LMX1B is a nuclear LIM-homeodomain DNA-binding transcriptional activator that recognizes regulatory DNA and works with context-dependent transcriptional coregulators. It establishes and maintains tissue-selective gene-expression programs in podocytes, the dorsal limb, and neuronal lineages including midbrain dopaminergic and central serotonergic neurons. In human cells, LMX1B directly promotes macroautophagy-gene expression and autophagic flux and binds ATG8-family ubiquitin-like proteins; this nutrient- and compartment-sensitive interaction enhances its transcriptional output and cellular stress resilience. Pathogenic LMX1B variants cause nail-patella syndrome and kidney-limited glomerular disease.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization is a core feature of this LIM-homeodomain transcription factor and is independently supported by direct imaging of human dopaminergic neurons. Reason: The IBA is biologically coherent with LMX1B's sequence-specific nuclear transcriptional activity. Human differentiated dopaminergic neurons show LMX1B in nuclei, so there is no indication of a faulty phylogenetic transfer. Propagation Review Root cause: NO FAILURE CORE Sources checked: FB:FBgn0267978 MGI:MGI:1096343 MGI:MGI:1100513 MGI:MGI:1306803 MGI:MGI:96785 MGI:MGI:99783 PANTHER:PTN000654232 RGD:71074 UniProtKB:O60663 UniProtKB:O97581 UniProtKB:P29674 UniProtKB:P53411 UniProtKB:Q9UPM6 WB:WBGene00000438 WB:WBGene00002987 WB:WBGene00002988 WB:WBGene00003167 WB:WBGene00006654 Supporting Evidence: PMID:24399192 LMX1b was expressed in all nuclei (inset). There was also unspecific cytoplasmic fluorescence. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: This IBA correctly captures the broad, unsigned process by which LMX1B regulates RNA polymerase II transcription across target and cofactor contexts. Reason: GO:0006357 is the valid RNA polymerase II regulation parent of the directly established positive-regulation processes and accurately preserves the broad phylogenetic inference. More specific positive-regulation annotations are retained separately. LDB1 can attenuate the magnitude of LMX1B-mediated activation, but this is not interpreted as evidence for negative regulation. Propagation Review Root cause: NO FAILURE CORE Sources checked: FB:FBgn0267978 MGI:MGI:102673 MGI:MGI:1100513 MGI:MGI:1888519 MGI:MGI:96785 PANTHER:PTN004680160 UniProtKB:C4TJC6 UniProtKB:P29674 UniProtKB:Q969G2 UniProtKB:Q9UBR4 WB:WBGene00000438 WB:WBGene00002987 WB:WBGene00002988 WB:WBGene00003167 WB:WBGene00006654 Supporting Evidence: PMID:11956244 We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. PMID:10767331 While co--transfections of E47/shPan1 with LMX1B result in a synergistic effect on reporter activity, LDB1 down-regulated LMX1B-mediated transactivation irrespective of E47/shPan1. |
| GO:0030182 neuron differentiation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: The broad neuron-differentiation inference is biologically defensible, but it describes one developmental context of a pleiotropic transcription factor rather than its molecular core. Reason: LMX1B contributes to development and maintenance of several neuronal populations, including mesodiencephalic dopaminergic neurons. Retain the broad process as contextual because LMX1B also has independent renal, limb, ocular, and serotonergic developmental roles. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: FB:FBgn0002023 FB:FBgn0267978 MGI:MGI:101776 MGI:MGI:102673 MGI:MGI:107792 MGI:MGI:1096343 MGI:MGI:1100513 MGI:MGI:1306803 MGI:MGI:1888519 MGI:MGI:96785 MGI:MGI:99783 PANTHER:PTN000654232 RGD:71076 UniProtKB:P53411 UniProtKB:Q8UVR3 UniProtKB:Q90881 WB:WBGene00000438 WB:WBGene00002987 WB:WBGene00002988 WB:WBGene00003000 WB:WBGene00003167 WB:WBGene00006654 ZFIN:ZDB-GENE-050114-2 ZFIN:ZDB-GENE-050114-3 ZFIN:ZDB-GENE-050417-210 ZFIN:ZDB-GENE-051220-1 ZFIN:ZDB-GENE-060728-1 ZFIN:ZDB-GENE-980526-131 Supporting Evidence: PMID:12897786 A major determinant in the cascades is an LIM homeodomain-containing gene, Lmx1b, which is required for the development of all 5-HT neurons in the central nervous system. PMID:23308148 The LIM homeodomain transcription factor Lmx1b is essential for the development of the isthmic organizer and mesodiencephalic dopaminergic neurons. |
| GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Sequence-specific binding to RNA polymerase II regulatory DNA is a core molecular function of LMX1B's homeodomain. Reason: Direct binding of LMX1B to regulatory sequences and activation through those sequences supports the IBA at an appropriate level of specificity. Propagation Review Root cause: NO FAILURE CORE Sources checked: FB:FBgn0267978 MGI:MGI:1100513 MGI:MGI:1888519 MGI:MGI:96785 PANTHER:PTN004680160 WB:WBGene00000438 WB:WBGene00002987 WB:WBGene00006654 Supporting Evidence: PMID:11956244 We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: RNA polymerase II-specific DNA-binding transcription factor activity is the central molecular function of LMX1B. Reason: The homeodomain supplies selective regulatory-DNA binding and LMX1B activates mammalian target-gene reporters; the IBA therefore captures the correct core activity without overclaiming a particular target or tissue. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:1100513 MGI:MGI:1888519 MGI:MGI:96785 PANTHER:PTN004680160 UniProtKB:Q969G2 UniProtKB:Q9UBR4 WB:WBGene00002987 WB:WBGene00003167 WB:WBGene00006654 Supporting Evidence: PMID:11956244 Thus, LMX1B regulates the expression of multiple podocyte genes critical for podocyte differentiation and function. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IEA GO_REF:0000002 | ACCEPT | Summary: The InterPro homeobox-signature mapping correctly predicts LMX1B's RNA polymerase II-specific DNA-binding transcription factor activity. Reason: The prediction is independently corroborated by direct LMX1B regulatory-DNA binding and transcriptional activation. The mapping is redundant with stronger evidence but not biologically erroneous. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR017970 Supporting Evidence: PMID:11956244 We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: The homeodomain mapping is directionally correct, but generic DNA binding loses the experimentally established sequence specificity and double-stranded substrate. Reason: LMX1B recognizes specific regulatory DNA sequences through its homeodomain. Replace the broad parent with sequence-specific double-stranded DNA binding, which is also directly supported in the existing annotation set. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: InterPro:IPR001356 Proposed replacements: sequence-specific double-stranded DNA binding Supporting Evidence: PMID:11956244 We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: The UniProt subcellular-location mapping correctly places LMX1B in the nucleus. Reason: Nuclear localization is independently demonstrated in human dopaminergic neurons and is the expected site of LMX1B's core transcription-factor activity. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0191 Supporting Evidence: PMID:24399192 LMX1b was expressed in all nuclei (inset). There was also unspecific cytoplasmic fluorescence. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: The InterPro mapping identifies a true unsigned transcriptional role, but its DNA-templated-transcription parent does not specify the relevant RNA polymerase. Reason: Refine the generic process to regulation of transcription by RNA polymerase II, the appropriate broad parent supported by the InterPro transcription-factor mapping. Direct experiments support separate positive-regulation rows, while this electronic mapping does not itself establish a signed regulatory effect. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: InterPro:IPR017970 Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:11956244 We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000117 | MODIFY | Summary: Sequence-specific DNA binding is correct, but LMX1B's regulatory substrate is double-stranded DNA, making the existing term less precise than a supported child term. Reason: The ARBA prediction captures specificity but not DNA strandedness. Direct LMX1B binding-site assays and the existing IDA annotation support sequence-specific double-stranded DNA binding. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: ARBA:ARBA00026779 Proposed replacements: sequence-specific double-stranded DNA binding Supporting Evidence: PMID:11956244 We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. |
| GO:0005515 protein binding | IPI PMID:12792813 Confirmation of CLIM2/LMX1B interaction by yeast two-hybrid ... | MODIFY | Summary: The LMX1B-LDB1 interaction is supported, but bare protein binding is uninformative; from LMX1B's perspective this is binding to a transcriptional coregulator. Reason: LDB1/CLIM2 is a LIM-homeodomain transcriptional coregulator. GO:0001221 therefore describes what LMX1B binds. LIM-domain binding would describe the reciprocal activity of LDB1 binding LMX1B's LIM domains, not LMX1B's activity, and is inappropriate for this gene-product annotation. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:12792813 By the yeast two-hybrid screening we detected the CLIM2 gene as a LMX1B interactor, confirming previous reports which described the same interaction by biochemical methods. |
