LHP1 (LIKE HETEROCHROMATIN PROTEIN 1; also TERMINAL FLOWER 2, TFL2) is the single Arabidopsis homolog of the HP1 chromodomain family. It carries an N-terminal chromodomain and a C-terminal chromo shadow domain, homodimerizes, and is a nuclear protein that associates almost exclusively with histone H3 lysine 27 trimethylation (H3K27me3)-marked genes in euchromatin. Its chromodomain binds H3K27me3, and LHP1 acts as a subunit of plant PRC1-like Polycomb complexes (with RING1A/B) while also interacting with PRC2-associated proteins such as MSI1, thereby helping to maintain and propagate H3K27me3-dependent epigenetic repression. Targets include floral regulators (FT, AG, AP3, PI, SEP3), KNOX genes and FLC; lhp1/tfl2 mutants flower early, form terminal flowers, are dwarfed, and fail to maintain vernalization-induced silencing of FLC after return to warm temperatures.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000791 euchromatin | IDA PMID:16244868 The Arabidopsis LHP1 protein is a component of euchromatin. | ACCEPT | Summary: A functional LHP1-GFP fusion that complements lhp1 localizes predominantly outside heterochromatic chromocenters, in euchromatic nuclear foci. Reason: Euchromatic localization is consistent with LHP1 binding H3K27me3-marked, Polycomb-repressed genes in gene-rich euchromatin rather than constitutive heterochromatin. Supporting Evidence: PMID:16244868 In A. thaliana interphase nuclei, LHP1 was predominantly located outside the heterochromatic chromocenters. |
| GO:0000792 heterochromatin | IDA PMID:16361394 Different domains control the localization and mobility of L... | KEEP AS NON CORE | Summary: Transient expression of LHP1-GFP showed chromocenter and punctate nuclear localization, dependent on the aromatic-cage residues of the chromodomain. Reason: Chromocenter association was seen in transient assays, whereas complementing LHP1-GFP in Arabidopsis and genome-wide mapping place LHP1 mainly on H3K27me3-marked facultative heterochromatin in euchromatic regions. Heterochromatin (which includes facultative heterochromatin) is a valid but non-core location. Supporting Evidence: PMID:16361394 localized to heterochromatic chromocenters and showed punctuated distribution within the nucleus PMID:17542647 in vivo TFL2/LHP1 associates almost exclusively and nearly co-extensively with H3K27me3 |
| GO:0000792 heterochromatin | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA-based heterochromatin location from HP1-family membership. Reason: Plausible in the sense of facultative (H3K27me3) heterochromatin, but LHP1 is mainly on euchromatic Polycomb targets rather than constitutive heterochromatin; keep as non-core. Supporting Evidence: PMID:16244868 LHP1 is mainly involved in euchromatin organization in A. thaliana |
| GO:0003677 DNA binding | IDA PMID:16972870 DamID, a new tool for studying plant chromatin profiling in ... | MODIFY | Summary: DamID showed LHP1 occupancy over promoters and transcribed regions of AG, AP3, FT and PI, with preference for A/T-rich regions. Reason: DamID measures in vivo association of a fusion protein with genomic loci, i.e. chromatin occupancy, not direct naked-DNA binding. LHP1 is recruited via its chromodomain to H3K27me3 nucleosomes; chromatin binding is the better-supported description of this result. Proposed replacements: chromatin binding Supporting Evidence: PMID:16972870 We showed that LHP1 was targeted to the promoter and transcribed regions of four genes: AG, AP3, FT and PI. |
| GO:0003682 chromatin binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for chromatin binding in the HP1/LHP1 chromodomain clade, consistent with LHP1's own experimental chromatin association. Reason: Chromatin binding is a direct consequence of the chromodomain H3K27me3 reader activity and is experimentally supported for LHP1. Supporting Evidence: PMID:17542647 in vivo TFL2/LHP1 associates almost exclusively and nearly co-extensively with H3K27me3 |
