TMF1

UniProt ID: P82094
Organism: Homo sapiens
Review Status: DRAFT
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Gene Description

Trans-Golgi golgin (TATA element modulatory factor 1 / ARA160). A long coiled-coil peripheral membrane protein recruited to the Golgi rim via a C-terminal Rab6-binding region, where it acts as a vesicle-tethering factor. Captures intra-Golgi transport vesicles via a conserved N-terminal motif (M-S-W-L/F, shared with the related intra-Golgi golgins GMAP-210 and golgin-84) and cooperates with the COG complex to dock retrograde vesicles. Required for Rab6-dependent retrograde transport from endosomes to the trans-Golgi network and from the Golgi to the ER (Shiga-toxin trafficking, GalNAc-T2 retention). Loss in mouse and Drosophila causes male-sterility acrosome biogenesis defects and altered Golgi-derived mucin glycosylation, consistent with a primary role in Golgi vesicle traffic. Despite the historical name and a small set of late-1990s overexpression studies that suggested a moonlighting role as a TBP-binding/androgen-receptor coactivator and a BC-box adaptor that targets STAT3 for proteasomal degradation, the bulk of mechanistically validated biology is at the Golgi and not in transcription.

Proposed New Ontology Terms

vesicle tethering activity

Definition: Binding activity of a long coiled-coil or multisubunit factor that bridges a transport vesicle membrane and a target organelle membrane prior to SNARE-mediated fusion. The molecular function counterpart of GO:0099022 vesicle tethering. Required for capturing incoming vesicles by golgins (e.g. TMF1, GMAP-210, golgin-84, the GRIP-domain golgins) at the Golgi and by analogous coiled-coil tethers at other compartments.

Justification: GO currently has the biological-process term GO:0099022 vesicle tethering and the cellular-component term GO:0099023 vesicle tethering complex, but no molecular-function term that captures the binding/bridging activity of an individual tether. Without such an MF, golgins like TMF1 default to GO:0005515 protein binding, which is explicitly discouraged. Per geneontology/go-annotation#6381 a "vesicle membrane tethering activity" term is being requested by curators (V. Wood, H. Attrill); GO:7770062 was referenced in that issue but is not yet present in GO at the time of this review (2026-05-02). Recording here so the term-request progress can be tracked alongside this review.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005794 Golgi apparatus
IBA
GO_REF:0000033
ACCEPT
Summary: IBA from PAINT. TMF1 is a canonical golgin and the Golgi rim is its primary, conserved localization (UniProt SUBCELLULAR LOCATION; PMID:17698061; PMID:23239882; PMID:28122620). Accept as core localization.
Supporting Evidence:
PMID:17698061
TMF signal surrounded Rab6-positive Golgi structures and immunoelectron microscopy revealed that TMF is concentrated at the budding structures localized at the tips of cisternae.
GO:0005783 endoplasmic reticulum
IBA
GO_REF:0000033
MARK AS OVER ANNOTATED
Summary: IBA from PAINT. TMF1 mediates Rab6-dependent retrograde transport from Golgi to ER (PMID:17698061), so it is transiently associated with ER-directed retrograde carriers, but it is not a steady-state ER-resident protein. Microscopy consistently shows the trans-Golgi rim, not the ER, as the primary localization. The annotation likely reflects over-propagation of yeast/fungal homolog data. Mark as over-annotated.
GO:0000139 Golgi membrane
IEA
GO_REF:0000044
ACCEPT
Summary: IEA from UniProt SubCell mapping. TMF1 is a peripheral Golgi-membrane protein concentrated at the tips of cisternae (UniProt SUBCELLULAR LOCATION; PMID:17698061). More precise than the bare Golgi apparatus annotation. Accept as core.
Supporting Evidence:
PMID:17698061
TMF is concentrated at the budding structures localized at the tips of cisternae.
GO:0005634 nucleus
IEA
GO_REF:0000044
MARK AS OVER ANNOTATED
Summary: IEA from UniProt SubCell mapping. A nuclear pool of one TMF isoform was reported (PMID:12044884), but the dominant localization in every cell type examined is the Golgi (PMID:15467733 explicitly describes TMF/ARA160 as a Golgi-resident protein). The IEA over-emphasizes a minor, isoform-restricted fraction; the primary biology of the protein is not nuclear. Mark as over-annotated.
Supporting Evidence:
PMID:12044884
TMF isoforms differentially localize in the Golgi apparatus and the nucleus.
GO:0005737 cytoplasm
IEA
GO_REF:0000044
KEEP AS NON CORE
Summary: IEA from UniProt SubCell mapping. Generic parent term subsumed by the more specific Golgi membrane / cytosol annotations. Keep as non-core.
GO:0005515 protein binding
IPI
PMID:20195357
A comprehensive resource of interacting protein regions for ...
MARK AS OVER ANNOTATED
Summary: High-throughput mRNA-display interactome screen reporting TMF1-NR3C1 binding. "Protein binding" is uninformative per project curation guidelines (CLAUDE.md). The relevant biology (interactions with Rab6, COG, AR, STAT3, FER, Elongin) is captured by more specific annotations. Mark as over-annotated.
GO:0005515 protein binding
IPI
PMID:32296183
A reference map of the human binary protein interactome.
MARK AS OVER ANNOTATED
Summary: High-throughput Y2H reference map (HuRI). Reports binding to CMTM5 isoform Q96DZ9-2; no functional follow-up. Uninformative MF per project guidelines. Mark as over-annotated.
GO:0005783 endoplasmic reticulum
IEA
GO_REF:0000107
MARK AS OVER ANNOTATED
Summary: IEA via Ensembl ortholog transfer from mouse Tmf1 (UniProtKB:B9EKI3). Same concern as the IBA ER annotation: TMF1 mediates retrograde traffic to the ER but is not an ER-resident protein. Mark as over-annotated.
GO:0005794 Golgi apparatus
IEA
GO_REF:0000107
ACCEPT
Summary: IEA via Ensembl ortholog transfer from mouse Tmf1. Redundant with the direct human IBA/IDA Golgi annotations but still correct. Accept.
GO:0061136 regulation of proteasomal protein catabolic process
IEA
GO_REF:0000107
KEEP AS NON CORE
Summary: IEA via Ensembl ortholog transfer from mouse Tmf1. Reflects PMID:15467733, which showed that the BC-box motif of TMF/ARA160 mediates its binding to Elongin C and that ectopic expression in serum-starved C2C12 cells drives Stat3 ubiquitination and proteasomal degradation. This is a discrete, mechanistically supported moonlighting activity at the Golgi cytoplasmic face but is not the protein's core function. Keep as non-core.
Supporting Evidence:
PMID:15467733
Amino-acid sequence analysis identified a BC-box element in TMF/ARA160 that mediated the binding of this protein to elongin C. Ectopic expression of TMF/ARA160 in serum-starved C2C12 cells drove the ubiquitination and proteasomal degradation of Stat3.
GO:0005794 Golgi apparatus
IDA
GO_REF:0000052
ACCEPT
Summary: IDA from Human Protein Atlas immunofluorescence. Direct experimental confirmation of Golgi localization. Accept as core.
GO:0003713 transcription coactivator activity
IDA
PMID:10428808
Isolation and characterization of ARA160 as the first androg...
MARK AS OVER ANNOTATED
Summary: IDA based on a single 1999 transient-transfection / reporter study in PC-3 cells. The same paper notes that a Gal4-DBD fusion to TMF1 fails to transactivate reporter genes (data not shown), which is inconsistent with a bona fide transcription coactivator (GO:0003713) sensu stricto - the authors propose that TMF acts only together with the AF-1 domain of steroid receptors. The mechanistically established function of TMF1 is at the Golgi (PMID:17698061; PMID:23239882; PMID:28122620); TMF1 has no DNA-binding domain (its "TMF_DNA_bd"/"TMF_TATA_bd" Pfam domains are operationally defined from the original 1992 HIV-1 LTR study and have not been validated as endogenous DNA-binding modules). The Pharos target development level is "Tbio" (no validated function). Down-rate from a core MF; flag as over-annotation pending orthogonal validation, but do not delete outright because a low-level moonlighting role at the AR cannot be formally excluded.
Supporting Evidence:
PMID:10428808
Transient transfection assays demonstrated that ARA160 might function as a coactivator for AR-mediated transactivation in human prostate cancer PC-3 cells.
GO:0030521 androgen receptor signaling pathway
IDA
PMID:10428808
Isolation and characterization of ARA160 as the first androg...
MARK AS OVER ANNOTATED
Summary: IDA from the same single 1999 overexpression study (PMID:10428808). The mouse TMF-/- testosterone/spermatogenesis phenotype (PMID:23000399) is more compatible with disrupted Leydig cell secretion / Golgi-dependent acrosome biogenesis than with cell-autonomous loss of an AR coregulator. Mark as over-annotated.
GO:0045944 positive regulation of transcription by RNA polymerase II
IDA
PMID:10428808
Isolation and characterization of ARA160 as the first androg...
MARK AS OVER ANNOTATED
Summary: IDA inferred from the same single transient transfection assay on an AR-responsive reporter in PC-3 cells. Not validated by orthogonal assays (ChIP-seq, KO RNA-seq) or independent groups. Mark as over-annotated.
GO:0050681 nuclear androgen receptor binding
IPI
PMID:10428808
Isolation and characterization of ARA160 as the first androg...
KEEP AS NON CORE
Summary: IPI based on far-Western blotting and co-immunoprecipitation between AR N-terminal peptide and TMF1/ARA160 (PMID:10428808). The physical interaction is reproducibly observed, but in the context of TMF1's overall biology the AR-binding role is a moonlighting feature of a Golgi protein, not a core function. Keep as non-core.
GO:0005829 cytosol
TAS
Reactome:R-HSA-6811431
KEEP AS NON CORE
Summary: TAS from Reactome "RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles". Reflects the Reactome cytosolic-pool placeholder for tethering factors. The diffuse cytoplasmic distribution observed under low-serum conditions (PMID:15467733) is real but the protein is concentrated at Golgi membranes. Keep as non-core.
GO:0005829 cytosol
TAS
Reactome:R-HSA-6814091
KEEP AS NON CORE
Summary: TAS from Reactome "ARL1 recruits TGN Golgin homodimers". Same comment as the previous cytosol annotation - reflects the Reactome cytosolic-pool placeholder. Keep as non-core.
GO:0005829 cytosol
TAS
Reactome:R-HSA-6814682
KEEP AS NON CORE
Summary: TAS from Reactome "Fusion of early-endosome derived vesicles at the TGN". Same comment - Reactome placeholder for the cytosolic tethering pool. Keep as non-core.
GO:0061136 regulation of proteasomal protein catabolic process
ISS
GO_REF:0000024
KEEP AS NON CORE
Summary: ISS from manual transfer of mouse Tmf1 (UniProtKB:B9EKI3). Reflects PMID:15467733 (TMF/ARA160 BC-box-Elongin C-mediated Stat3 ubiquitination). Mechanistically supported but is a moonlighting activity of the Golgi pool, not the core function. Keep as non-core.
Supporting Evidence:
PMID:15467733
Amino-acid sequence analysis identified a BC-box element in TMF/ARA160 that mediated the binding of this protein to elongin C.
GO:0060090 molecular adaptor activity
NAS NEW
Summary: Added to align core_functions with existing annotations. Captures the vesicle-tethering bridging activity of TMF1 (closest existing MF; a more specific "vesicle tethering activity" term is requested in proposed_new_terms).
Reason: Core function term not present in existing_annotations.
Supporting Evidence:
PMID:28122620
When relocated to mitochondria, TMF captures intra-Golgi transport vesicles.
file:human/TMF1/TMF1-deep-research-falcon.md
TMF1 is best supported as a **Golgi tether/scaffold (golgin) and Rab6 effector** that contributes to Golgi ribbon morphology and to specific retrograde trafficking pathways.
GO:0099041 vesicle tethering to Golgi
NAS NEW
Summary: Added to align core_functions with existing annotations. Direct demonstration by mitochondrial-relocation assay (PMID:28122620) and by interaction with the COG complex (PMID:23239882).
Reason: Core function term not present in existing_annotations.
Supporting Evidence:
PMID:28122620
When relocated to mitochondria, TMF captures intra-Golgi transport vesicles.
GO:0006891 intra-Golgi vesicle-mediated transport
NAS NEW
Summary: Added to align core_functions with existing annotations. Supported by vesicle-capture assays (PMID:28122620), COG-TMF tethering model (PMID:23239882), and Drosophila in vivo data (PMID:36103876).
Reason: Core function term not present in existing_annotations.
Supporting Evidence:
PMID:23239882
We find that the COG complex interacts with two different Rabs in addition to each end of the golgin "TATA element modulatory factor" (TMF).
GO:0031267 small GTPase binding
NAS NEW
Summary: Added to align core_functions with existing annotations. Captures the Rab6-GTP binding activity that recruits TMF1 to the trans-Golgi.
Reason: Core function term not present in existing_annotations.
Supporting Evidence:
PMID:17698061
TMF signal surrounded Rab6-positive Golgi structures.
GO:0042147 retrograde transport, endosome to Golgi
NAS NEW
Summary: Added to align core_functions with existing annotations. TMF1 knockdown blocks Rab6-dependent retrograde transport of Shiga toxin from early/recycling endosomes to the trans-Golgi network (PMID:17698061).
Reason: Core function term not present in existing_annotations.
Supporting Evidence:
PMID:17698061
The knockdown of either TMF or Rab6 by RNA interference blocked retrograde transport of endocytosed Shiga toxin from early/recycling endosomes to the trans-Golgi network.
GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
NAS NEW
Summary: Added to align core_functions with existing annotations. PMID:17698061 establishes a role for TMF1 in Rab6-dependent Golgi-to-ER retrograde traffic.
Reason: Core function term not present in existing_annotations.
Supporting Evidence:
PMID:17698061
critical roles for TMF in two Rab6-dependent retrograde transport processes - one from endosomes to the Golgi and the other from the Golgi to the ER.