| GO:0005515 protein binding | IPI PMID:20211142 An atlas of combinatorial transcriptional regulation in mous... | MODIFY | Summary: The interaction atlas supports LMX1B association with LDB1 and SSBP3, but the generic protein-binding label obscures their role as LIM-homeodomain transcriptional coregulators. Reason: Replace generic protein binding with transcription coregulator binding. LDB1 is the established LIM-domain-interacting coregulator and SSBP3 is a component of LDB1-centered transcriptional complexes. The replacement is assigned from LMX1B's perspective; LIM-domain binding would reverse the direction of the molecular function. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:10767331 Transfection studies showed that both the LIM domain-interacting protein, LDB1, and the helix-loop-helix protein, E47/shPan1, can regulate LMX1B action. |
| GO:0005515 protein binding | IPI PMID:30833792 A protein-interaction network of interferon-stimulated genes... | MODIFY | Summary: This high-throughput IPI records the reproducible LMX1B-SSBP3 interaction, but bare protein binding is not functionally informative. Reason: SSBP3 functions as a transcriptional coregulator in LDB1/LIM-homeodomain complexes, making transcription coregulator binding the appropriate gene-product-perspective replacement. The immune-network assay context does not itself make an innate-immune role for LMX1B. Proposed replacements: transcription coregulator binding |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MODIFY | Summary: Proteome-scale affinity purification recovers LDB1 and SSBP3 with LMX1B, but generic protein binding should be replaced by the shared mechanistic class of these partners. Reason: Both partners participate in LIM-homeodomain transcriptional regulatory complexes, so transcription coregulator binding is informative and directionally correct for LMX1B. The proteome-scale cell-line setting supports physical association but does not establish a tissue-specific biological process. Proposed replacements: transcription coregulator binding Supporting Evidence: PMID:33961781 Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | MODIFY | Summary: The multimodal interaction map again supports LMX1B association with LDB1 and SSBP3, while generic protein binding fails to capture their transcriptional role. Reason: Replace with transcription coregulator binding. LDB1 and SSBP3 are partners in transcriptional regulatory complexes, and this term describes LMX1B binding those partners without incorrectly assigning the reciprocal LIM-domain-binding activity to LMX1B. Proposed replacements: transcription coregulator binding |
| GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding | ISS GO_REF:0000024 | ACCEPT | Summary: Manual transfer from mouse Lmx1b correctly captures the conserved, core regulatory-DNA-binding activity of human LMX1B. Reason: The mouse ortholog is one-to-one and the transfer is independently corroborated by human and mammalian binding-site assays. No paralog-specific divergence is evident for the homeodomain activity. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:O88609 Supporting Evidence: PMID:11956244 We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | ISS GO_REF:0000024 | ACCEPT | Summary: The RNA polymerase II-specific transcription-factor activity is core; the five extensions preserve the target scope of the manually transferred mouse annotation. Reason: Retain the manually curated orthology transfer, because mammalian evidence supports LMX1B regulation of this midbrain network and human assays independently establish the core molecular activity. Evidence strength is not identical for every WNT1, PITX3, NR4A2, LMX1A, and MSX1 target relationship in human cells, but that caveat does not invalidate the conserved transcription-factor activity. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:O88609 Supporting Evidence: PMID:23308148 The (partial) loss of Pitx3 and later of Th in the Lmx1b null mutant suggest that Lmx1b may act as an upstream activator of these genes in the development of mdDA neurons [1]β[3], or Lmx1b may be involved in specifying the dopaminergic niche in the midbrain region. |
| GO:1990837 sequence-specific double-stranded DNA binding | IDA PMID:28473536 Impact of cytosine methylation on DNA binding specificities ... | ACCEPT | Summary: Methylation-sensitive SELEX directly supports sequence-specific double-stranded DNA binding by human LMX1B; this is an appropriate core molecular-function term. Reason: The high-throughput study experimentally profiled human transcription-factor DNA specificity. Independent target-regulatory-region assays corroborate the sequence-specific double-stranded DNA-binding function without requiring a more motif-specific GO term. Supporting Evidence: PMID:28473536 By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. PMID:11956244 We identified several LMX1B binding sites in the putative regulatory regions of both CD2AP and NPHS2 (podocin) and demonstrated that LMX1B binds to these sequences in vitro and can activate transcription through them in cotransfection assays. |