| GO:0003682 chromatin binding | IDA PMID:27495811 The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LH... | ACCEPT | Summary: Genome-wide ChIP mapping of LHP1 and LIF2 showed LHP1 occupancy of clustered regions of chromatin. Reason: Direct experimental evidence for chromatin association. Supporting Evidence: PMID:27495811 we mapped their genome-wide distributions in wild-type, lif2, and lhp1 backgrounds |
| GO:0003723 RNA binding | IPI PMID:35150931 The lncRNA MARS modulates the epigenetic reprogramming of th... | KEEP AS NON CORE | Summary: The lncRNA MARS associates with LHP1 and titrates it away from the marneral gene cluster in response to ABA. Reason: LHP1 interaction with lncRNAs (MARS; also APOLO in other studies) is a recognized regulatory input modulating LHP1 chromatin occupancy, but RNA binding is a locus-specific modulatory property rather than LHP1's core activity. Deferring to the curator on the IPI evidence. Supporting Evidence: PMID:35150931 MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1 (PRC1) component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binding throughout the cluster |
| GO:0003935 GTP cyclohydrolase II activity | IDA PMID:23203051 Arabidopsis RIBA proteins: two out of three isoforms have lo... | REMOVE | Summary: GTP cyclohydrolase II activity attributed to LHP1 from a paper on RIBA enzymes. Reason: The full text of this paper (cached) characterizes the riboflavin-biosynthetic RIBA1-3 proteins (At5g64300, At2g22450, At5g59750) and never mentions LHP1/TFL2 (At5g17690). LHP1 is a chromodomain/chromo-shadow protein with no GTP cyclohydrolase II or DHBPS domain. This is a gene-attribution error in the annotation (the activity belongs to RIBA1/RIBA3), verified against the full text, and is contradicted by LHP1 domain architecture. Supporting Evidence: PMID:23203051 while AtRIBA2 is lacking GCHII activity, AtRIBA3 does not display DHBPS function file:ARATH/LHP1/LHP1-uniprot.txt Chromo 1 |
| GO:0005515 protein binding | IPI PMID:19097900 Polycomb silencing of KNOX genes confines shoot stem cell ni... | REMOVE | Summary: LHP1 binds AtRING1a, a RING1 homolog of the PRC1 core, supporting a plant PRC1-like complex. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. The informative content (LHP1 as a subunit of a PRC1-like complex with RING1A/B) is captured in core_functions as in_complex PRC1 complex. Supporting Evidence: PMID:19097900 AtRING1a binds to itself and to AtRING1b, to CURLY LEAF (CLF), a PRC2 core component catalyzing H3K27-methylation, and to LIKE HETEROCHROMATIN PROTEIN1 (LHP1), a chromodomain protein binding trimethyl-H3K27 |
| GO:0005515 protein binding | IPI PMID:19947980 EARLY IN SHORT DAYS 7 (ESD7) encodes the catalytic subunit o... | REMOVE | Summary: In vitro interaction between the ESD7/POL2A (DNA polymerase epsilon) C-terminus and TFL2/LHP1. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. No more informative MF term describes this contact; the link to replication-coupled maintenance of H3K27me3 is noted in the gene notes. Supporting Evidence: PMID:19947980 a molecular interaction between the carboxy terminus of ESD7 and TFL2 was demonstrated in vitro |
| GO:0005515 protein binding | IPI PMID:21304947 Control of flowering and cell fate by LIF2, an RNA binding p... | REMOVE | Summary: LHP1 interacts in vivo (BiFC, nucleus) with the hnRNP-Q protein LIF2. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. LIF2 is an RNA-binding modulator of LHP1 targets; no specific MF term captures LHP1's side of this interaction. Supporting Evidence: PMID:21304947 Thus, LIF2 and LHP1 interact in vivo, in the nucleus of plant cells. |
| GO:0005515 protein binding | IPI PMID:23778966 Arabidopsis MSI1 connects LHP1 to PRC2 complexes. | REMOVE | Summary: MSI1 interacts with LHP1 and links it to PRC2. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. The informative content is LHP1's bridging of H3K27me3 to PRC2 (captured via the H3K27me3 reader activity in core_functions); bare protein binding adds nothing. Supporting Evidence: PMID:23778966 We found that MSI1 serves to link PRC2 to LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), a protein that binds H3K27me3 in vitro and in vivo and is required for a functional plant PcG system. |