Core Functions

Acts as a long coiled-coil vesicle-tethering factor (golgin) at the trans-Golgi rim that bridges incoming transport vesicles and the Golgi membrane prior to SNARE-mediated fusion. The N-terminal disordered region (~residues 1-36, containing the conserved M-S-W-L/F motif shared with golgin-84 and GMAP-210) and the central/C-terminal coiled-coil each independently capture intra-Golgi transport vesicles in the mitochondrial-relocation assay; the C-terminal Rab6-binding coiled-coil recruits TMF1 to the Golgi membrane and cooperates with the COG complex to dock retrograde vesicles. (A specific MF "vesicle tethering activity" is requested in proposed_new_terms; GO:0060090 is used here as the closest available existing MF.)

Supporting Evidence:
  • PMID:28122620
    When relocated to mitochondria, TMF captures intra-Golgi transport vesicles.
  • PMID:23239882
    We find that the COG complex interacts with two different Rabs in addition to each end of the golgin "TATA element modulatory factor" (TMF).
  • file:human/TMF1/TMF1-deep-research-falcon.md
    TMF1 is best supported as a **Golgi tether/scaffold (golgin) and Rab6 effector** that contributes to Golgi ribbon morphology and to specific retrograde trafficking pathways.

Binds Rab6 in its GTP-bound active state via the C-terminal coiled-coil region; this interaction is required for recruitment of TMF1 to the trans-Golgi rim and for its function in Rab6-dependent retrograde transport from endosomes to the trans-Golgi network and from the Golgi to the ER.

Supporting Evidence:
  • PMID:17698061
    TMF signal surrounded Rab6-positive Golgi structures... critical roles for TMF in two Rab6-dependent retrograde transport processes - one from endosomes to the Golgi and the other from the Golgi to the ER.
  • file:human/TMF1/TMF1-deep-research-falcon.md
    TMF1/ARA160 is a **Golgi-associated coiled-coil "golgin"** that binds **Rab6** family GTPases and contributes to Golgi organization.

References

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Gene Ontology annotation based on curation of immunofluorescence data
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
Cloning and chromosomal mapping of a human immunodeficiency virus 1 "TATA" element modulatory factor.
  • TMF was originally identified as a 123 kDa cellular protein that binds the HIV-1 LTR TATA element in gel-retardation assays and inhibits TBP-mediated transcriptional activation in vitro.
    "TMF binds to the human immunodeficiency virus 1 TATA element in gel-retardation assays and inhibits activation of the viral long terminal repeat by the TATA-binding protein in in vitro transcription assays."
  • The original characterisation was a viral-promoter / in vitro context; no endogenous cellular target genes were demonstrated.
    "TMF is a transcription factor that likely regulates the expression of both viral and cellular genes."
Isolation and characterization of ARA160 as the first androgen receptor N-terminal-associated coactivator in human prostate cells.
  • AR N-terminal peptide directly binds TMF1/ARA160 in far-Western and co-IP assays in vitro.
    "The far-Western blotting and co-immunoprecipitation assays demonstrate that the AR can interact directly with ARA160/TMF."
  • A transient transfection AR-reporter assay in PC-3 cells suggests TMF1/ARA160 enhances AR transactivation.
    "Transient transfection assays demonstrated that ARA160 might function as a coactivator for AR-mediated transactivation in human prostate cancer PC-3 cells."
A putative nuclear receptor coactivator (TMF/ARA160) associates with hbrm/hSNF2 alpha and BRG-1/hSNF2 beta and localizes in the Golgi apparatus.
  • TMF1 isoforms differentially localize between Golgi and nucleus; the Golgi pool is dominant.
    "Immunofluorescence and Western blot studies revealed that the TMF isoforms differentially localize in the Golgi apparatus and the nucleus."
  • The C-terminal region of TMF1 binds the conserved N-terminal regions of the SWI/SNF ATPases hbrm/hSNF2alpha and BRG-1/hSNF2beta in vitro and in vivo.
    "hbrm/hSNF2 alpha and BRG-1/hSNF2 beta, the ATPase subunits of the human SNF/SWI complexes, specifically associate in vitro and in vivo with TATA element modulatory factor (TMF)/ARA160."
TMF/ARA160 is a BC-box-containing protein that mediates the degradation of Stat3.
  • TMF/ARA160 is described as a Golgi-resident protein.
    "TMF/ARA160 is a Golgi resident protein whose cellular functions have not been conclusively revealed."
  • TMF/ARA160 contains a BC-box motif that binds Elongin C and directs Stat3 ubiquitination/proteasomal degradation in serum-starved C2C12 cells.
    "Amino-acid sequence analysis identified a BC-box element in TMF/ARA160 that mediated the binding of this protein to elongin C. Ectopic expression of TMF/ARA160 in serum-starved C2C12 cells drove the ubiquitination and proteasomal degradation of Stat3."
Functional involvement of TMF/ARA160 in Rab6-dependent retrograde membrane traffic.
  • TMF1 surrounds Rab6-positive Golgi structures and is concentrated at cisternal-tip budding structures.
    "TMF signal surrounded Rab6-positive Golgi structures and immunoelectron microscopy revealed that TMF is concentrated at the budding structures localized at the tips of cisternae."
  • TMF1 knockdown phenocopies Rab6 knockdown for retrograde transport of Shiga toxin from early/recycling endosomes to the trans-Golgi network.
    "The knockdown of either TMF or Rab6 by RNA interference blocked retrograde transport of endocytosed Shiga toxin from early/recycling endosomes to the trans-Golgi network, causing missorting of the toxin to late endosomes/lysosomes."
  • TMF1 is required for Golgi retention of GalNAc-T2 (but not GalT), and is implicated in Rab6-dependent retrograde transport from Golgi to ER.
    "These observations suggest critical roles for TMF in two Rab6-dependent retrograde transport processes - one from endosomes to the Golgi and the other from the Golgi to the ER."
A comprehensive resource of interacting protein regions for refining human transcription factor networks.
  • High-throughput mRNA-display screen reports a TMF1-NR3C1 (glucocorticoid receptor) interaction; no functional follow-up.
    "present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs)."
Testosterone deficiency accompanied by testicular and epididymal abnormalities in TMF(-/-) mice.
  • TMF/ARA160 is a Golgi-associated protein essential for spermiogenesis; its loss in mouse causes Leydig-cell proliferation, testosterone deficiency and epididymal apoptosis - a phenotype consistent with disrupted Golgi-derived acrosome biogenesis and secretion rather than loss of an AR coregulator.
    "TMF/ARA160 is a Golgi-associated protein, which is essential for spermiogenesis. In this study, we show that lack of TMF/ARA160 leads to defects in both the testis and the epididymis."
Molecular insights into vesicle tethering at the Golgi by the conserved oligomeric Golgi (COG) complex and the golgin TATA element modulatory factor (TMF).
  • TMF1 is a Golgi-tethering coiled-coil ("golgin") that binds the COG complex at both ends and to Golgi membranes via its central coiled-coil after COPI uncoating.
    "We find that the COG complex interacts with two different Rabs in addition to each end of the golgin "TATA element modulatory factor" (TMF). This allows COG to potentially bridge the distance between the distal end of the golgin and the target membrane thereby promoting tighter docking. Concurrently we show that the central portion of TMF can bind to Golgi membranes that are liberated of their COPI cover."
Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in TMF-/- mice.
  • TMF/ARA160 is referred to as a multifunctional Golgi-associated protein; TMF-/- colon shows altered MUC2 mucin oligomerisation, consistent with disrupted Golgi-dependent glycosylation/secretion.
    "Tata Element Modulatory Factor (TMF/ARA160) is a multifunctional Golgi-associated protein, which accumulates in colonic enterocytes and goblet cells."
The golgin coiled-coil proteins capture different types of transport carriers via distinct N-terminal motifs.
  • TMF1, when relocated to mitochondria, captures intra-Golgi transport vesicles - direct demonstration of vesicle-tethering activity.
    "When relocated to mitochondria, TMF captures intra-Golgi transport vesicles, but these contain some proteins from later in the stack than those captured by GMAP-210 and golgin-84."
  • A short N-terminal motif (M-S-W-L/F, conserved across metazoa and shared with golgin-84 and GMAP-210) and a central/C-terminal coiled-coil region both contribute vesicle-capture activity.
    "The first 36 residues of the protein are necessary for the capture activity of the N-terminal half, and sufficient to confer capture activity when attached to two different heterologous coiled-coil proteins."
A reference map of the human binary protein interactome.
  • HuRI Y2H interactome map reports a TMF1-CMTM5 (isoform Q96DZ9-2) binary interaction; no functional follow-up.
    "A reference map of the human binary protein interactome."
In vivo characterization of Drosophila golgins reveals redundancy and plasticity of vesicle capture at the Golgi apparatus.
  • In Drosophila, ectopic TMF captures intra-Golgi transport vesicles and the loss-of-function mutant recapitulates the male-fertility phenotype seen in mouse Tmf1 knockouts, supporting a conserved role in Golgi vesicle traffic.
    "We show that ectopic forms can capture intra-Golgi transport vesicles, but strikingly, the cargo present in the vesicles captured by each golgin varies between tissues. Loss-of-function mutants show that the golgins are individually dispensable, although the loss of TMF recapitulates the male fertility defects observed in mice."
Reactome:R-HSA-6811431
RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
Reactome:R-HSA-6814091
ARL1 recruits TGN Golgin homodimers
Reactome:R-HSA-6814682
Fusion of early-endosome derived vesicles at the TGN
file:human/TMF1/TMF1-notes.md
TMF1 research notes (this review)
file:human/TMF1/TMF1-deep-research-falcon.md
Falcon deep research report for TMF1
  • Falcon supports the Golgi-associated golgin/Rab6-effector role as the most reproducible TMF1 function, while treating transcriptional, proteostasis, and nuclear RTK roles as conditional or context-dependent.
    "The Golgi/tethering axis is supported by multiple cell biological methods (Golgi localization, Rab6-binding, trafficking defects, Golgi morphology quantification)."

Suggested Questions for Experts

Q: Is the apparent transcription-coactivator activity of TMF1 (PMID:10428808) a true endogenous function or an overexpression artefact? Has it been validated by AR ChIP-seq or by RNA-seq of TMF1 KO prostate cells?

Suggested experts: GO Consortium (R. Lovering, A. Lock, ARUK-UCL), Steroid-receptor coactivator field (e.g. C. Chang lab)

Q: Does any tissue/cell type maintain a functional nuclear pool of TMF1, and if so what is its target-gene repertoire?

Suggested experts: SWI/SNF / chromatin-remodeling researchers, Neuro-andrology / prostate-cancer transcription researchers

Suggested Experiments

Experiment: ChIP-seq for endogenous TMF1 in LNCaP/22Rv1 (AR-positive prostate) cells +/- DHT, paired with AR ChIP-seq. Compute peak overlap with AR cistrome and motif enrichment. Validate top putative TMF1 chromatin sites by ChIP-qPCR after TMF1 knockdown. Couple with RNA-seq of TMF1 KO cells +/- DHT to ask whether AR target genes are preferentially affected.

Hypothesis: If TMF1 is an endogenous AR coactivator, AR-target promoters should be enriched among TMF1 ChIP-seq peaks; if not, TMF1 should occupy few or no chromatin sites and the existing IDA annotations to GO:0003713/GO:0045944/GO:0030521 should be retired rather than merely demoted.

Type: Genome-wide ChIP-seq for TMF1 in AR-positive prostate cells

Experiment: Generate stable lines expressing TurboID-TMF1 (full length and isoform P82094-2) at near-endogenous level. Perform 10-min biotin labelling, streptavidin enrichment and TMT-MS3 quantitation. Compare with TurboID-only and a TurboID-Rab6 control. Quantify the relative enrichment of trafficking vs. chromatin/transcription GO categories.

Hypothesis: TMF1 BioID interactomes will be dominated by Golgi-tethering machinery (Rab6, COG subunits, intra-Golgi cargo, glycosyltransferases) rather than by transcription/chromatin factors, reinforcing that the core function is at the Golgi.

Type: Quantitative proximity labelling (BioID/TurboID) at the trans-Golgi rim and at chromatin

Experiment: Cryo-electron tomography of vitrified Golgi-membrane-enriched HeLa extracts immuno-labelled for TMF1, with sub-tomogram averaging of TMF1-decorated vesicle-Golgi contacts. Compare WT to a TMF1 N-terminal motif (M-S-W-L/F) mutant and to Rab6-knockdown.

Hypothesis: TMF1 will be observed as elongated coiled-coil bridges between intra-Golgi transport vesicles and cisternal rims, with Rab6-binding ends anchored at the Golgi, providing a structural counterpart of the mitochondrial-relocation capture assay (PMID:28122620).

Type: Cryo-ET of TMF1 at intra-Golgi vesicle tethering sites

Deep Research

Falcon

(TMF1-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 36 citations 2026-05-11T00:34:42.272352

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: Human TMF1 (UniProt P82094) / TMF-1 / ARA160 (TATA element modulatory factor)

1) Gene/protein identity verification and nomenclature

Human TMF1 encodes a ~160 kDa, ~1,093 amino-acid protein historically identified under multiple names, including TATA element modulatory factor (TMF) and androgen receptor-associated protein of 160 kDa (ARA160). ARA160 was cloned as an androgen receptor (AR) N-terminalโ€“associated protein and was reported to be identical in sequence to TMF (a factor previously described in the context of TATA element modulation), thereby linking the gene symbol TMF1 to the protein described in UniProt accession P82094 (Hsiao & Chang, 1999; publication date Aug 1999; https://doi.org/10.1074/jbc.274.32.22373) (hsiao1999isolationandcharacterization pages 1-1).

2) Key concepts/definitions and current understanding of TMF1 function

2.1 TMF1 as a Golgi-associated golgin and Rab6 effector

A major validated concept is that TMF1/ARA160 is a Golgi-associated coiled-coil โ€œgolginโ€ that binds Rab6 family GTPases and contributes to Golgi organization. Fridmann-Sirkis et al. (May 2004; https://doi.org/10.1186/1471-2121-5-18) localized TMF to the Golgi by immunofluorescence and biochemical fractionation, and showed that a C-terminal fragment of TMF localizes to the Golgi and binds Rab6, consistent with the notion that Rab6 recruits this golgin (fridmannsirkis2004tmfisa pages 5-7). Functionally, partial TMF depletion by RNAi correlated with Golgi dispersal, supporting an architectural role in maintaining compact Golgi organization (fridmannsirkis2004tmfisa pages 5-7).