| GO:0000785 chromatin | ISA GO_REF:0000113 | ACCEPT | Summary: Chromatin is an appropriate active location for a sequence-specific DNA-binding transcription factor and is corroborated by direct LMX1B promoter occupancy assays. Reason: TFClass correctly classifies LMX1B as a LIM-homeodomain DNA-binding transcription factor. Direct chromatin immunoprecipitation in human cells confirms occupancy at target promoters, supporting chromatin as a core activity location. Propagation Review Root cause: NO FAILURE CORE Sources checked: tfclass:3.1.5 Supporting Evidence: PMID:37014324 Using an arbitrary twofold cut-off for targets of interest, promoter occupancy was confirmed for several core autophagy genes, including ULK1, ATG3, ATG16L1, UVRAG, as well as the autolysosomal transcription factor TFEB and the receptors and/or mitophagy genes, NDP52, OPTN, and PINK1 (Fig. 1 A). |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | ISA GO_REF:0000113 | ACCEPT | Summary: TFClass correctly assigns RNA polymerase II-specific DNA-binding transcription factor activity to LMX1B. Reason: The classification is consistent with the homeodomain and with direct regulatory-DNA binding, reporter activation, and endogenous target-gene regulation. It captures the core molecular function at a suitable level of specificity. Propagation Review Root cause: NO FAILURE CORE Sources checked: tfclass:3.1.5 Supporting Evidence: PMID:11956244 Thus, LMX1B regulates the expression of multiple podocyte genes critical for podocyte differentiation and function. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | TAS PMID:24431302 Wnt signaling in midbrain dopaminergic neuron development an... | KEEP AS NON CORE | Summary: LMX1B-dependent activation of WNT1 transcription at the midbrain-hindbrain boundary is biologically coherent, but this extended annotation is a specific developmental context rather than the gene's general core function. Reason: Retain the curator-authored TAS annotation. The cited review is not direct primary evidence, but full-text mouse work independently places Lmx1b upstream of Wnt1 in isthmic-organizer development. The tissue and dopaminergic-differentiation extensions make the row appropriately contextual. Supporting Evidence: PMID:23308148 This possibility is underlined by the fact that Lmx1b is also involved in regulation of Fgf8 and Wnt1, and several isthmus-related transcription factors, and it is essential for inductive activity of the isthmic organizer (IsO) [4], [5]. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Positive transcriptional regulation of the transferred midbrain target set is supported in mouse, but the target-specific extensions describe a developmental program rather than the general molecular core. Reason: Manual orthology transfer from mouse Lmx1b is reasonable and is supported by conserved human transcription-factor activity. Retain as non-core because the WNT1, PITX3, NR4A2, and LMX1A target restrictions are developmental-context statements and are not all equally demonstrated as direct targets in human cells. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:O88609 Supporting Evidence: PMID:23308148 The (partial) loss of Pitx3 and later of Th in the Lmx1b null mutant suggest that Lmx1b may act as an upstream activator of these genes in the development of mdDA neurons [1]β[3], or Lmx1b may be involved in specifying the dopaminergic niche in the midbrain region. |
| GO:0071542 dopaminergic neuron differentiation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Mouse Lmx1b evidence supports a role in dopaminergic neuron development, but this is one tissue-specific developmental role of a pleiotropic transcription factor. Reason: Retain the manually transferred process as contextual. Lmx1b is important for establishment of the isthmic organizer and the mesodiencephalic dopaminergic field, although stage- and cell-type-specific knockout studies make its role more nuanced than an invariant cell-autonomous differentiation requirement. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:O88609 Supporting Evidence: PMID:23308148 The LIM homeodomain transcription factor Lmx1b is essential for the development of the isthmic organizer and mesodiencephalic dopaminergic neurons. |
| GO:0005634 nucleus | IDA PMID:24399192 Differentiation of human epidermal neural crest stem cells (... | ACCEPT | Summary: Direct immunocytochemistry places human LMX1B in nuclei of differentiated dopaminergic neurons. Reason: The figure description explicitly reports nuclear LMX1B staining in all scored day-25 dopaminergic neurons. The cell-type extension accurately preserves the experimental context while nucleus remains a core activity location. Supporting Evidence: PMID:24399192 LMX1b was expressed in all nuclei (inset). There was also unspecific cytoplasmic fluorescence. |