| GO:0005515 protein binding | IPI PMID:26538092 AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis... | REMOVE | Summary: The Agenet/Tudor protein AIP1 interacts with LHP1 in vivo. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. No informative MF term applies to LHP1's side of this interaction. Supporting Evidence: PMID:26538092 here we have identified that AIP1 interacts in vivo with the plant histone modification |
| GO:0005515 protein binding | IPI PMID:28428341 Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3... | REMOVE | Summary: The Ctf4-related protein EOL1 interacts with LHP1 and PRC2 subunits CLF and SWN. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. The interaction places LHP1-PRC2 at replication to maintain H3K27me3; the functional content is captured by the reader activity and epigenetic repression in core_functions. Supporting Evidence: PMID:28428341 EOL1 physically interacted with CLF, its partially redundant paralog SWINGER (SWN), and LHP1. |
| GO:0005515 protein binding | IPI PMID:29314758 Arabidopsis PWWP domain proteins mediate H3K27 trimethylatio... | REMOVE | Summary: MSI4/FVE co-purified with LHP1 in a study of PWWP-domain proteins regulating FLC H3K27me3. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. Co-purification indicates LHP1-associated PRC2-related complexes; no more informative MF term for LHP1 applies. Supporting Evidence: PMID:29314758 We demonstrated that FVE, MSI5, and PDP3 were co-purified with LHP1. |
| GO:0005515 protein binding | IPI PMID:29314758 Arabidopsis PWWP domain proteins mediate H3K27 trimethylatio... | REMOVE | Summary: PDP3 co-purified with LHP1 in a study of PWWP-domain proteins regulating FLC H3K27me3. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. Co-purification indicates LHP1-associated PRC2-related complexes; no more informative MF term for LHP1 applies. Supporting Evidence: PMID:29314758 We demonstrated that FVE, MSI5, and PDP3 were co-purified with LHP1. |
| GO:0005515 protein binding | IPI PMID:29314758 Arabidopsis PWWP domain proteins mediate H3K27 trimethylatio... | REMOVE | Summary: MSI5 co-purified with LHP1 in a study of PWWP-domain proteins regulating FLC H3K27me3. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. Co-purification indicates LHP1-associated PRC2-related complexes; no more informative MF term for LHP1 applies. Supporting Evidence: PMID:29314758 We demonstrated that FVE, MSI5, and PDP3 were co-purified with LHP1. |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: High-throughput binary Y2H interaction with MYB73 from the phytohormone interactome map. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. This is an unvalidated systematic Y2H pair with no functional characterization for LHP1. Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: High-throughput binary Y2H interaction with CPK1 from the phytohormone interactome map. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. This is an unvalidated systematic Y2H pair with no functional characterization for LHP1. Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: High-throughput binary Y2H interaction with TIFY4A/PPD1 from the phytohormone interactome map. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. This is an unvalidated systematic Y2H pair with no functional characterization for LHP1. Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions |
| GO:0005515 protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | REMOVE | Summary: High-throughput binary Y2H interaction with IAA26 from the phytohormone interactome map. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. This is an unvalidated systematic Y2H pair with no functional characterization for LHP1. Supporting Evidence: PMID:32612234 we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions |
| GO:0005515 protein binding | IPI PMID:38558017 Interaction of ubiquitin-like protein SILENCING DEFECTIVE 2 ... | REMOVE | Summary: The cleaved SDE2-C fragment interacts with LHP1 in vitro and in vivo and both repress sucrose-induced anthocyanin genes. Reason: Removal reflects only the lack of functional information in a bare protein-binding row, not doubt that the interaction occurred. No informative MF term captures LHP1's side of this interaction. Supporting Evidence: PMID:38558017 physically interacts with LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) in vitro and in vivo |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear localization from phylogenetic/electronic inference, consistent with extensive experimental evidence. Reason: LHP1 is a nuclear chromatin protein. Supporting Evidence: file:ARATH/LHP1/LHP1-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | IDA PMID:21304947 Control of flowering and cell fate by LIF2, an RNA binding p... | ACCEPT | Summary: BiFC and fluorescent-protein fusions show LHP1 and LHP1 complexes in the nucleus. Reason: Direct experimental support for nuclear location. Supporting Evidence: PMID:21304947 We firstly confirmed that the LHP1 dimerization occurred in vivo in the plant nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Nuclear localization from phylogenetic/electronic inference, consistent with extensive experimental evidence. Reason: LHP1 is a nuclear chromatin protein. Supporting Evidence: file:ARATH/LHP1/LHP1-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: Nuclear localization from phylogenetic/electronic inference, consistent with extensive experimental evidence. Reason: LHP1 is a nuclear chromatin protein. Supporting Evidence: file:ARATH/LHP1/LHP1-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0006325 chromatin organization | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO chromatin organization from the HP1/LHP1 chromodomain family. Reason: Correct but very general; the specific process LHP1 contributes to is H3K27me3-dependent facultative heterochromatin formation/maintenance as a PRC1-like subunit, captured in core_functions. Kept as non-core, consistent with the IMP row for the same term. Supporting Evidence: PMID:28428341 RING domain proteins are responsible for H2A ubiquitination and interact with LHP1, whose chromodomain binds to H3K27me3 |
| GO:0006325 chromatin organization | IMP PMID:16244868 The Arabidopsis LHP1 protein is a component of euchromatin. | KEEP AS NON CORE | Summary: lhp1 mutant nuclei were analysed for chromatin organization; no major heterochromatin defects were seen, and LHP1 was concluded to act mainly in euchromatin organization. Reason: Mutant-based (acts_upstream_of_or_within) and general; consistent with LHP1 biology but non-core relative to the specific facultative heterochromatin/epigenetic repression role. Supporting Evidence: PMID:16244868 These data indicate that LHP1 is mainly involved in euchromatin organization in A. thaliana. |
| GO:0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity | IDA NOT PMID:23203051 Arabidopsis RIBA proteins: two out of three isoforms have lo... | REMOVE | Summary: Negative (NOT) DHBPS activity attributed to LHP1 from a paper on RIBA enzymes. Reason: The full text of this paper (cached) characterizes the riboflavin-biosynthetic RIBA1-3 proteins (At5g64300, At2g22450, At5g59750) and never mentions LHP1/TFL2 (At5g17690). LHP1 is a chromodomain/chromo-shadow protein with no GTP cyclohydrolase II or DHBPS domain. Although LHP1 certainly lacks DHBPS activity, this NOT row was evidently made for RIBA3 (which lost DHBPS activity) and mis-attributed to LHP1; it carries no information about LHP1. Supporting Evidence: PMID:23203051 while AtRIBA2 is lacking GCHII activity, AtRIBA3 does not display DHBPS function |
| GO:0009507 chloroplast | IDA PMID:23203051 Arabidopsis RIBA proteins: two out of three isoforms have lo... | REMOVE | Summary: Chloroplast location attributed to LHP1 from GFP localization of RIBA proteins. Reason: The full text of this paper (cached) characterizes the riboflavin-biosynthetic RIBA1-3 proteins (At5g64300, At2g22450, At5g59750) and never mentions LHP1/TFL2 (At5g17690). LHP1 is a chromodomain/chromo-shadow protein with no GTP cyclohydrolase II or DHBPS domain. The plastid localization was shown for RIBA-GFP fusions; LHP1 is a nuclear chromatin protein. Supporting Evidence: PMID:23203051 All three AtRIBA proteins possess N-terminal sequences that exclusively direct GFP fusions to plastids PMID:21304947 Upper panel: LHP1 dimerization in the nucleus. |