Yamane et al. (Oct 2007; https://doi.org/10.1016/j.yexcr.2007.07.010) extended this to trafficking function: TMF localized around Rab6-positive Golgi structures and, by immuno-EM, concentrated near budding structures of Golgi cisternae. TMF knockdown (and Rab6 perturbation) disrupted Rab6-dependent retrograde traffic, including endosomeโ†’TGN transport of Shiga toxin and aspects of Golgiโ†’ER recycling, and affected Golgi retention of specific resident enzymes such as GalNAc-T2 (yamane2007functionalinvolvementof pages 1-2).

Definition (functional): In mammalian cells, TMF1 is best supported as a Golgi tether/scaffold (golgin) and Rab6 effector that contributes to Golgi ribbon morphology and to specific retrograde trafficking pathways (fridmannsirkis2004tmfisa pages 5-7, yamane2007functionalinvolvementof pages 1-2).

2.2 TMF1 as a nuclear receptor coactivator (ARA160)

TMF1/ARA160 was originally cloned as the first reported AR N-terminalโ€“associated coactivator in prostate cells. Hsiao & Chang (Aug 1999; https://doi.org/10.1074/jbc.274.32.22373) demonstrated direct ARโ€“ARA160 binding using far-Western, pull-down, co-immunoprecipitation, and mammalian two-hybrid assays, and showed functional coactivation in androgen-dependent reporter systems (hsiao1999isolationandcharacterization pages 1-1, hsiao1999isolationandcharacterization pages 3-3). Interaction mapping supported engagement with the AR N-terminal/AF-1 region and an internal ARA160 region (e.g., ARA160 aa 410โ€“888 used in binding assays) (hsiao1999isolationandcharacterization pages 1-3, hsiao1999isolationandcharacterization pages 3-3). ARA160 enhanced AR transactivation and could synergize with another AR coactivator (ARA70), consistent with coactivator network behavior (hsiao1999isolationandcharacterization pages 4-5).

Definition (functional): TMF1 can function as an AR coactivator in transcriptional reporter contexts, with ligand-enhanced ARโ€“TMF/ARA160 interaction and mapped preference for AR AF-1 (hsiao1999isolationandcharacterization pages 4-5, hsiao1999isolationandcharacterization pages 3-3).

2.3 TMF1 as a BC-box protein coupling signaling to proteasomal degradation

Another central concept is that TMF1/ARA160 contains a BC-box motif capable of binding elongin C (an adaptor module often used in Cullin-based ubiquitin ligase complexes), enabling TMF1 to promote ubiquitination and proteasomal turnover of select targets.

Perry et al. (Nov 2004; https://doi.org/10.1038/sj.onc.1208149) described TMF/ARA160 as a Golgi-confined coiled-coil protein that can redistribute into the cytoplasm under serum starvation, associate with the non-receptor tyrosine kinase Fer and transcription factor STAT3, and promote STAT3 ubiquitination and proteasomal degradation in a BC-boxโ€“dependent manner (perry2004tmfara160isa pages 1-2, perry2004tmfara160isa pages 8-9). Proteasome inhibition (MG132) blocked TMF-induced STAT3/Fer loss, supporting a proteasome-dependent mechanism (perry2004tmfara160isa pages 8-9).

Abrham et al. (Jul 2009; https://doi.org/10.1002/ijc.24277) further linked TMF to stress-conditional proteostasis control in cancer models: in PC3 xenografts, TMF expression correlated with lower abundance of NF-ฮบB p65/RelA and downregulation of proangiogenic cytokines (e.g., IL-8, IL-1ฮฒ), consistent with TMF-mediated suppression of NF-ฮบBโ€“dependent proangiogenic programs under metabolic constraints (abrham2009tmfara160downregulatesproangiogenic pages 1-2, abrham2009tmfara160downregulatesproangiogenic pages 7-8).

Definition (functional): TMF1 can act as a BC-boxโ€“dependent regulator of protein stability, linking signaling/stress states to selective ubiquitin-proteasome control of factors such as STAT3 and (in stressed tumor settings) NF-ฮบB p65/RelA (perry2004tmfara160isa pages 8-9, abrham2009tmfara160downregulatesproangiogenic pages 7-8).

2.4 TMF1 in nuclear receptor tyrosine kinase (RTK) trafficking and chromatin remodeling

A modern mechanistic axis connecting TMF1 to nuclear signaling is the PDGFRฮฒโ€“Ferโ€“TMF-1โ€“Brg-1 pathway.

Papadopoulos et al. (May 2018; https://doi.org/10.1083/jcb.201706118) showed that PDGF-BB stimulation causes a fraction of full-length PDGFRฮฒ to accumulate in the nucleus (chromatin and nuclear matrix), where it forms ligand-inducible complexes with Fer and TMF-1 (papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2, papadopoulos2018pdgfrฮฒtranslocatesto pages 9-11). PDGF-BB stimulation decreased TMF-1 association with Brg-1 and released Brg-1 from the SWIโ€“SNF chromatin remodeling complex, linking RTK nuclear trafficking to chromatin remodeling (papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2). TMF-1 knockdown reduced PDGFRฮฒ nuclear translocation and increased expression of the cell cycle inhibitor CDKN1A (p21), while immediate-early PDGFRฮฒ responses were largely unaffectedโ€”supporting a selective chromatin-mediated proliferation control route (papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2, papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8).

A 2024 review on RTK signaling in neurodegenerative contexts explicitly cites this mechanismโ€”โ€œPDGFRฮฒ translocates to the nucleus and regulates chromatin remodeling via TATA elementโ€“modifying factor 1โ€โ€”placing TMF1 within an ongoing shift in RTK biology toward nuclear functions and chromatin regulation (Feb 2024; https://doi.org/10.37349/en.2024.00033) (sengupta2024connectingtheends pages 21-23).

Definition (functional): TMF1 functions as a cofactor/trafficking-linked regulator of nuclear PDGFRฮฒ signaling, impacting SWIโ€“SNF chromatin remodeling (via Brg-1) and cell-cycle control genes such as p21 (papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2, papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8, sengupta2024connectingtheends pages 21-23).

3) Domain architecture and subcellular localization

Subcellular localization is context-dependent, with strong evidence for Golgi association but also documented nuclear/cytoplasmic roles.

  • Golgi localization: TMF localizes to Golgi membranes by immunofluorescence and Golgi fractionation and exhibits a characteristic Golgi โ€œringโ€ pattern; a C-terminal fragment is sufficient for Golgi localization and Rab6-dependent recruitment (fridmannsirkis2004tmfisa pages 5-7). TMF also surrounds Rab6-positive Golgi structures and is observed at budding regions by immuno-EM (yamane2007functionalinvolvementof pages 1-2).
  • Cytoplasmic redistribution under stress: In serum-starved myoblasts, TMF redistributes from Golgi to the cytoplasm and associates with Fer/STAT3 in a proteasome-regulated complex (perry2004tmfara160isa pages 8-9).
  • Nuclear functions/associations: TMF-1 is found in nuclear complexes with PDGFRฮฒ/Fer and is implicated in chromatin remodeling via Brg-1 (papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2, papadopoulos2018pdgfrฮฒtranslocatesto pages 9-11).

Structural motifs (functionally inferred/validated):
* Coiled-coil architecture: TMF is described as a coiled-coil rich protein consistent with golgin family features (perry2004tmfara160isa pages 1-2, fridmannsirkis2004tmfisa pages 5-7).
* C-terminal Rab6-binding region: Experiments localize Rab6 interaction/Golgi targeting to the C-terminal region (fridmannsirkis2004tmfisa pages 5-7).
* BC-box motif: Required for elongin C binding and for STAT3 degradation activity (perry2004tmfara160isa pages 1-2, perry2004tmfara160isa pages 8-9).
* Microtubule-interacting domain (MIT) (shown in mouse TMF): A C-terminal MIT domain plus coiled-coil regions are required for stable Golgi association and microtubule binding in spermatogenic contexts, supporting cytoskeletal coupling of Golgi behavior (elkis2015tmfara160governsthe pages 11-13, elkis2015tmfara160governsthe pages 15-17).

4) Biological roles and pathways (experimentally supported)

4.1 Golgi organization and retrograde membrane traffic (Rab6 pathway)

TMF1 is implicated in maintaining compact Golgi organization and in Rab6-dependent retrograde trafficking. In NRK cells, TMF RNAi correlated with loss of a compact Golgi ribbon: 58% of cells with normal TMF levels exhibited a compact Golgi versus 8% of TMF-depleted cells (Fridmann-Sirkis et al., 2004; Fig. 4C image evidence) (fridmannsirkis2004tmfisa pages 5-7, fridmannsirkis2004tmfisa media a620ef8a). TMF knockdown also disrupted Shiga toxin retrograde routing to the TGN and altered retention of select Golgi enzymes (GalNAc-T2) (yamane2007functionalinvolvementof pages 1-2).

4.2 AR transcriptional coactivation (steroid receptor signaling)

ARA160/TMF interacts with AR (ligand enhanced) and augments AR transcriptional output in prostate cell reporter assays, with stronger enhancement of AR AF-1 activity than AF-2 in mapping experiments. Reporter outcomes include DHT-induced transactivation increased from approximately 5-fold to ~17-fold with ARA160 coexpression in one assay configuration (hsiao1999isolationandcharacterization pages 3-3). These data support a role for TMF1 as a transcriptional cofactor in steroid receptor signaling contexts (hsiao1999isolationandcharacterization pages 4-5, hsiao1999isolationandcharacterization pages 3-3).

4.3 Proteostasis control of STAT3 and NF-ฮบB under growth arrest/metabolic stress

Under serum deprivation, TMF associates with Fer and STAT3 and promotes STAT3 ubiquitination and proteasomal degradation in a BC-boxโ€“dependent manner; MG132 blocks this loss (perry2004tmfara160isa pages 8-9). In tumor contexts where metabolic stress is expected, TMF expression correlated with reduced NF-ฮบB p65/RelA (~2-fold in xenograft tumors) and downregulation of NF-ฮบBโ€“regulated proangiogenic cytokines (IL-8, IL-1ฮฒ) (abrham2009tmfara160downregulatesproangiogenic pages 5-7, abrham2009tmfara160downregulatesproangiogenic pages 7-8).

4.4 Nuclear PDGFRฮฒ signaling to chromatin remodeling and cell-cycle control

Papadopoulos et al. provide direct quantification of PDGFRฮฒ nuclear trafficking: nuclear PDGFRฮฒ increased from ~7% of total receptor (basal) to a peak of ~26% at 30 minutes after PDGF-BB stimulation (papadopoulos2018pdgfrฮฒtranslocatesto pages 2-4). They also quantified plasma-membraneโ€“derived (biotinylated) PDGFRฮฒ clusters colocalizing with TMF-1 in Golgi and nucleus (e.g., ~13 Golgi clusters and ~14 nuclear clusters per cell; n=29; and ~2.5 vs ~2.4 triple-positive dots per cell using a Pearson cutoff) (papadopoulos2018pdgfrฮฒtranslocatesto pages 4-5). Functionally, Fer/TMF-1/Brg-1 depletion increased the fraction of p21-positive cells (control 6.5% vs 21% Fer KD, 25% TMF-1 KD, 50% Brg-1 KD), and impaired PDGF-driven proliferation (papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8). These findings support an expert-level mechanistic model in which TMF-1-positive trafficking routes contribute to nuclear receptor delivery and to chromatin remodeling events that modulate p53/p21-linked proliferation control (papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2, papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8).

4.5 Spermiogenesis and Golgi orientation (in vivo developmental cell biology)

In TMF knockout mice, TMF is required for correct Golgi spatial orientation in developing spermatids and for pro-acrosomal vesicle targeting to the nucleus during acrosome formation. TMF displays dynamic localization across Golgi regions during spermiogenesis. The work supports TMF as a Golgi- and microtubule-associated factor: TMF co-immunoprecipitates with tubulin and associates with polymerized microtubules; disrupting microtubules (colchicine) disrupts Golgi association of TMF constructs. A C-terminal MIT domain and coiled-coil regions are required for stable TMF association with Golgi in NIH3T3 mapping experiments (Dec 2015; https://doi.org/10.1371/journal.pone.0145277) (elkis2015tmfara160governsthe pages 11-13, elkis2015tmfara160governsthe pages 15-17).

4.6 Mucus secretion, mucus barrier function, microbiota composition, and colitis susceptibility

In the colon, TMF is linked to regulated secretion of the major gel-forming mucin MUC2, and to downstream ecological effects on microbiota. Bel et al. (Mar 2014; https://doi.org/10.1073/pnas.1319114111) showed that TMFโˆ’/โˆ’ goblet cells display altered secretory granule behavior by TEM (granules โ€œdo not fuse before mucus secretionโ€ and are discharged late), consistent with a vesicle fusion/tethering defect affecting mucus granule exocytosis (bel2014reprogrammedandtransmissible pages 4-5). TMF colocalized with MUC2 in human colonic goblet cells by immunofluorescence (bel2014reprogrammedandtransmissible pages 2-3). Biochemically, mucus from TMFโˆ’/โˆ’ mice contained highly oligomerized MUC2 that resisted natural degradation: under nonreducing conditions WT MUC2 appeared as a smear (degraded) whereas TMFโˆ’/โˆ’ MUC2 appeared as an undegraded highโ€“molecular-weight species (bel2014reprogrammedandtransmissible pages 2-3).

Phenotypically, TMFโˆ’/โˆ’ mice had altered microbiota (higher diversity; shifts toward Firmicutes taxa described as beneficial) and showed reduced susceptibility to DSS-induced colitis; the protective microbiota was transmissible to WT mice by cohousing, and DSS outcomes (weight loss, fecal/histopathology scoring, cytokine mRNAs) showed significant differences (p<0.05; n=5 in reported DSS experiments) (bel2014reprogrammedandtransmissible pages 4-5, bel2014reprogrammedandtransmissible pages 4-4).