| GO:0006355 regulation of DNA-templated transcription | IDA PMID:10767331 LMX1B transactivation and expression in nail-patella syndrom... | MODIFY | Summary: The experiment demonstrates transcriptional activation, but regulation of DNA-templated transcription is an unsigned and polymerase-unspecified parent. Reason: LMX1B activates reporter transcription, and independent target-site studies show positive transcriptional regulation. Replace the generic process with positive regulation of transcription by RNA polymerase II. Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:10767331 Mutant LMX1B proteins containing human mutations affecting each of the helices or the N-terminal arm of the homeodomain abolished transactivation, while LIM B and truncation mutations retained residual activity. |
| GO:0009953 dorsal/ventral pattern formation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: The mouse-ortholog transfer correctly captures LMX1B's conserved role in dorsal-ventral patterning, especially dorsal limb fate, but this is a developmental context rather than its molecular core. Reason: Human nail-patella phenotypes and mouse loss-of-function data strongly support the process. Retain as non-core because the term describes a pleiotropic developmental outcome downstream of LMX1B's transcription-factor activity. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:O88609 Supporting Evidence: PMID:10767331 Lmx1b, a member of the LIM homeodomain protein family, is essential for the specification of dorsal limb fates at the zeugopodal and autopodal level in vertebrates. |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:10767331 LMX1B transactivation and expression in nail-patella syndrom... | MODIFY | Summary: The direct reporter assay establishes DNA-binding transcription-factor activity, but the generic term omits both the activating sign and RNA polymerase II context. Reason: Replace with DNA-binding transcription activator activity, RNA polymerase II-specific. LMX1B's homeodomain binds regulatory DNA and the tested wild-type protein positively drives reporter and endogenous target-gene transcription. Proposed replacements: DNA-binding transcription activator activity, RNA polymerase II-specific Supporting Evidence: PMID:10767331 Mutant LMX1B proteins containing human mutations affecting each of the helices or the N-terminal arm of the homeodomain abolished transactivation, while LIM B and truncation mutations retained residual activity. |
| GO:0005634 nucleus | IDA PMID:10767331 LMX1B transactivation and expression in nail-patella syndrom... | ACCEPT | Summary: Nuclear localization is correct for LMX1B and is corroborated by later direct human-cell imaging. Reason: The source paper is abstract-only in the local cache, so its precise localization assay cannot be re-audited; the experimental annotation should not be overruled. Independent full-text imaging shows human LMX1B in dopaminergic-neuron nuclei, and nuclear localization is consistent with its core transcription-factor function. Supporting Evidence: PMID:24399192 LMX1b was expressed in all nuclei (inset). There was also unspecific cytoplasmic fluorescence. |
| GO:0030182 neuron differentiation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Broad neuron differentiation is a defensible transfer from mouse Lmx1b, but it is less specific than the dopaminergic context and represents a secondary developmental role. Reason: Retain the curator-judged orthology transfer. LMX1B contributes to development and maintenance of neuronal populations, but its molecular core is sequence-specific transcriptional regulation and it also has substantial non-neuronal functions. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:O88609 Supporting Evidence: PMID:12897786 A major determinant in the cascades is an LIM homeodomain-containing gene, Lmx1b, which is required for the development of all 5-HT neurons in the central nervous system. PMID:37014324 The LIM homeodomain transcription factors LMX1A and LMX1B are essential mediators of midbrain dopaminergic neuronal (mDAN) differentiation and survival. |
| GO:0016239 positive regulation of macroautophagy | IMP PMID:37014324 ATG8-dependent LMX1B-autophagy crosstalk shapes human midbra... | NEW | Summary: Direct perturbation and rescue experiments in human cells show that LMX1B promotes basal and nutrient-stress-induced macroautophagic flux. Reason: LMX1B depletion or knockout reduced expression of multiple autophagy genes and dampened autophagic flux in HEK293T cells, while LMX1B suppression in human iPSC-derived midbrain dopaminergic neurons reduced autophagy-gene expression and autophagosome assembly sites. These direct human phenotypes support positive regulation of macroautophagy without relying on mouse orthology. Supporting Evidence: PMID:37014324 Together, these data demonstrate that LMX1B contributes to the control of autophagy gene expression in HEK293T cells, and that LMX1B depletion dampens basal/housekeeping and nutrient stress-induced autophagic flux responses. |