| GO:0009648 photoperiodism | IMP PMID:9611176 The TERMINAL FLOWER2 (TFL2) gene controls the reproductive t... | KEEP AS NON CORE | Summary: tfl2 mutants have reduced photoperiod sensitivity. Reason: A pleiotropic downstream consequence of derepression of LHP1 targets (notably FT); not a direct LHP1 process. Supporting Evidence: PMID:9611176 have reduced photoperiod sensitivity |
| GO:0009744 response to sucrose | IEP PMID:38558017 Interaction of ubiquitin-like protein SILENCING DEFECTIVE 2 ... | KEEP AS NON CORE | Summary: Sucrose induces LHP1 expression. Reason: Expression response (IEP) to sugar; not a core function. Supporting Evidence: PMID:38558017 we found that sugar can induce expression of SDE2 and LHP1 |
| GO:0009825 multidimensional cell growth | IMP PMID:9611176 The TERMINAL FLOWER2 (TFL2) gene controls the reproductive t... | KEEP AS NON CORE | Summary: tfl2 mutant plants are dwarfed. Reason: Pleiotropic growth phenotype of a global chromatin repressor mutant; not a direct LHP1 process. Supporting Evidence: PMID:9611176 tfl2 mutant plants are also dwarfed in appearance |
| GO:0009910 negative regulation of flower development | IMP PMID:9611176 The TERMINAL FLOWER2 (TFL2) gene controls the reproductive t... | ACCEPT | Summary: tfl2 mutants flower early and form terminal flowers; LHP1 represses floral regulators such as FT and floral homeotic genes. Reason: Early flowering is the defining tfl2 phenotype and reflects direct LHP1-dependent repression of H3K27me3-marked flowering genes (FT, AG, AP3, PI); the acts_upstream_of_or_within qualifier is appropriate. Supporting Evidence: PMID:9611176 initiates flowering early and terminates the inflorescence with floral structures PMID:17542647 These results suggest that TFL2/LHP1 represses transcription of genes that act during different stages of reproductive development. |
| GO:0010016 shoot system morphogenesis | IMP PMID:9611176 The TERMINAL FLOWER2 (TFL2) gene controls the reproductive t... | KEEP AS NON CORE | Summary: tfl2 mutants have altered shoot/inflorescence architecture (terminal flowers, dwarfism). Reason: Pleiotropic developmental phenotype; non-core. Supporting Evidence: PMID:9611176 The complex nature of the tfl2 single mutant phenotype suggests that TFL2 has a regulatory role more global than that of TFL1. |
| GO:0010048 vernalization response | IMP PMID:16682972 Epigenetic maintenance of the vernalized state in Arabidopsi... | ACCEPT | Summary: LHP1 is required to maintain vernalization-induced FLC repression after return to warm conditions and is enriched at FLC chromatin after cold. Reason: Core, well-replicated role (two independent 2006 studies): LHP1 is needed for the maintenance phase of the vernalization response at FLC. Supporting Evidence: PMID:16682972 is necessary to maintain the epigenetically repressed state of FLC upon return to warm conditions typical of spring PMID:16549797 lhp1 mutants revealed a role for LHP1 in maintaining epigenetic silencing of FLC |
| GO:0010468 regulation of gene expression | IEA GO_REF:0000117 | MODIFY | Summary: ARBA-based regulation of gene expression. Reason: Correct but too general; LHP1 mediates epigenetic (Polycomb/H3K27me3) repression of gene expression, already annotated by IMP and IBA. Proposed replacements: negative regulation of gene expression, epigenetic Supporting Evidence: PMID:16549797 lhp1 mutants revealed a role for LHP1 in maintaining epigenetic silencing of FLC |