5) Disease relevance, real-world applications, and implementations

5.1 Cancer biology: antiangiogenic activity in prostate xenografts

In vivo, ectopic TMF expression in PC3 xenografts attenuated tumor progression, associated with reduced angiogenesis and increased apoptotic markers (activated caspase-3, TUNEL), while proliferation markers (PCNA) were not changedโ€”supporting a model where TMF influences tumor microenvironment (angiogenesis) and stress-driven survival rather than baseline proliferation (Jul 2009; https://doi.org/10.1002/ijc.24277) (abrham2009tmfara160downregulatesproangiogenic pages 5-7). Vessel mass reduction was supported by CD31 staining with reported significance (p<0.04, n=6) (abrham2009tmfara160downregulatesproangiogenic pages 5-7). This suggests TMF1-related pathways may be relevant for interpreting tumor stress responses and angiogenic transcription programs involving NF-ฮบB/STAT3, though clinical translation remains investigational in the cited record.

5.2 Reproductive health and infertility associations

Mechanistic mouse studies demonstrate TMFโ€™s necessity for normal spermiogenesis and acrosome formation (elkis2015tmfara160governsthe pages 9-11, elkis2015tmfara160governsthe pages 11-13). Consistent with this biology, Open Targets lists TMF1 disease associations enriched in male infertility-related phenotypes (e.g., azoospermia and spermatogenic failure terms) with multiple literature evidence links (evidence count=5 in the returned Open Targets results for each listed disease) (OpenTargets Search: -TMF1). These database associations should be interpreted as curated linkage signals rather than mechanistic proof, but they align with in vivo functional roles in male germ cell development.

5.3 Systems/cell biology implementations

TMF1 is used in real-world research implementations as:
* A Golgi scaffold/tether perturbation target (RNAi/siRNA or knockout) to assay Golgi ribbon morphology and retrograde traffic pathways (fridmannsirkis2004tmfisa pages 5-7, yamane2007functionalinvolvementof pages 1-2).
* A component in nuclear RTK trafficking studies leveraging surface biotinylation, colocalization pipelines, and chromatin fractionation (papadopoulos2018pdgfrฮฒtranslocatesto pages 4-5, papadopoulos2018pdgfrฮฒtranslocatesto pages 2-4).
* A regulator of mucus barrier biology and microbiome transmissibility studies using cohousing paradigms and DSS colitis induction (bel2014reprogrammedandtransmissible pages 4-4).

6) Expert synthesis and analysis (integrating the evidence)

The literature supports TMF1 as a multifunctional, localization-flexible scaffold that links membrane trafficking architecture to signal-dependent transcriptional control.

  1. Primary/most reproducible cellular role: The Golgi/tethering axis is supported by multiple cell biological methods (Golgi localization, Rab6-binding, trafficking defects, Golgi morphology quantification). These findings converge on TMF1 acting as a Rab6 effector/golgin mediating aspects of retrograde trafficking and maintaining Golgi compactness (fridmannsirkis2004tmfisa pages 5-7, yamane2007functionalinvolvementof pages 1-2).

  2. Conditional regulatory role in proteostasis: TMF1โ€™s BC-box-dependent proteasome coupling appears to become prominent under growth arrest or metabolic stress, consistent with its cytoplasmic redistribution under serum starvation and xenograft-specific effects absent in standard culture (perry2004tmfara160isa pages 8-9, abrham2009tmfara160downregulatesproangiogenic pages 8-10). This conditionality is important for functional annotation: TMF1 is not a constitutive E3 ligase, but rather an adaptor-like factor whose activity depends on cellular state.

  3. Emerging nuclear signaling integration: The PDGFRฮฒ nuclear trafficking/chromatin axis provides a mechanistic bridge between TMF1โ€™s trafficking identity and transcriptional outcomes, and has been highlighted in recent (2024) synthesis of RTK nuclear functions (papadopoulos2018pdgfrฮฒtranslocatesto pages 4-5, papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8, sengupta2024connectingtheends pages 21-23).

  4. Physiological specialization: TMF1โ€™s roles in spermiogenesis and in goblet cell mucin secretion indicate it contributes to specialized secretory processes requiring oriented Golgi dynamics and regulated granule fusion (elkis2015tmfara160governsthe pages 9-11, bel2014reprogrammedandtransmissible pages 4-5).

7) Quantitative highlights (selected)

  • Golgi morphology: compact Golgi in 58% of TMF-normal cells vs 8% of TMF-reduced cells after RNAi (Fridmann-Sirkis et al., 2004; Fig. 4C) (fridmannsirkis2004tmfisa media a620ef8a).
  • Nuclear PDGFRฮฒ: ~7% basal โ†’ ~26% at 30 min after PDGF-BB (Papadopoulos et al., 2018) (papadopoulos2018pdgfrฮฒtranslocatesto pages 2-4).
  • Nuclear PDGFRฮฒ/TMF-1 trafficking quantification: ~13 Golgi and 14 nuclear biotinylated PDGFRฮฒ clusters per cell; ~2.5 (Golgi) and 2.4 (nucleus) triple-positive dots per cell (Pearson >0.2; n=29) (papadopoulos2018pdgfrฮฒtranslocatesto pages 4-5).
  • p21-positive cells after knockdown: control 6.5% vs 21% (Fer KD), 25% (TMF-1 KD), 50% (Brg-1 KD) (Papadopoulos et al., 2018) (papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8).
  • PC3 xenografts: group size n=8 per group; reduced CD31 vessel mass with p<0.04 (n=6); IL-8 and IL-1ฮฒ reduced across three independent xenografts (Abrham et al., 2009) (abrham2009tmfara160downregulatesproangiogenic pages 5-7, abrham2009tmfara160downregulatesproangiogenic pages 3-5).
  • DSS colitis: 3% DSS, with significant outcomes (p<0.05) and n=5 in reported experiments; transmissible microbiota protective effect after 4 weeks cohousing (Bel et al., 2014) (bel2014reprogrammedandtransmissible pages 4-4).

8) Summary table (evidence-grounded)

The following table consolidates the validated functional areas, partners, evidence types, quantitative highlights, and DOI links.

Functional area Key partners Key experimental evidence (assay types) Quantitative/statistical highlights Primary sources with year + DOI URL
Golgi tethering / retrograde traffic Rab6; GalNAc-T2; Golgi membranes/cisternae Golgi fraction immunoblotting; immunofluorescence ring pattern in COS cells; C-terminal Rab6-binding fragment localization; RNAi in NRK cells; immuno-EM and toxin-trafficking assays showing endosome-to-Golgi and Golgi-to-ER roles (fridmannsirkis2004tmfisa pages 5-7, yamane2007functionalinvolvementof pages 1-2, fridmannsirkis2004tmfisa media a620ef8a) After TMF knockdown, compact Golgi seen in 58% of cells with normal TMF vs 8% of cells with reduced TMF; 10-15% of RNAi-transfected cells showed markedly lowered TMF; TMF/Rab6 loss redirected internalized Shiga toxin toward late endosomes/lysosomes (fridmannsirkis2004tmfisa pages 5-7, yamane2007functionalinvolvementof pages 1-2, fridmannsirkis2004tmfisa media a620ef8a) Fridmann-Sirkis et al., 2004, https://doi.org/10.1186/1471-2121-5-18; Yamane et al., 2007, https://doi.org/10.1016/j.yexcr.2007.07.010
Transcription / nuclear receptor coactivation Androgen receptor (AR); AR AF-1/AF-2; GR; PR Far-Western blotting; affinity pull-downs; co-immunoprecipitation; mammalian two-hybrid; luciferase/CAT reporter assays in PC-3 and other cells; expression detected with anti-ARA160/TMF antibody (hsiao1999isolationandcharacterization pages 1-3, hsiao1999isolationandcharacterization pages 4-5, hsiao1999isolationandcharacterization pages 1-1, hsiao1999isolationandcharacterization pages 3-3, hsiao1999isolationandcharacterization pages 3-4, hsiao1999isolationandcharacterization pages 5-7) ARA160/TMF enhanced DHT/AR transactivation from about 5-fold to about 17-fold in reporter assays; coexpression with ARA70 produced up to about 15-fold synergistic activation; interaction mapped to AR N-terminal region with ARA160 internal region aa 410-888 used in binding assays (hsiao1999isolationandcharacterization pages 4-5, hsiao1999isolationandcharacterization pages 3-3) Hsiao and Chang, 1999, https://doi.org/10.1074/jbc.274.32.22373
Ubiquitin-mediated degradation Elongin C; BC-box E3 ligase machinery; STAT3; Fer; p65/RelA Serum-starvation paradigms; ectopic expression; ubiquitination/proteasome assays; MG132 rescue; co-IP; immunoblotting; BC-box deletion/mutant analyses; TMF knockdown under starvation (perry2004tmfara160isa pages 1-2, perry2004tmfara160isa pages 8-9, abrham2009tmfara160downregulatesproangiogenic pages 1-2, abrham2009tmfara160downregulatesproangiogenic pages 8-10, abrham2009tmfara160downregulatesproangiogenic pages 7-8) Fer/STAT3 association strongest at 24 h starvation; Stat3/Fer downregulation most apparent at 24-48 h and significant by 72 h; MG132 blocked TMF-induced Stat3/Fer loss; TMF reduced p65/RelA protein by about 2-fold in xenografts, with significance reported at p less than 0.04, n=3 for western quantification (perry2004tmfara160isa pages 8-9, abrham2009tmfara160downregulatesproangiogenic pages 5-7, abrham2009tmfara160downregulatesproangiogenic pages 7-8) Perry et al., 2004, https://doi.org/10.1038/sj.onc.1208149; Abrham et al., 2009, https://doi.org/10.1002/ijc.24277
RTK nuclear signaling / chromatin remodeling PDGFR-beta; Fer; TMF-1; Brg-1/SWI-SNF; p21/CDKN1A; p53-regulated axis Nuclear/cytoplasmic/chromatin/matrix fractionation; phosphotyrosine immunoblot; siRNA knockdowns; confocal colocalization; cell-surface biotinylation plus triple-colocalization; qPCR; proliferation assays; p21 immunostaining quantified with CellProfiler (papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8, papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2, papadopoulos2018pdgfrฮฒtranslocatesto pages 2-4, papadopoulos2018pdgfrฮฒtranslocatesto pages 9-11, papadopoulos2018pdgfrฮฒtranslocatesto pages 15-16, papadopoulos2018pdgfrฮฒtranslocatesto pages 4-5, papadopoulos2018pdgfrฮฒtranslocatesto pages 8-9) Nuclear PDGFR-beta rose from about 7% basal to about 26% of total receptor at 30 min after PDGF-BB; AG1296 reduced nuclear translocation by about 50%; biotinylated PDGFR-beta clusters averaged 13 in Golgi and 14 in nucleus per cell, n=29, with about 2.5 and 2.4 triple-positive dots per cell respectively; p21-positive cells increased to 21% after Fer knockdown, 25% after TMF-1 knockdown, and 50% after Brg-1 knockdown vs 6.5% control; knockdown impaired proliferation with reported significance from p less than 0.05 to p less than 0.001 (papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8, papadopoulos2018pdgfrฮฒtranslocatesto pages 2-4, papadopoulos2018pdgfrฮฒtranslocatesto pages 4-5) Papadopoulos et al., 2018, https://doi.org/10.1083/jcb.201706118
Spermiogenesis / Golgi orientation Tubulin; microtubules; Golgi apparatus; pro-acrosomal vesicles; acroplaxome; KIF17B TMF knockout mouse; TEM; immunofluorescence with TGN38/Golgin97/phalloidin/KIF17B; co-IP with tubulin; microtubule co-precipitation; colchicine sensitivity; NIH3T3 EGFP-fragment mapping; immunogold EM (elkis2015tmfara160governsthe pages 17-18, elkis2015tmfara160governsthe pages 15-17, elkis2015tmfara160governsthe pages 9-11, elkis2015tmfara160governsthe pages 11-13) TMF contains coiled-coil and MIT domain required for stable Golgi association; colchicine dispersed ectopic TMF from Golgi; reported reproducibility included 4 independent transfections, 5 independent western analyses, and representative imaging from 1 of 20 cells across multiple sections or suspensions; TMF loss caused abnormal Golgi orientation, absent acroplaxome or chromatoid body, and failed vesicle targeting to nucleus (elkis2015tmfara160governsthe pages 15-17, elkis2015tmfara160governsthe pages 9-11, elkis2015tmfara160governsthe pages 11-13) Lerer-Goldshtein et al., 2010, https://doi.org/10.1016/j.ydbio.2010.07.033; Elkis et al., 2015, https://doi.org/10.1371/journal.pone.0145277
Mucus secretion / microbiome MUC2; goblet-cell mucus granules; colonic microbiota TMF knockout mouse; TEM of goblet cells; nonreducing/reducing MUC2 western blot; muc2 transcription analysis; 16S rRNA microbiome sequencing; weighted UniFrac PCoA; cohousing/reseparation DSS-colitis experiments; human colonic biopsy co-immunofluorescence showing TMF/MUC2 colocalization (bel2014reprogrammedandtransmissible pages 4-5, bel2014reprogrammedandtransmissible pages 2-3, bel2014reprogrammedandtransmissible pages 1-2, bel2014reprogrammedandtransmissible pages 3-4, bel2014reprogrammedandtransmissible pages 5-6, bel2014reprogrammedandtransmissible pages 4-4) TMF knockout mucus showed undegraded high-molecular-weight MUC2 under nonreducing conditions; wild-type showed smear consistent with degradation; DSS paradigms used 3% DSS for 5-7 days, with improved weight loss, fecal score, and histopathology outcomes in TMF knockout mice, p less than 0.05, n=5; protective microbiota transferred to wild-type after 4 weeks cohousing and was reversible after reseparation; Shannon diversity was higher in TMF knockout mice (bel2014reprogrammedandtransmissible pages 4-5, bel2014reprogrammedandtransmissible pages 2-3, bel2014reprogrammedandtransmissible pages 4-4) Bel et al., 2014, https://doi.org/10.1073/pnas.1319114111
Cancer / angiogenesis p65/RelA; IL-8; IL-1beta; laminin alpha3/beta3/gamma2; apoptotic machinery PC3 xenografts in athymic mice; HA-TMF ectopic expression; CD31 immunostaining; activated caspase-3 and TUNEL staining; Affymetrix expression profiling; semiquantitative RT-PCR validation; in vitro proliferation/MTT and flow cytometry controls (abrham2009tmfara160downregulatesproangiogenic pages 5-7, abrham2009tmfara160downregulatesproangiogenic pages 1-2, abrham2009tmfara160downregulatesproangiogenic pages 8-10, abrham2009tmfara160downregulatesproangiogenic pages 3-5, abrham2009tmfara160downregulatesproangiogenic pages 7-8, abrham2009tmfara160downregulatesproangiogenic pages 10-11) Xenograft study used 1 x 10^6 cells per mouse, n=8 per group; tumor impairment was significant at days 15, 19, 22, and 25; CD31-positive blood-vessel mass was reduced with p less than 0.04, n=6; IL-8 and IL-1beta decreased in three independent HA-TMF xenografts; in vitro proliferation was unchanged despite in vivo tumor suppression, consistent with stress-dependent antiangiogenic activity (abrham2009tmfara160downregulatesproangiogenic pages 5-7, abrham2009tmfara160downregulatesproangiogenic pages 3-5, abrham2009tmfara160downregulatesproangiogenic pages 7-8) Abrham et al., 2009, https://doi.org/10.1002/ijc.24277

Table: This table summarizes experimentally validated functions of human TMF1/P82094 across trafficking, nuclear signaling, proteostasis, reproduction, mucosal biology, and cancer. It highlights key partners, assay types, quantitative findings, and the primary supporting papers with DOI links.