| GO:0032182 ubiquitin-like protein binding | IPI PMID:37014324 ATG8-dependent LMX1B-autophagy crosstalk shapes human midbra... | NEW | Summary: Endogenous co-immunoprecipitation in human HEK293T cells demonstrates binding between native LMX1B and the ATG8-family ubiquitin-like protein LC3B. Reason: The endogenous LMX1B-LC3B co-immunoprecipitation supports ubiquitin-like protein binding and is encoded with LC3B as the sole supporting entity. Complementary tagged assays recovered LMX1B with all six human ATG8-family proteins, but those five additional partners are not added as entities because their evidence was not an endogenous interaction assay. This is a regulated cofactor interaction, not evidence that LMX1B is a stable complex subunit. Supporting Evidence: PMID:37014324 Importantly, we observed coIP of endogenous LC3B using antibodies against native LMX1B in HEK293T cells (Fig. 5 E). |
| GO:0072248 metanephric podocyte differentiation | ISO PMID:11956244 Transcriptional induction of slit diaphragm genes by Lmx1b i... | NEW | Summary: Mouse Lmx1b loss causes developmental arrest and structural dysplasia of podocytes in the developing definitive kidney, supporting transfer of metanephric podocyte differentiation to human LMX1B. Reason: The mouse null phenotype directly establishes a requirement for Lmx1b in metanephric podocyte differentiation, and the one-to-one human ortholog has a conserved renal disease role. The more specific metanephric child term matches the mammalian definitive-kidney experiment. The ISO annotation does not assert that any proposed COL4A3, COL4A4, NPHS2, or CD2AP target relationship is universal in human podocytes. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:O88609 SUPPORTS TRANSFER The experimentally tested mouse Lmx1b ortholog supplies the podocyte differentiation phenotype; the proposed human annotation is an orthology transfer. Supporting Evidence: PMID:11956244 Here, we show that Lmx1b(-/-) podocytes have reduced numbers of foot processes, are dysplastic, and lack typical slit diaphragms, indicating an arrest in development. |
| GO:0032956 regulation of actin cytoskeleton organization | ISO PMID:23990680 LMX1B is essential for the maintenance of differentiated pod... | NEW | Summary: Conditional loss of mouse Lmx1b in adult podocytes dysregulates actin cytoskeleton organization, supporting a podocyte-restricted transfer to human LMX1B. Reason: The acute adult mouse phenotype supports regulation of actin cytoskeleton organization as part of LMX1B-dependent podocyte maintenance. Human-podocyte ChIP and gel-shift assays independently show direct promoter recognition of ABRA and ARL4C, genes identified in the same study as actin-cytoskeleton-associated targets. Thus, the regulation is transcription-mediated rather than inferred from a bare downstream phenotype. ISO and the podocyte extension preserve the species and cell-type boundaries without asserting that this target program is universal. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:O88609 SUPPORTS TRANSFER Conditional mouse Lmx1b inactivation supplies the adult podocyte phenotype; the proposed human annotation is an orthology transfer. Supporting Evidence: PMID:23990680 Cell biological and biophysical experiments with primary podocytes isolated after 1 week of Lmx1b inactivation indicated dysregulation of actin cytoskeleton organization PMID:23990680 Chromatin immunoprecipitation experiments in conditionally immortalized human podocytes and gel shift assays showed that LMX1B recognizes AT-rich binding sites (FLAT elements) in the promoter regions of ABRA and ARL4C |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: Which endogenous direct LMX1B targets, rather than secondary differentiation markers, are required for human podocyte maturation and long-term filtration-barrier maintenance?
Suggested experts: podocyte developmental biologists, human glomerular-disease geneticists
Q: Which endogenous LC3/GABARAP paralogs modulate LMX1B transcription in human midbrain dopaminergic neurons, and how does nutrient state redistribute the functional interaction between nucleus and cytosol?
Suggested experts: autophagy interaction specialists, human midbrain dopaminergic-neuron biologists
Q: Do O60663-1, O60663-2, and O60663-3 have distinct transcriptional targets, interaction partners, or tissue-specific functions in vivo?
Suggested experts: LMX1B isoform specialists
Experiment: Engineer an endogenous degron in human iPSC-derived podocytes and perform a short time course of LMX1B CUT&RUN, PRO-seq, single-cell RNA-seq, quantitative cytoskeletal imaging, and filtration-barrier assays. Rescue with wild-type LMX1B and edit candidate ABRA/ARL4C enhancers to distinguish direct effectors from secondary target changes.