| GO:0031507 heterochromatin formation | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO heterochromatin formation from HP1-family membership. Reason: Animal HP1 proteins act in H3K9me-dependent constitutive heterochromatin, but plant LHP1 reads H3K27me3 and acts in Polycomb-type facultative heterochromatin; the child term facultative heterochromatin formation is more accurate. Proposed replacements: facultative heterochromatin formation Supporting Evidence: PMID:17542647 in vivo TFL2/LHP1 associates almost exclusively and nearly co-extensively with H3K27me3 |
| GO:0042802 identical protein binding | IPI PMID:32612234 Extensive signal integration by the phytohormone protein net... | MODIFY | Summary: LHP1 self-interaction in a binary Y2H screen; LHP1 homodimerizes in vivo via its chromo shadow domain region. Reason: Self-binding is better described as protein homodimerization activity, which is independently supported by in vivo BiFC data. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:32612234 consisting of more than 2,000 binary protein-protein interactions PMID:21304947 We firstly confirmed that the LHP1 dimerization occurred in vivo in the plant nucleus |
| GO:0043565 sequence-specific DNA binding | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA for sequence-specific DNA binding in the LHP1 clade, whose only experimental grounding is LHP1's own IDA (motif enrichment in ChIP-defined regions). Reason: LHP1 has no sequence-specific DNA-binding domain; it is recruited to chromatin through its chromodomain (H3K27me3) and partner proteins. Enrichment of motifs (G-box-like, GAGA, telo-box) in LHP1-bound regions reflects recruitment by DNA-binding partners rather than LHP1 itself binding these sequences. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: AGI_LocusCode:AT5G17690 · LHP1 SOURCE WEAK OR INFERRED The only experimental grounding is LHP1's own IDA (PMID:27495811), which reports motif enrichment in LHP1-bound regions rather than direct sequence-specific DNA binding; LHP1 has no sequence-specific DNA-binding domain. Supporting Evidence: PMID:17676062 The LHP1 chromodomain also binds H3K27me3 with high affinity |
| GO:0043565 sequence-specific DNA binding | IDA PMID:27495811 The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LH... | MARK AS OVER ANNOTATED | Summary: Motifs were identified in LHP1/LIF2-targeted genomic regions from ChIP-chip/seq. Reason: Motif enrichment in occupied regions does not demonstrate direct sequence-specific DNA binding by LHP1, which lacks a DNA-binding domain. The full text was not available; deferring on the existence of the data but marking the MF as an over-interpretation; chromatin binding (row above) captures the result. Supporting Evidence: PMID:27495811 We identified specific motifs within the targeted regions, including a G-box-like motif, a GAGA motif, and a telo-box. |
| GO:0045814 negative regulation of gene expression, epigenetic | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for epigenetic negative regulation of gene expression, grounded in LHP1's own IMP. Reason: Core process: LHP1 maintains Polycomb (H3K27me3)-dependent epigenetic silencing. Supporting Evidence: PMID:16549797 lhp1 mutants revealed a role for LHP1 in maintaining epigenetic silencing of FLC |
| GO:0045814 negative regulation of gene expression, epigenetic | IMP PMID:16549797 LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1,... | ACCEPT | Summary: lhp1 mutants fail to maintain epigenetic silencing of FLC after vernalization. Reason: Core process, directly supported by full-text evidence. Supporting Evidence: PMID:16549797 lhp1 mutants revealed a role for LHP1 in maintaining epigenetic silencing of FLC |
| GO:0045892 negative regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for negative regulation of transcription in the chromodomain clade. Reason: LHP1 represses transcription of its H3K27me3-marked targets; consistent with experimental data. Supporting Evidence: PMID:17542647 These results suggest that TFL2/LHP1 represses transcription of genes that act during different stages of reproductive development. |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:27495811 The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LH... | ACCEPT | Summary: LHP1 and LIF2 regulate transcription of stress-responsive target genes; LHP1 acts as a repressor at many targets. Reason: Consistent with LHP1's role in transcriptional repression; deferring to the curator on the full-text details. Supporting Evidence: PMID:27495811 LIF2 and LHP1 can operate both antagonistically and synergistically. |