9) Notes on evidence gaps and 2023โ€“2024 coverage

Within the retrieved corpus, TMF1-specific mechanistic advances in 2023โ€“2024 were limited; however, a 2024 review explicitly positions TMF1 in the contemporary framework of nuclear RTK signaling/chromatin remodeling (sengupta2024connectingtheends pages 21-23). Most definitive mechanistic and in vivo functional studies currently available here span 1999โ€“2018 (AR coactivation; Rab6/golgin trafficking; BC-box proteostasis; PDGFRฮฒ nuclear chromatin axis) plus strong in vivo phenotypes in 2014โ€“2015 (mucus secretion/microbiome; spermiogenesis) (hsiao1999isolationandcharacterization pages 3-3, yamane2007functionalinvolvementof pages 1-2, perry2004tmfara160isa pages 8-9, papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2, bel2014reprogrammedandtransmissible pages 2-3, elkis2015tmfara160governsthe pages 11-13).

References

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  2. (fridmannsirkis2004tmfisa pages 5-7): Yael Fridmann-Sirkis, Symeon Siniossoglou, and Hugh RB Pelham. Tmf is a golgin that binds rab6 and influences golgi morphology. BMC Cell Biology, 5:18-18, May 2004. URL: https://doi.org/10.1186/1471-2121-5-18, doi:10.1186/1471-2121-5-18. This article has 119 citations.

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  5. (hsiao1999isolationandcharacterization pages 1-3): Pei-Wen Hsiao and Chawnshang Chang. Isolation and characterization of ara160 as the first androgen receptor n-terminal-associated coactivator in human prostate cells*. The Journal of Biological Chemistry, 274:22373-22379, Aug 1999. URL: https://doi.org/10.1074/jbc.274.32.22373, doi:10.1074/jbc.274.32.22373. This article has 180 citations.

  6. (hsiao1999isolationandcharacterization pages 4-5): Pei-Wen Hsiao and Chawnshang Chang. Isolation and characterization of ara160 as the first androgen receptor n-terminal-associated coactivator in human prostate cells*. The Journal of Biological Chemistry, 274:22373-22379, Aug 1999. URL: https://doi.org/10.1074/jbc.274.32.22373, doi:10.1074/jbc.274.32.22373. This article has 180 citations.

  7. (perry2004tmfara160isa pages 1-2): Erez Perry, Rachel Tsruya, Pavel Levitsky, Oz Pomp, Michal Taller, Shira Weisberg, Wendy Parris, Sarang Kulkarni, Hana Malovani, Tony Pawson, Sally Shpungin, and Uri Nir. Tmf/ara160 is a bc-box-containing protein that mediates the degradation of stat3. Oncogene, 23:8908-8919, Nov 2004. URL: https://doi.org/10.1038/sj.onc.1208149, doi:10.1038/sj.onc.1208149. This article has 70 citations and is from a domain leading peer-reviewed journal.

  8. (perry2004tmfara160isa pages 8-9): Erez Perry, Rachel Tsruya, Pavel Levitsky, Oz Pomp, Michal Taller, Shira Weisberg, Wendy Parris, Sarang Kulkarni, Hana Malovani, Tony Pawson, Sally Shpungin, and Uri Nir. Tmf/ara160 is a bc-box-containing protein that mediates the degradation of stat3. Oncogene, 23:8908-8919, Nov 2004. URL: https://doi.org/10.1038/sj.onc.1208149, doi:10.1038/sj.onc.1208149. This article has 70 citations and is from a domain leading peer-reviewed journal.

  9. (abrham2009tmfara160downregulatesproangiogenic pages 1-2): Galya Abrham, Marina Volpe, Sally Shpungin, and Uri Nir. Tmf/ara160 downregulates proangiogenic genes and attenuates the progression of pc3 xenografts. International Journal of Cancer, 125:43-53, Jul 2009. URL: https://doi.org/10.1002/ijc.24277, doi:10.1002/ijc.24277. This article has 24 citations and is from a domain leading peer-reviewed journal.

  10. (abrham2009tmfara160downregulatesproangiogenic pages 7-8): Galya Abrham, Marina Volpe, Sally Shpungin, and Uri Nir. Tmf/ara160 downregulates proangiogenic genes and attenuates the progression of pc3 xenografts. International Journal of Cancer, 125:43-53, Jul 2009. URL: https://doi.org/10.1002/ijc.24277, doi:10.1002/ijc.24277. This article has 24 citations and is from a domain leading peer-reviewed journal.

  11. (papadopoulos2018pdgfrฮฒtranslocatesto pages 1-2): Natalia Papadopoulos, Johan Lennartsson, and Carl-Henrik Heldin. Pdgfrฮฒ translocates to the nucleus and regulates chromatin remodeling via tata elementโ€“modifying factor 1. The Journal of Cell Biology, 217:1701-1717, May 2018. URL: https://doi.org/10.1083/jcb.201706118, doi:10.1083/jcb.201706118. This article has 35 citations.

  12. (papadopoulos2018pdgfrฮฒtranslocatesto pages 9-11): Natalia Papadopoulos, Johan Lennartsson, and Carl-Henrik Heldin. Pdgfrฮฒ translocates to the nucleus and regulates chromatin remodeling via tata elementโ€“modifying factor 1. The Journal of Cell Biology, 217:1701-1717, May 2018. URL: https://doi.org/10.1083/jcb.201706118, doi:10.1083/jcb.201706118. This article has 35 citations.

  13. (papadopoulos2018pdgfrฮฒtranslocatesto pages 7-8): Natalia Papadopoulos, Johan Lennartsson, and Carl-Henrik Heldin. Pdgfrฮฒ translocates to the nucleus and regulates chromatin remodeling via tata elementโ€“modifying factor 1. The Journal of Cell Biology, 217:1701-1717, May 2018. URL: https://doi.org/10.1083/jcb.201706118, doi:10.1083/jcb.201706118. This article has 35 citations.

  14. (sengupta2024connectingtheends pages 21-23): Priyanka Sengupta, Russa Das, Piyali Majumder, and Debashis Mukhopadhyay. Connecting the ends: signaling via receptor tyrosine kinases and cytoskeletal degradation in neurodegeneration. Exploration of Neuroscience, 3:1-26, Feb 2024. URL: https://doi.org/10.37349/en.2024.00033, doi:10.37349/en.2024.00033. This article has 18 citations.

  15. (elkis2015tmfara160governsthe pages 11-13): Yoav Elkis, Shai Bel, Roni Rahimi, Tali Lerer-Goldstein, Smadar Levin-Zaidman, Tatiana Babushkin, Sally Shpungin, and Uri Nir. Tmf/ara160 governs the dynamic spatial orientation of the golgi apparatus during sperm development. PLoS ONE, 10:e0145277, Dec 2015. URL: https://doi.org/10.1371/journal.pone.0145277, doi:10.1371/journal.pone.0145277. This article has 29 citations and is from a peer-reviewed journal.

  16. (elkis2015tmfara160governsthe pages 15-17): Yoav Elkis, Shai Bel, Roni Rahimi, Tali Lerer-Goldstein, Smadar Levin-Zaidman, Tatiana Babushkin, Sally Shpungin, and Uri Nir. Tmf/ara160 governs the dynamic spatial orientation of the golgi apparatus during sperm development. PLoS ONE, 10:e0145277, Dec 2015. URL: https://doi.org/10.1371/journal.pone.0145277, doi:10.1371/journal.pone.0145277. This article has 29 citations and is from a peer-reviewed journal.

  17. (fridmannsirkis2004tmfisa media a620ef8a): Yael Fridmann-Sirkis, Symeon Siniossoglou, and Hugh RB Pelham. Tmf is a golgin that binds rab6 and influences golgi morphology. BMC Cell Biology, 5:18-18, May 2004. URL: https://doi.org/10.1186/1471-2121-5-18, doi:10.1186/1471-2121-5-18. This article has 119 citations.

  18. (abrham2009tmfara160downregulatesproangiogenic pages 5-7): Galya Abrham, Marina Volpe, Sally Shpungin, and Uri Nir. Tmf/ara160 downregulates proangiogenic genes and attenuates the progression of pc3 xenografts. International Journal of Cancer, 125:43-53, Jul 2009. URL: https://doi.org/10.1002/ijc.24277, doi:10.1002/ijc.24277. This article has 24 citations and is from a domain leading peer-reviewed journal.

  19. (papadopoulos2018pdgfrฮฒtranslocatesto pages 2-4): Natalia Papadopoulos, Johan Lennartsson, and Carl-Henrik Heldin. Pdgfrฮฒ translocates to the nucleus and regulates chromatin remodeling via tata elementโ€“modifying factor 1. The Journal of Cell Biology, 217:1701-1717, May 2018. URL: https://doi.org/10.1083/jcb.201706118, doi:10.1083/jcb.201706118. This article has 35 citations.

  20. (papadopoulos2018pdgfrฮฒtranslocatesto pages 4-5): Natalia Papadopoulos, Johan Lennartsson, and Carl-Henrik Heldin. Pdgfrฮฒ translocates to the nucleus and regulates chromatin remodeling via tata elementโ€“modifying factor 1. The Journal of Cell Biology, 217:1701-1717, May 2018. URL: https://doi.org/10.1083/jcb.201706118, doi:10.1083/jcb.201706118. This article has 35 citations.

  21. (bel2014reprogrammedandtransmissible pages 4-5): Shai Bel, Yoav Elkis, Hila Elifantz, Omry Koren, Rotem Ben-Hamo, Tal Lerer-Goldshtein, Roni Rahimi, Shomron Ben Horin, Abraham Nyska, Sally Shpungin, and Uri Nir. Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in tmfโˆ’/โˆ’ mice. Proceedings of the National Academy of Sciences, 111:4964-4969, Mar 2014. URL: https://doi.org/10.1073/pnas.1319114111, doi:10.1073/pnas.1319114111. This article has 64 citations and is from a highest quality peer-reviewed journal.

  22. (bel2014reprogrammedandtransmissible pages 2-3): Shai Bel, Yoav Elkis, Hila Elifantz, Omry Koren, Rotem Ben-Hamo, Tal Lerer-Goldshtein, Roni Rahimi, Shomron Ben Horin, Abraham Nyska, Sally Shpungin, and Uri Nir. Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in tmfโˆ’/โˆ’ mice. Proceedings of the National Academy of Sciences, 111:4964-4969, Mar 2014. URL: https://doi.org/10.1073/pnas.1319114111, doi:10.1073/pnas.1319114111. This article has 64 citations and is from a highest quality peer-reviewed journal.

  23. (bel2014reprogrammedandtransmissible pages 4-4): Shai Bel, Yoav Elkis, Hila Elifantz, Omry Koren, Rotem Ben-Hamo, Tal Lerer-Goldshtein, Roni Rahimi, Shomron Ben Horin, Abraham Nyska, Sally Shpungin, and Uri Nir. Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in tmfโˆ’/โˆ’ mice. Proceedings of the National Academy of Sciences, 111:4964-4969, Mar 2014. URL: https://doi.org/10.1073/pnas.1319114111, doi:10.1073/pnas.1319114111. This article has 64 citations and is from a highest quality peer-reviewed journal.

  24. (elkis2015tmfara160governsthe pages 9-11): Yoav Elkis, Shai Bel, Roni Rahimi, Tali Lerer-Goldstein, Smadar Levin-Zaidman, Tatiana Babushkin, Sally Shpungin, and Uri Nir. Tmf/ara160 governs the dynamic spatial orientation of the golgi apparatus during sperm development. PLoS ONE, 10:e0145277, Dec 2015. URL: https://doi.org/10.1371/journal.pone.0145277, doi:10.1371/journal.pone.0145277. This article has 29 citations and is from a peer-reviewed journal.

  25. (OpenTargets Search: -TMF1): Open Targets Query (-TMF1, 5 results). Buniello, A. et al. (2025). Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery. Nucleic Acids Research.

  26. (abrham2009tmfara160downregulatesproangiogenic pages 8-10): Galya Abrham, Marina Volpe, Sally Shpungin, and Uri Nir. Tmf/ara160 downregulates proangiogenic genes and attenuates the progression of pc3 xenografts. International Journal of Cancer, 125:43-53, Jul 2009. URL: https://doi.org/10.1002/ijc.24277, doi:10.1002/ijc.24277. This article has 24 citations and is from a domain leading peer-reviewed journal.

  27. (abrham2009tmfara160downregulatesproangiogenic pages 3-5): Galya Abrham, Marina Volpe, Sally Shpungin, and Uri Nir. Tmf/ara160 downregulates proangiogenic genes and attenuates the progression of pc3 xenografts. International Journal of Cancer, 125:43-53, Jul 2009. URL: https://doi.org/10.1002/ijc.24277, doi:10.1002/ijc.24277. This article has 24 citations and is from a domain leading peer-reviewed journal.

  28. (hsiao1999isolationandcharacterization pages 3-4): Pei-Wen Hsiao and Chawnshang Chang. Isolation and characterization of ara160 as the first androgen receptor n-terminal-associated coactivator in human prostate cells*. The Journal of Biological Chemistry, 274:22373-22379, Aug 1999. URL: https://doi.org/10.1074/jbc.274.32.22373, doi:10.1074/jbc.274.32.22373. This article has 180 citations.