Hypothesis: Acute loss of LMX1B in human podocytes directly alters an actin-regulatory transcriptional program before secondary loss of differentiation markers.
Type: acute perturbation, chromatin occupancy, and podocyte functional rescue
Experiment: Introduce endogenous LMX1B interaction-interface mutations and paralog-selective ATG8 knockouts in isogenic human iPSC-derived midbrain dopaminergic neurons; quantify compartment-resolved binding, LMX1B chromatin occupancy, nascent target-gene transcription, autophagic flux, mitochondrial ROS, and rotenone survival, with wild-type and interaction-restoring rescue constructs.
Hypothesis: A defined endogenous ATG8 paralog and compartment-specific interaction with LMX1B are required to couple transcriptional activation to autophagic flux and stress resilience in human midbrain dopaminergic neurons.
Type: endogenous interaction genetics and compartment-resolved functional assay
Experiment: Create isoform-selective splice edits and endogenous epitope tags in matched human podocyte and midbrain dopaminergic-neuron models, then compare localization, DNA occupancy, transcriptomes, LDB1/SSBP3 and ATG8 interactions, and rescue of podocyte or autophagy phenotypes at matched expression levels.
Hypothesis: The three human LMX1B splice isoforms have distinguishable, cell-type-dependent transcriptional and protein-interaction outputs.
Type: isoform-resolved endogenous perturbation and multi-omics comparison
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The endogenous LMX1B target genes that are necessary and sufficient for human podocyte differentiation and adult maintenance remain unresolved; in particular, COL4A3, COL4A4, NPHS2, and CD2AP should not be treated as a universal direct LMX1B target set.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Mouse null and conditional-knockout studies establish Lmx1b-dependent podocyte differentiation, adult maintenance, and actin-cytoskeleton organization, and human-podocyte assays show LMX1B occupancy at ABRA and ARL4C regulatory regions. However, severely affected human nail-patella syndrome kidneys retained the classic collagen and slit-diaphragm proteins, and adult conditional-knockout work supports an alternative actin-centered mechanism.
Significance: Resolving this target network is necessary to connect LMX1B's established transcription-factor activity to human glomerular disease without overgeneralizing reporter assays or mouse developmental phenotypes.
What would resolve it: Combine acute endogenous LMX1B degradation with CUT&RUN, nascent-transcription profiling, and morphology/filtration-barrier phenotyping in human iPSC-derived podocytes, followed by target-specific rescue and enhancer editing.
Provenance (the field's own admissions):
Gap: It is not known which ATG8-family paralogs are endogenous LMX1B cofactors in human midbrain dopaminergic neurons, how their contributions differ between basal nuclear and starvation-induced cytosolic binding, or what interaction stoichiometry produces the transcriptional effect.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Human HEK293T experiments demonstrate endogenous LMX1B-LC3B co-immunoprecipitation, tagged interaction with all six human ATG8-family proteins, compartment- and nutrient-dependent LC3B binding, and loss of transcriptional and stress-protective output from an LMX1B 308-317 deletion mutant.
Significance: Defining the endogenous cofactor species and compartmental mechanism would explain how ubiquitin-like protein binding modulates LMX1B's core transcriptional activity in the neuronal context most relevant to stress resilience.
What would resolve it: Endogenously tag LMX1B and individual ATG8 paralogs in human iPSC-derived midbrain dopaminergic neurons, then combine paralog-selective perturbation, compartment-resolved interaction assays, LMX1B chromatin occupancy, nascent RNA, autophagic-flux measurements, and rotenone-stress rescue.
Provenance (the field's own admissions):
Gap: Whether the three annotated human LMX1B splice isoforms differ in regulatory-DNA selection, coregulator binding, ATG8 binding, localization, or tissue-specific biological output has not been established.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: UniProtKB records three human isoforms, but the current GOA source annotations are not isoform-specific and the direct human autophagy study does not establish an isoform-exclusive function.
Significance: Functional isoform resolution could reveal tissue-selective mechanisms while preventing experimentally tested constructs from being interpreted as proof that a function is unique to one isoform.
What would resolve it: Use isoform-selective splice editing and endogenous tagging in human podocytes and iPSC-derived midbrain dopaminergic neurons, with matched DNA-occupancy, interactome, transcriptome, localization, autophagic-flux, and rescue assays.
Provenance (the field's own admissions):
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)