| GO:0048364 root development | IMP NOT PMID:9611176 The TERMINAL FLOWER2 (TFL2) gene controls the reproductive t... | ACCEPT | Summary: NOT annotation: tfl2 mutants were reported without a root development defect. Reason: The original tfl2 characterization focused on shoot phenotypes; the curator recorded absence of a root phenotype from the full text, which is not cached. Deferring to the curator. Supporting Evidence: PMID:9611176 The complex nature of the tfl2 single mutant phenotype |
| GO:0048573 photoperiodism, flowering | IMP PMID:18799658 Diversification of photoperiodic response patterns in a coll... | KEEP AS NON CORE | Summary: Screen of early-flowering mutants for quantitative photoperiod response; tfl2/lhp1 is presumably among the mutants analysed. Reason: Photoperiodic flowering response alterations are a downstream consequence of LHP1 repression of FT; non-core. Full text not available; deferring to the curator on gene identity. Supporting Evidence: PMID:18799658 We studied the quantitative response to photoperiod in 49 mutants selected for early flowering in SDs. |
| GO:0061628 histone H3K27me3 reader activity | IDA PMID:17542647 Arabidopsis TFL2/LHP1 specifically associates with genes mar... | ACCEPT | Summary: TFL2/LHP1 binds H3K27me3 (and H3K9me peptides in vitro) and co-localizes nearly exclusively with H3K27me3 genome-wide. Reason: Core molecular function: the LHP1 chromodomain reads H3K27me3. Supporting Evidence: PMID:17542647 in vivo TFL2/LHP1 associates almost exclusively and nearly co-extensively with H3K27me3 |
| GO:0061628 histone H3K27me3 reader activity | IDA PMID:17676062 The Arabidopsis LHP1 protein colocalizes with histone H3 Lys... | ACCEPT | Summary: The LHP1 chromodomain binds H3K27me3 with high affinity, and LHP1 co-localizes with H3K27me3 genome-wide. Reason: Core molecular function, independently confirmed. Supporting Evidence: PMID:17676062 The LHP1 chromodomain also binds H3K27me3 with high affinity, suggesting that LHP1 has functions similar to those of Polycomb. |
| GO:0035102 PRC1 complex | IPI PMID:19097900 Polycomb silencing of KNOX genes confines shoot stem cell ni... | NEW | Summary: NEW annotation. LHP1 binds the RING1 homologs AtRING1a/b, and genetic, molecular and functional evidence supports an Arabidopsis PRC1-like complex of AtRING1a, AtRING1b and LHP1 that binds H3K27me3 deposited by PRC2. This replaces the information lost by removing the bare protein-binding rows for RING1A. Reason: Complex membership is supported by direct interaction data, genetic enhancement, and later work describing LHP1 as a PRC1 subunit; the plant PRC1-like assembly is the appropriate GO complex term. Supporting Evidence: PMID:19097900 We propose a model in which AtRING1a, AtRING1b, and LHP1 form a PRC1-like complex, which binds trimethyl-H3K27 marked by the CLF-containing PRC2 PMID:28428341 PRC1 variants contain seven proteins, including LHP1, EMF1, and five RING-domain proteins |
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Download this section (compressed HTML)Q: Does LHP1 contribute any activity of its own to H3K27me3 spreading or chromatin compaction at FLC beyond reading the mark, e.g. by bridging PRC2 (via MSI1) to modified nucleosomes during replication?
Q: The GOA rows for GTP cyclohydrolase II activity, NOT DHBPS activity and chloroplast from PMID:23203051 appear to belong to RIBA1/RIBA3; can the TAIR curators confirm and correct the gene attribution?
Experiment: Separation-of-function LHP1 alleles (chromodomain aromatic-cage vs chromo-shadow dimerization mutants) introduced into lhp1 to test which interaction is required for maintenance of FLC silencing after vernalization, monitored by FLC-Venus imaging and H3K27me3 ChIP.
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