  29. (hsiao1999isolationandcharacterization pages 5-7): Pei-Wen Hsiao and Chawnshang Chang. Isolation and characterization of ara160 as the first androgen receptor n-terminal-associated coactivator in human prostate cells*. The Journal of Biological Chemistry, 274:22373-22379, Aug 1999. URL: https://doi.org/10.1074/jbc.274.32.22373, doi:10.1074/jbc.274.32.22373. This article has 180 citations.

  30. (papadopoulos2018pdgfrฮฒtranslocatesto pages 15-16): Natalia Papadopoulos, Johan Lennartsson, and Carl-Henrik Heldin. Pdgfrฮฒ translocates to the nucleus and regulates chromatin remodeling via tata elementโ€“modifying factor 1. The Journal of Cell Biology, 217:1701-1717, May 2018. URL: https://doi.org/10.1083/jcb.201706118, doi:10.1083/jcb.201706118. This article has 35 citations.

  31. (papadopoulos2018pdgfrฮฒtranslocatesto pages 8-9): Natalia Papadopoulos, Johan Lennartsson, and Carl-Henrik Heldin. Pdgfrฮฒ translocates to the nucleus and regulates chromatin remodeling via tata elementโ€“modifying factor 1. The Journal of Cell Biology, 217:1701-1717, May 2018. URL: https://doi.org/10.1083/jcb.201706118, doi:10.1083/jcb.201706118. This article has 35 citations.

  32. (elkis2015tmfara160governsthe pages 17-18): Yoav Elkis, Shai Bel, Roni Rahimi, Tali Lerer-Goldstein, Smadar Levin-Zaidman, Tatiana Babushkin, Sally Shpungin, and Uri Nir. Tmf/ara160 governs the dynamic spatial orientation of the golgi apparatus during sperm development. PLoS ONE, 10:e0145277, Dec 2015. URL: https://doi.org/10.1371/journal.pone.0145277, doi:10.1371/journal.pone.0145277. This article has 29 citations and is from a peer-reviewed journal.

  33. (bel2014reprogrammedandtransmissible pages 1-2): Shai Bel, Yoav Elkis, Hila Elifantz, Omry Koren, Rotem Ben-Hamo, Tal Lerer-Goldshtein, Roni Rahimi, Shomron Ben Horin, Abraham Nyska, Sally Shpungin, and Uri Nir. Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in tmfโˆ’/โˆ’ mice. Proceedings of the National Academy of Sciences, 111:4964-4969, Mar 2014. URL: https://doi.org/10.1073/pnas.1319114111, doi:10.1073/pnas.1319114111. This article has 64 citations and is from a highest quality peer-reviewed journal.

  34. (bel2014reprogrammedandtransmissible pages 3-4): Shai Bel, Yoav Elkis, Hila Elifantz, Omry Koren, Rotem Ben-Hamo, Tal Lerer-Goldshtein, Roni Rahimi, Shomron Ben Horin, Abraham Nyska, Sally Shpungin, and Uri Nir. Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in tmfโˆ’/โˆ’ mice. Proceedings of the National Academy of Sciences, 111:4964-4969, Mar 2014. URL: https://doi.org/10.1073/pnas.1319114111, doi:10.1073/pnas.1319114111. This article has 64 citations and is from a highest quality peer-reviewed journal.

  35. (bel2014reprogrammedandtransmissible pages 5-6): Shai Bel, Yoav Elkis, Hila Elifantz, Omry Koren, Rotem Ben-Hamo, Tal Lerer-Goldshtein, Roni Rahimi, Shomron Ben Horin, Abraham Nyska, Sally Shpungin, and Uri Nir. Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in tmfโˆ’/โˆ’ mice. Proceedings of the National Academy of Sciences, 111:4964-4969, Mar 2014. URL: https://doi.org/10.1073/pnas.1319114111, doi:10.1073/pnas.1319114111. This article has 64 citations and is from a highest quality peer-reviewed journal.

  36. (abrham2009tmfara160downregulatesproangiogenic pages 10-11): Galya Abrham, Marina Volpe, Sally Shpungin, and Uri Nir. Tmf/ara160 downregulates proangiogenic genes and attenuates the progression of pc3 xenografts. International Journal of Cancer, 125:43-53, Jul 2009. URL: https://doi.org/10.1002/ijc.24277, doi:10.1002/ijc.24277. This article has 24 citations and is from a domain leading peer-reviewed journal.

Citations

  1. hsiao1999isolationandcharacterization pages 1-1
  2. fridmannsirkis2004tmfisa pages 5-7
  3. yamane2007functionalinvolvementof pages 1-2
  4. hsiao1999isolationandcharacterization pages 4-5
  5. sengupta2024connectingtheends pages 21-23
  6. hsiao1999isolationandcharacterization pages 3-3
  7. bel2014reprogrammedandtransmissible pages 4-5
  8. bel2014reprogrammedandtransmissible pages 2-3
  9. bel2014reprogrammedandtransmissible pages 4-4
  10. hsiao1999isolationandcharacterization pages 1-3
  11. hsiao1999isolationandcharacterization pages 3-4
  12. hsiao1999isolationandcharacterization pages 5-7
  13. bel2014reprogrammedandtransmissible pages 1-2
  14. bel2014reprogrammedandtransmissible pages 3-4
  15. bel2014reprogrammedandtransmissible pages 5-6
  16. https://doi.org/10.1074/jbc.274.32.22373
  17. https://doi.org/10.1186/1471-2121-5-18
  18. https://doi.org/10.1016/j.yexcr.2007.07.010
  19. https://doi.org/10.1038/sj.onc.1208149
  20. https://doi.org/10.1002/ijc.24277
  21. https://doi.org/10.1083/jcb.201706118
  22. https://doi.org/10.37349/en.2024.00033
  23. https://doi.org/10.1371/journal.pone.0145277
  24. https://doi.org/10.1073/pnas.1319114111
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  30. https://doi.org/10.1016/j.yexcr.2007.07.010,
  31. https://doi.org/10.1038/sj.onc.1208149,
  32. https://doi.org/10.1002/ijc.24277,
  33. https://doi.org/10.1083/jcb.201706118,
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  36. https://doi.org/10.1073/pnas.1319114111,

๐Ÿ“š Additional Documentation

Notes

(TMF1-notes.md)

TMF1 (TATA element modulatory factor 1) โ€” research notes

Context

This review was triggered by geneontology/go-annotation#6381 ("TMF1 annotation review"). Curators (V. Wood, H. Attrill, S. Munro group, L. Breuza, R. Lovering, P. Gaudet) flagged that the human TMF1 GO annotations are still dominated by transcription-related terms (transcription coactivator activity, androgen receptor signaling, positive regulation of transcription by RNA Pol II) that trace back to a small set of late-1990s/early-2000s overexpression studies, while the well-supported biology is now Golgi vesicle tethering (golgin) in retrograde and intra-Golgi vesicle traffic.

FlyBase already updated the D. melanogaster TMF1 ortholog to "vesicle membrane tethering activity" via P2GO (per @hattrill in #6381).

Summary of evidence

TMF1 is a golgin (vesicle tethering factor) on the trans-Golgi rim

  • PMID:17698061. Knockdown of TMF or Rab6 blocks retrograde transport of Shiga toxin from early/recycling endosomes to the TGN and causes Rab6-dependent displacement of GalNAc-T2 (but not GalT) from the Golgi. The authors conclude "critical roles for TMF in two Rab6-dependent retrograde transport processes: one from endosomes to the Golgi and the other from the Golgi to the ER."
  • PMID:23239882. Establishes TMF as the long coiled-coil tether that, together with the COG complex, mediates retrograde tethering of intra-Golgi vesicles.
  • PMID:28122620. Mitochondrial-relocation assay shows that TMF1 acts as a vesicle-capture (tethering) golgin. The first 36 residues of TMF are necessary and sufficient for intra-Golgi vesicle capture; the C-terminal coiled-coil with the Rab6-binding region also contributes capture activity.
  • PMID:36103876. Drosophila in vivo characterisation reaffirms TMF as an intra-Golgi vesicle-capturing golgin with conserved tissue-level functions.

Mechanism / structure

  • TMF is recruited to the Golgi membrane via a C-terminal Rab6-binding coiled-coil (UniProt SUBCELLULAR LOCATION; PMID:17698061; PMID:23239882; PMID:28122620). It contains predicted disordered N-terminus (~residues 1โ€“400) followed by extensive coiled-coil (residues 439โ€“922, 984โ€“1092 per UniProt feature table).
  • The N-terminal region has a conserved M-S-W-L/F motif shared with the other intra-Golgi tethering golgins GMAP-210 and golgin-84 PMID:28122620.

Mouse phenotype consistent with Golgi/secretion role, not transcription

  • PMID:23000399. The endocrine phenotype is consistent with disrupted Leydig cell secretion / spermiogenesis acrosome biogenesis (a Golgi-derived organelle), not with loss of a transcription coactivator.
  • PMID:24639530. The colon mucus phenotype is consistent with disrupted Golgi-mediated mucin glycosylation/secretion.
  • PMID:1409643. The original cloning paper used HIV-1 LTR reporter and in vitro TBP assays; the protein was characterised in a viral context, not in regulation of endogenous cellular genes.
  • PMID:10428808. Hedged language ("might function"); transient overexpression in PC-3 cells; a Gal4-DNA binding domain fusion to TMF1 reportedly does not work as a dbTF (data not shown), inconsistent with a bona fide transcription coactivator activity (GO:0003713 sensu stricto).
  • PMID:12044884. Reports interaction with hbrm/hSNF2ฮฑ and BRG-1/hSNF2ฮฒ SWI/SNF subunits. The bulk of TMF1 is at the Golgi; nuclear pool is a minor fraction.
  • PMID:15467733. Reports a BC-box-mediated role in Stat3 ubiquitination; this is the basis of the regulation-of-proteasomal-protein-catabolic-process annotations.
  • The 2025 Pharos status for TMF1 is "Tbio" (proteins with virtually no functional/drug characterisation), reflecting the field's view that transcription coactivator function is not solidly established.

Implications for GO annotation

Existing annotation (Aspect) Recommendation Rationale
GO:0005794 Golgi apparatus, GO:0000139 Golgi membrane (CC) ACCEPT โ€” core Multiple IDA/IBA studies; UniProt SUBCELLULAR LOCATION; canonical golgin localization.
GO:0005829 cytosol (CC, TAS Reactome) KEEP_AS_NON_CORE Reflects diffuse cytoplasmic pool described in PMID:15467733; TMF is concentrated at Golgi.
GO:0005634 nucleus (CC, IEA) MARK_AS_OVER_ANNOTATED A minor isoform-dependent nuclear pool was reported (PMID:12044884) but the protein's primary localization is Golgi; the SubCell-derived IEA over-emphasizes this fraction.
GO:0005737 cytoplasm (CC, IEA) KEEP_AS_NON_CORE Generic; subsumed by Golgi/cytosol.
GO:0005783 endoplasmic reticulum (IBA, IEA-Ensembl) MARK_AS_OVER_ANNOTATED TMF mediates retrograde traffic to the ER but is not a steady-state ER-resident protein.
GO:0006891 intra-Golgi vesicle-mediated transport (NEW) NEW Strongly supported by PMID:28122620, PMID:23239882, PMID:36103876.
GO:0099041 vesicle tethering to Golgi (NEW) NEW Best existing BP for the golgin tethering activity (PMID:23239882, PMID:28122620).
GO:0006895 retrograde transport, Golgi to endoplasmic reticulum (NEW) NEW Established by PMID:17698061 (Rab6-dependent retrograde traffic).
GO:0042147 retrograde transport, endosome to Golgi (NEW) NEW Established by PMID:17698061 (Shiga toxin retrograde trafficking).
GO:0003713 transcription coactivator activity (IDA, PMID:10428808) MARK_AS_OVER_ANNOTATED Single overexpression study with hedged conclusions; Gal4-DBD fusion fails to transactivate; primary biology is at the Golgi. Demote from core; do not delete because a low-level moonlighting role cannot be excluded.
GO:0030521 androgen receptor signaling pathway (IDA, PMID:10428808) MARK_AS_OVER_ANNOTATED Same single overexpression study; mouse KO testosterone phenotype is more compatible with disrupted Leydig/spermiogenesis secretion than with cell-autonomous loss of an AR coregulator.
GO:0045944 positive regulation of transcription by RNA Pol II (IDA, PMID:10428808) MARK_AS_OVER_ANNOTATED Inferred from the same single transient transfection assay; not validated by orthogonal assays.
GO:0050681 nuclear androgen receptor binding (IPI, PMID:10428808) KEEP_AS_NON_CORE The far-Western/co-IP interaction is real, but is a moonlighting feature, not a core function.
GO:0061136 regulation of proteasomal protein catabolic process (ISS/IEA) KEEP_AS_NON_CORE PMID:15467733 supports a BC-box/Elongin-C-mediated role in Stat3 ubiquitination; this is a discrete moonlighting activity at the Golgi, not the core function.
GO:0005515 protein binding (IPI x2) REMOVE / MARK_AS_OVER_ANNOTATED Uninformative per project guideline.

Suggested new term

A molecular-function counterpart of GO:0099022 ("vesicle tethering" โ€” currently a BP) would let us annotate golgins like TMF1, GMAP-210, golgin-84 and the GRIP-domain golgins to a meaningful MF beyond "protein binding". ValWood (#6381) referred to a prospective "vesicle membrane tethering activity" term (not yet present in GO at time of writing โ€” GO:7770062 returned 404 from the GO API on 2026-05-02). Until such a term is added, GO:0099041 (vesicle tethering to Golgi) is the most informative existing BP, and we record the missing MF in proposed_new_terms.

๐Ÿ“„ View Raw YAML

id: P82094
gene_symbol: TMF1
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: 'Trans-Golgi golgin (TATA element modulatory factor 1 / ARA160). A long
  coiled-coil peripheral membrane protein recruited to the Golgi rim via a C-terminal
  Rab6-binding region, where it acts as a vesicle-tethering factor. Captures intra-Golgi
  transport vesicles via a conserved N-terminal motif (M-S-W-L/F, shared with the
  related intra-Golgi golgins GMAP-210 and golgin-84) and cooperates with the COG
  complex to dock retrograde vesicles. Required for Rab6-dependent retrograde transport
  from endosomes to the trans-Golgi network and from the Golgi to the ER (Shiga-toxin
  trafficking, GalNAc-T2 retention). Loss in mouse and Drosophila causes male-sterility
  acrosome biogenesis defects and altered Golgi-derived mucin glycosylation, consistent
  with a primary role in Golgi vesicle traffic. Despite the historical name and a
  small set of late-1990s overexpression studies that suggested a moonlighting role
  as a TBP-binding/androgen-receptor coactivator and a BC-box adaptor that targets
  STAT3 for proteasomal degradation, the bulk of mechanistically validated biology
  is at the Golgi and not in transcription.

  '
alternative_products:
- name: '1'
  id: P82094-1
- name: '2'
  id: P82094-2
  sequence_note: VSP_037411
existing_annotations:
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'IBA from PAINT. TMF1 is a canonical golgin and the Golgi rim is its
      primary, conserved localization (UniProt SUBCELLULAR LOCATION; PMID:17698061;
      PMID:23239882; PMID:28122620). Accept as core localization.

      '
    action: ACCEPT
    supported_by:
    - reference_id: PMID:17698061
      supporting_text: TMF signal surrounded Rab6-positive Golgi structures and immunoelectron
        microscopy revealed that TMF is concentrated at the budding structures localized
        at the tips of cisternae.
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'IBA from PAINT. TMF1 mediates Rab6-dependent retrograde transport from
      Golgi to ER (PMID:17698061), so it is transiently associated with ER-directed
      retrograde carriers, but it is not a steady-state ER-resident protein. Microscopy
      consistently shows the trans-Golgi rim, not the ER, as the primary localization.
      The annotation likely reflects over-propagation of yeast/fungal homolog data.
      Mark as over-annotated.

      '
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0000139
    label: Golgi membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: 'IEA from UniProt SubCell mapping. TMF1 is a peripheral Golgi-membrane
      protein concentrated at the tips of cisternae (UniProt SUBCELLULAR LOCATION;
      PMID:17698061). More precise than the bare Golgi apparatus annotation. Accept
      as core.

      '
    action: ACCEPT
    supported_by:
    - reference_id: PMID:17698061
      supporting_text: TMF is concentrated at the budding structures localized at
        the tips of cisternae.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: 'IEA from UniProt SubCell mapping. A nuclear pool of one TMF isoform
      was reported (PMID:12044884), but the dominant localization in every cell type
      examined is the Golgi (PMID:15467733 explicitly describes TMF/ARA160 as a Golgi-resident
      protein). The IEA over-emphasizes a minor, isoform-restricted fraction; the
      primary biology of the protein is not nuclear. Mark as over-annotated.

      '
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: PMID:12044884
      supporting_text: TMF isoforms differentially localize in the Golgi apparatus
        and the nucleus.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: 'IEA from UniProt SubCell mapping. Generic parent term subsumed by the
      more specific Golgi membrane / cytosol annotations. Keep as non-core.

      '
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20195357
  review:
    summary: 'High-throughput mRNA-display interactome screen reporting TMF1-NR3C1
      binding. "Protein binding" is uninformative per project curation guidelines
      (CLAUDE.md). The relevant biology (interactions with Rab6, COG, AR, STAT3, FER,
      Elongin) is captured by more specific annotations. Mark as over-annotated.

      '
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  review:
    summary: 'High-throughput Y2H reference map (HuRI). Reports binding to CMTM5 isoform
      Q96DZ9-2; no functional follow-up. Uninformative MF per project guidelines.
      Mark as over-annotated.

      '
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: 'IEA via Ensembl ortholog transfer from mouse Tmf1 (UniProtKB:B9EKI3).
      Same concern as the IBA ER annotation: TMF1 mediates retrograde traffic to the
      ER but is not an ER-resident protein. Mark as over-annotated.

      '
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: 'IEA via Ensembl ortholog transfer from mouse Tmf1. Redundant with the
      direct human IBA/IDA Golgi annotations but still correct. Accept.

      '
    action: ACCEPT
- term:
    id: GO:0061136
    label: regulation of proteasomal protein catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: 'IEA via Ensembl ortholog transfer from mouse Tmf1. Reflects PMID:15467733,
      which showed that the BC-box motif of TMF/ARA160 mediates its binding to Elongin
      C and that ectopic expression in serum-starved C2C12 cells drives Stat3 ubiquitination
      and proteasomal degradation. This is a discrete, mechanistically supported moonlighting
      activity at the Golgi cytoplasmic face but is not the protein''s core function.
      Keep as non-core.

      '
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:15467733
      supporting_text: Amino-acid sequence analysis identified a BC-box element in
        TMF/ARA160 that mediated the binding of this protein to elongin C. Ectopic
        expression of TMF/ARA160 in serum-starved C2C12 cells drove the ubiquitination
        and proteasomal degradation of Stat3.
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: 'IDA from Human Protein Atlas immunofluorescence. Direct experimental
      confirmation of Golgi localization. Accept as core.

      '
    action: ACCEPT
- term:
    id: GO:0003713
    label: transcription coactivator activity
  evidence_type: IDA
  original_reference_id: PMID:10428808
  review:
    summary: 'IDA based on a single 1999 transient-transfection / reporter study in
      PC-3 cells. The same paper notes that a Gal4-DBD fusion to TMF1 fails to transactivate
      reporter genes (data not shown), which is inconsistent with a bona fide transcription
      coactivator (GO:0003713) sensu stricto - the authors propose that TMF acts only
      together with the AF-1 domain of steroid receptors. The mechanistically established
      function of TMF1 is at the Golgi (PMID:17698061; PMID:23239882; PMID:28122620);
      TMF1 has no DNA-binding domain (its "TMF_DNA_bd"/"TMF_TATA_bd" Pfam domains
      are operationally defined from the original 1992 HIV-1 LTR study and have not
      been validated as endogenous DNA-binding modules). The Pharos target development
      level is "Tbio" (no validated function). Down-rate from a core MF; flag as over-annotation
      pending orthogonal validation, but do not delete outright because a low-level
      moonlighting role at the AR cannot be formally excluded.

      '
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: PMID:10428808
      supporting_text: Transient transfection assays demonstrated that ARA160 might
        function as a coactivator for AR-mediated transactivation in human prostate
        cancer PC-3 cells.
- term:
    id: GO:0030521
    label: androgen receptor signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:10428808
  review:
    summary: 'IDA from the same single 1999 overexpression study (PMID:10428808).
      The mouse TMF-/- testosterone/spermatogenesis phenotype (PMID:23000399) is more
      compatible with disrupted Leydig cell secretion / Golgi-dependent acrosome biogenesis
      than with cell-autonomous loss of an AR coregulator. Mark as over-annotated.

      '
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: IDA
  original_reference_id: PMID:10428808
  review:
    summary: 'IDA inferred from the same single transient transfection assay on an
      AR-responsive reporter in PC-3 cells. Not validated by orthogonal assays (ChIP-seq,
      KO RNA-seq) or independent groups. Mark as over-annotated.

      '
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0050681
    label: nuclear androgen receptor binding
  evidence_type: IPI
  original_reference_id: PMID:10428808
  review:
    summary: 'IPI based on far-Western blotting and co-immunoprecipitation between
      AR N-terminal peptide and TMF1/ARA160 (PMID:10428808). The physical interaction
      is reproducibly observed, but in the context of TMF1''s overall biology the
      AR-binding role is a moonlighting feature of a Golgi protein, not a core function.
      Keep as non-core.

      '
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6811431
  review:
    summary: 'TAS from Reactome "RAB6:GTP binds the GARP and COG complexes, t-SNAREs
      and endosome-derived vesicles". Reflects the Reactome cytosolic-pool placeholder
      for tethering factors. The diffuse cytoplasmic distribution observed under low-serum
      conditions (PMID:15467733) is real but the protein is concentrated at Golgi
      membranes. Keep as non-core.

      '
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6814091
  review:
    summary: 'TAS from Reactome "ARL1 recruits TGN Golgin homodimers". Same comment
      as the previous cytosol annotation - reflects the Reactome cytosolic-pool placeholder.
      Keep as non-core.

      '
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-6814682
  review:
    summary: 'TAS from Reactome "Fusion of early-endosome derived vesicles at the
      TGN". Same comment - Reactome placeholder for the cytosolic tethering pool.
      Keep as non-core.

      '
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0061136
    label: regulation of proteasomal protein catabolic process
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: 'ISS from manual transfer of mouse Tmf1 (UniProtKB:B9EKI3). Reflects
      PMID:15467733 (TMF/ARA160 BC-box-Elongin C-mediated Stat3 ubiquitination). Mechanistically
      supported but is a moonlighting activity of the Golgi pool, not the core function.
      Keep as non-core.

      '
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:15467733
      supporting_text: Amino-acid sequence analysis identified a BC-box element in
        TMF/ARA160 that mediated the binding of this protein to elongin C.
- term:
    id: GO:0060090
    label: molecular adaptor activity
  evidence_type: NAS
  review:
    summary: 'Added to align core_functions with existing annotations. Captures the
      vesicle-tethering bridging activity of TMF1 (closest existing MF; a more specific
      "vesicle tethering activity" term is requested in proposed_new_terms).

      '
    action: NEW
    reason: Core function term not present in existing_annotations.
    supported_by:
    - reference_id: PMID:28122620
      supporting_text: When relocated to mitochondria, TMF captures intra-Golgi transport
        vesicles.
    - reference_id: file:human/TMF1/TMF1-deep-research-falcon.md
      supporting_text: >-
        TMF1 is best supported as a **Golgi tether/scaffold (golgin) and Rab6
        effector** that contributes to Golgi ribbon morphology and to specific
        retrograde trafficking pathways.
- term:
    id: GO:0099041
    label: vesicle tethering to Golgi
  evidence_type: NAS
  review:
    summary: 'Added to align core_functions with existing annotations. Direct demonstration
      by mitochondrial-relocation assay (PMID:28122620) and by interaction with the
      COG complex (PMID:23239882).

      '
    action: NEW
    reason: Core function term not present in existing_annotations.
    supported_by:
    - reference_id: PMID:28122620
      supporting_text: When relocated to mitochondria, TMF captures intra-Golgi transport
        vesicles.
- term:
    id: GO:0006891
    label: intra-Golgi vesicle-mediated transport
  evidence_type: NAS
  review:
    summary: 'Added to align core_functions with existing annotations. Supported by
      vesicle-capture assays (PMID:28122620), COG-TMF tethering model (PMID:23239882),
      and Drosophila in vivo data (PMID:36103876).

      '
    action: NEW
    reason: Core function term not present in existing_annotations.
    supported_by:
    - reference_id: PMID:23239882
      supporting_text: We find that the COG complex interacts with two different Rabs
        in addition to each end of the golgin "TATA element modulatory factor" (TMF).
- term:
    id: GO:0031267
    label: small GTPase binding
  evidence_type: NAS
  review:
    summary: 'Added to align core_functions with existing annotations. Captures the
      Rab6-GTP binding activity that recruits TMF1 to the trans-Golgi.

      '
    action: NEW
    reason: Core function term not present in existing_annotations.
    supported_by:
    - reference_id: PMID:17698061
      supporting_text: TMF signal surrounded Rab6-positive Golgi structures.
- term:
    id: GO:0042147
    label: retrograde transport, endosome to Golgi
  evidence_type: NAS
  review:
    summary: 'Added to align core_functions with existing annotations. TMF1 knockdown
      blocks Rab6-dependent retrograde transport of Shiga toxin from early/recycling
      endosomes to the trans-Golgi network (PMID:17698061).

      '
    action: NEW
    reason: Core function term not present in existing_annotations.
    supported_by:
    - reference_id: PMID:17698061
      supporting_text: The knockdown of either TMF or Rab6 by RNA interference blocked
        retrograde transport of endocytosed Shiga toxin from early/recycling endosomes
        to the trans-Golgi network.
- term:
    id: GO:0006890
    label: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
  evidence_type: NAS
  review:
    summary: 'Added to align core_functions with existing annotations. PMID:17698061
      establishes a role for TMF1 in Rab6-dependent Golgi-to-ER retrograde traffic.

      '
    action: NEW
    reason: Core function term not present in existing_annotations.
    supported_by:
    - reference_id: PMID:17698061
      supporting_text: critical roles for TMF in two Rab6-dependent retrograde transport
        processes - one from endosomes to the Golgi and the other from the Golgi to
        the ER.
references:
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  findings: []
- id: PMID:1409643
  title: Cloning and chromosomal mapping of a human immunodeficiency virus 1 "TATA"
    element modulatory factor.
  findings:
  - statement: TMF was originally identified as a 123 kDa cellular protein that binds
      the HIV-1 LTR TATA element in gel-retardation assays and inhibits TBP-mediated
      transcriptional activation in vitro.
    supporting_text: TMF binds to the human immunodeficiency virus 1 TATA element
      in gel-retardation assays and inhibits activation of the viral long terminal
      repeat by the TATA-binding protein in in vitro transcription assays.
  - statement: The original characterisation was a viral-promoter / in vitro context;
      no endogenous cellular target genes were demonstrated.
    supporting_text: TMF is a transcription factor that likely regulates the expression
      of both viral and cellular genes.
- id: PMID:10428808
  title: Isolation and characterization of ARA160 as the first androgen receptor N-terminal-associated
    coactivator in human prostate cells.
  findings:
  - statement: AR N-terminal peptide directly binds TMF1/ARA160 in far-Western and
      co-IP assays in vitro.
    supporting_text: The far-Western blotting and co-immunoprecipitation assays demonstrate
      that the AR can interact directly with ARA160/TMF.
  - statement: A transient transfection AR-reporter assay in PC-3 cells suggests TMF1/ARA160
      enhances AR transactivation.
    supporting_text: Transient transfection assays demonstrated that ARA160 might
      function as a coactivator for AR-mediated transactivation in human prostate
      cancer PC-3 cells.
- id: PMID:12044884
  title: A putative nuclear receptor coactivator (TMF/ARA160) associates with hbrm/hSNF2
    alpha and BRG-1/hSNF2 beta and localizes in the Golgi apparatus.
  findings:
  - statement: TMF1 isoforms differentially localize between Golgi and nucleus; the
      Golgi pool is dominant.
    supporting_text: Immunofluorescence and Western blot studies revealed that the
      TMF isoforms differentially localize in the Golgi apparatus and the nucleus.
  - statement: The C-terminal region of TMF1 binds the conserved N-terminal regions
      of the SWI/SNF ATPases hbrm/hSNF2alpha and BRG-1/hSNF2beta in vitro and in vivo.
    supporting_text: hbrm/hSNF2 alpha and BRG-1/hSNF2 beta, the ATPase subunits of
      the human SNF/SWI complexes, specifically associate in vitro and in vivo with
      TATA element modulatory factor (TMF)/ARA160.
- id: PMID:15467733
  title: TMF/ARA160 is a BC-box-containing protein that mediates the degradation of
    Stat3.
  findings:
  - statement: TMF/ARA160 is described as a Golgi-resident protein.
    supporting_text: TMF/ARA160 is a Golgi resident protein whose cellular functions
      have not been conclusively revealed.
  - statement: TMF/ARA160 contains a BC-box motif that binds Elongin C and directs
      Stat3 ubiquitination/proteasomal degradation in serum-starved C2C12 cells.
    supporting_text: Amino-acid sequence analysis identified a BC-box element in TMF/ARA160
      that mediated the binding of this protein to elongin C. Ectopic expression of
      TMF/ARA160 in serum-starved C2C12 cells drove the ubiquitination and proteasomal
      degradation of Stat3.
- id: PMID:17698061
  title: Functional involvement of TMF/ARA160 in Rab6-dependent retrograde membrane
    traffic.
  findings:
  - statement: TMF1 surrounds Rab6-positive Golgi structures and is concentrated at
      cisternal-tip budding structures.
    supporting_text: TMF signal surrounded Rab6-positive Golgi structures and immunoelectron
      microscopy revealed that TMF is concentrated at the budding structures localized
      at the tips of cisternae.
  - statement: TMF1 knockdown phenocopies Rab6 knockdown for retrograde transport
      of Shiga toxin from early/recycling endosomes to the trans-Golgi network.
    supporting_text: The knockdown of either TMF or Rab6 by RNA interference blocked
      retrograde transport of endocytosed Shiga toxin from early/recycling endosomes
      to the trans-Golgi network, causing missorting of the toxin to late endosomes/lysosomes.
  - statement: TMF1 is required for Golgi retention of GalNAc-T2 (but not GalT), and
      is implicated in Rab6-dependent retrograde transport from Golgi to ER.
    supporting_text: These observations suggest critical roles for TMF in two Rab6-dependent
      retrograde transport processes - one from endosomes to the Golgi and the other
      from the Golgi to the ER.
- id: PMID:20195357
  title: A comprehensive resource of interacting protein regions for refining human
    transcription factor networks.
  findings:
  - statement: High-throughput mRNA-display screen reports a TMF1-NR3C1 (glucocorticoid
      receptor) interaction; no functional follow-up.
    supporting_text: present the first large-scale IR data set obtained using mRNA
      display for 50 human transcription factors (TFs).
- id: PMID:23000399
  title: Testosterone deficiency accompanied by testicular and epididymal abnormalities
    in TMF(-/-) mice.
  findings:
  - statement: TMF/ARA160 is a Golgi-associated protein essential for spermiogenesis;
      its loss in mouse causes Leydig-cell proliferation, testosterone deficiency
      and epididymal apoptosis - a phenotype consistent with disrupted Golgi-derived
      acrosome biogenesis and secretion rather than loss of an AR coregulator.
    supporting_text: TMF/ARA160 is a Golgi-associated protein, which is essential
      for spermiogenesis. In this study, we show that lack of TMF/ARA160 leads to
      defects in both the testis and the epididymis.
- id: PMID:23239882
  title: Molecular insights into vesicle tethering at the Golgi by the conserved oligomeric
    Golgi (COG) complex and the golgin TATA element modulatory factor (TMF).
  findings:
  - statement: TMF1 is a Golgi-tethering coiled-coil ("golgin") that binds the COG
      complex at both ends and to Golgi membranes via its central coiled-coil after
      COPI uncoating.
    supporting_text: We find that the COG complex interacts with two different Rabs
      in addition to each end of the golgin "TATA element modulatory factor" (TMF).
      This allows COG to potentially bridge the distance between the distal end of
      the golgin and the target membrane thereby promoting tighter docking. Concurrently
      we show that the central portion of TMF can bind to Golgi membranes that are
      liberated of their COPI cover.
- id: PMID:24639530
  title: Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility
    to induced colitis in TMF-/- mice.
  findings:
  - statement: TMF/ARA160 is referred to as a multifunctional Golgi-associated protein;
      TMF-/- colon shows altered MUC2 mucin oligomerisation, consistent with disrupted
      Golgi-dependent glycosylation/secretion.
    supporting_text: Tata Element Modulatory Factor (TMF/ARA160) is a multifunctional
      Golgi-associated protein, which accumulates in colonic enterocytes and goblet
      cells.
- id: PMID:28122620
  title: The golgin coiled-coil proteins capture different types of transport carriers
    via distinct N-terminal motifs.
  findings:
  - statement: TMF1, when relocated to mitochondria, captures intra-Golgi transport
      vesicles - direct demonstration of vesicle-tethering activity.
    supporting_text: When relocated to mitochondria, TMF captures intra-Golgi transport
      vesicles, but these contain some proteins from later in the stack than those
      captured by GMAP-210 and golgin-84.
  - statement: A short N-terminal motif (M-S-W-L/F, conserved across metazoa and shared
      with golgin-84 and GMAP-210) and a central/C-terminal coiled-coil region both
      contribute vesicle-capture activity.
    supporting_text: The first 36 residues of the protein are necessary for the capture
      activity of the N-terminal half, and sufficient to confer capture activity when
      attached to two different heterologous coiled-coil proteins.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings:
  - statement: HuRI Y2H interactome map reports a TMF1-CMTM5 (isoform Q96DZ9-2) binary
      interaction; no functional follow-up.
    supporting_text: A reference map of the human binary protein interactome.
- id: PMID:36103876
  title: In vivo characterization of Drosophila golgins reveals redundancy and plasticity
    of vesicle capture at the Golgi apparatus.
  findings:
  - statement: In Drosophila, ectopic TMF captures intra-Golgi transport vesicles
      and the loss-of-function mutant recapitulates the male-fertility phenotype seen
      in mouse Tmf1 knockouts, supporting a conserved role in Golgi vesicle traffic.
    supporting_text: We show that ectopic forms can capture intra-Golgi transport
      vesicles, but strikingly, the cargo present in the vesicles captured by each
      golgin varies between tissues. Loss-of-function mutants show that the golgins
      are individually dispensable, although the loss of TMF recapitulates the male
      fertility defects observed in mice.
- id: Reactome:R-HSA-6811431
  title: RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived
    vesicles
  findings: []
- id: Reactome:R-HSA-6814091
  title: ARL1 recruits TGN Golgin homodimers
  findings: []
- id: Reactome:R-HSA-6814682
  title: Fusion of early-endosome derived vesicles at the TGN
  findings: []
- id: file:human/TMF1/TMF1-notes.md
  title: TMF1 research notes (this review)
  findings: []
- id: file:human/TMF1/TMF1-deep-research-falcon.md
  title: Falcon deep research report for TMF1
  findings:
  - statement: >-
      Falcon supports the Golgi-associated golgin/Rab6-effector role as the
      most reproducible TMF1 function, while treating transcriptional,
      proteostasis, and nuclear RTK roles as conditional or context-dependent.
    supporting_text: >-
      The Golgi/tethering axis is supported by multiple cell biological methods
      (Golgi localization, Rab6-binding, trafficking defects, Golgi morphology
      quantification).
core_functions:
- molecular_function:
    id: GO:0060090
    label: molecular adaptor activity
  description: Acts as a long coiled-coil vesicle-tethering factor (golgin) at the
    trans-Golgi rim that bridges incoming transport vesicles and the Golgi membrane
    prior to SNARE-mediated fusion. The N-terminal disordered region (~residues 1-36,
    containing the conserved M-S-W-L/F motif shared with golgin-84 and GMAP-210) and
    the central/C-terminal coiled-coil each independently capture intra-Golgi transport
    vesicles in the mitochondrial-relocation assay; the C-terminal Rab6-binding coiled-coil
    recruits TMF1 to the Golgi membrane and cooperates with the COG complex to dock
    retrograde vesicles. (A specific MF "vesicle tethering activity" is requested
    in proposed_new_terms; GO:0060090 is used here as the closest available existing
    MF.)
  directly_involved_in:
  - id: GO:0099041
    label: vesicle tethering to Golgi
  - id: GO:0006891
    label: intra-Golgi vesicle-mediated transport
  supported_by:
  - reference_id: PMID:28122620
    supporting_text: When relocated to mitochondria, TMF captures intra-Golgi transport
      vesicles.
  - reference_id: PMID:23239882
    supporting_text: We find that the COG complex interacts with two different Rabs
      in addition to each end of the golgin "TATA element modulatory factor" (TMF).
  - reference_id: file:human/TMF1/TMF1-deep-research-falcon.md
    supporting_text: >-
      TMF1 is best supported as a **Golgi tether/scaffold (golgin) and Rab6
      effector** that contributes to Golgi ribbon morphology and to specific
      retrograde trafficking pathways.
- molecular_function:
    id: GO:0031267
    label: small GTPase binding
  description: Binds Rab6 in its GTP-bound active state via the C-terminal coiled-coil
    region; this interaction is required for recruitment of TMF1 to the trans-Golgi
    rim and for its function in Rab6-dependent retrograde transport from endosomes
    to the trans-Golgi network and from the Golgi to the ER.
  directly_involved_in:
  - id: GO:0042147
    label: retrograde transport, endosome to Golgi
  - id: GO:0006890
    label: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
  supported_by:
  - reference_id: PMID:17698061
    supporting_text: TMF signal surrounded Rab6-positive Golgi structures... critical
      roles for TMF in two Rab6-dependent retrograde transport processes - one from
      endosomes to the Golgi and the other from the Golgi to the ER.
  - reference_id: file:human/TMF1/TMF1-deep-research-falcon.md
    supporting_text: >-
      TMF1/ARA160 is a **Golgi-associated coiled-coil "golgin"** that binds
      **Rab6** family GTPases and contributes to Golgi organization.
proposed_new_terms:
- proposed_name: vesicle tethering activity
  proposed_definition: Binding activity of a long coiled-coil or multisubunit factor
    that bridges a transport vesicle membrane and a target organelle membrane prior
    to SNARE-mediated fusion. The molecular function counterpart of GO:0099022 vesicle
    tethering. Required for capturing incoming vesicles by golgins (e.g. TMF1, GMAP-210,
    golgin-84, the GRIP-domain golgins) at the Golgi and by analogous coiled-coil
    tethers at other compartments.
  justification: GO currently has the biological-process term GO:0099022 vesicle tethering
    and the cellular-component term GO:0099023 vesicle tethering complex, but no molecular-function
    term that captures the binding/bridging activity of an individual tether. Without
    such an MF, golgins like TMF1 default to GO:0005515 protein binding, which is
    explicitly discouraged. Per geneontology/go-annotation#6381 a "vesicle membrane
    tethering activity" term is being requested by curators (V. Wood, H. Attrill);
    GO:7770062 was referenced in that issue but is not yet present in GO at the time
    of this review (2026-05-02). Recording here so the term-request progress can be
    tracked alongside this review.
suggested_questions:
- question: Is the apparent transcription-coactivator activity of TMF1 (PMID:10428808)
    a true endogenous function or an overexpression artefact? Has it been validated
    by AR ChIP-seq or by RNA-seq of TMF1 KO prostate cells?
  experts:
  - GO Consortium (R. Lovering, A. Lock, ARUK-UCL)
  - Steroid-receptor coactivator field (e.g. C. Chang lab)
- question: Does any tissue/cell type maintain a functional nuclear pool of TMF1,
    and if so what is its target-gene repertoire?
  experts:
  - SWI/SNF / chromatin-remodeling researchers
  - Neuro-andrology / prostate-cancer transcription researchers
suggested_experiments:
- experiment_type: Genome-wide ChIP-seq for TMF1 in AR-positive prostate cells
  hypothesis: If TMF1 is an endogenous AR coactivator, AR-target promoters should
    be enriched among TMF1 ChIP-seq peaks; if not, TMF1 should occupy few or no chromatin
    sites and the existing IDA annotations to GO:0003713/GO:0045944/GO:0030521 should
    be retired rather than merely demoted.
  description: ChIP-seq for endogenous TMF1 in LNCaP/22Rv1 (AR-positive prostate)
    cells +/- DHT, paired with AR ChIP-seq. Compute peak overlap with AR cistrome
    and motif enrichment. Validate top putative TMF1 chromatin sites by ChIP-qPCR
    after TMF1 knockdown. Couple with RNA-seq of TMF1 KO cells +/- DHT to ask whether
    AR target genes are preferentially affected.
- experiment_type: Quantitative proximity labelling (BioID/TurboID) at the trans-Golgi
    rim and at chromatin
  hypothesis: TMF1 BioID interactomes will be dominated by Golgi-tethering machinery
    (Rab6, COG subunits, intra-Golgi cargo, glycosyltransferases) rather than by transcription/chromatin
    factors, reinforcing that the core function is at the Golgi.
  description: Generate stable lines expressing TurboID-TMF1 (full length and isoform
    P82094-2) at near-endogenous level. Perform 10-min biotin labelling, streptavidin
    enrichment and TMT-MS3 quantitation. Compare with TurboID-only and a TurboID-Rab6
    control. Quantify the relative enrichment of trafficking vs. chromatin/transcription
    GO categories.
- experiment_type: Cryo-ET of TMF1 at intra-Golgi vesicle tethering sites
  hypothesis: TMF1 will be observed as elongated coiled-coil bridges between intra-Golgi
    transport vesicles and cisternal rims, with Rab6-binding ends anchored at the
    Golgi, providing a structural counterpart of the mitochondrial-relocation capture
    assay (PMID:28122620).
  description: Cryo-electron tomography of vitrified Golgi-membrane-enriched HeLa
    extracts immuno-labelled for TMF1, with sub-tomogram averaging of TMF1-decorated
    vesicle-Golgi contacts. Compare WT to a TMF1 N-terminal motif (M-S-W-L/F) mutant
    and to Rab6-knockdown.