Cyclin T1 is the cyclin regulatory subunit of P-TEFb, partnering with CDK9 to promote RNA polymerase II pause release and productive transcription elongation. It binds 7SK snRNA in the inactive 7SK snRNP/P-TEFb regulatory pool and is recruited to chromatin and transcription factors during gene activation. The histidine-rich region can support transcription-associated condensate/scaffold behavior, but the conserved core role is activation and targeting of CDK9-dependent transcription elongation rather than general DNA binding or cell division.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Cyclin-T1 carries an NLS and functions in the nucleus as the cyclin subunit of P-TEFb regulating Pol II transcription elongation; primary site of action. Reason: Core localization; IDA-supported and matches UniProt. |
| GO:0032786 positive regulation of DNA-templated transcription, elongation | IBA GO_REF:0000033 | MODIFY | Summary: Cyclin-T1 specifically promotes RNA Pol II elongation; the Pol II-specific child term more precisely captures P-TEFb's role than the generic DNA-templated parent. Reason: Generic parent; Pol II-specific elongation child (GO:0032968) is more precise. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000002653 SUPPORTS TRANSFER The elongation-control IBD sits at this node, whose seed set spans human, Drosophila and budding-yeast members. Positive control of transcription elongation is therefore an inherited property of the group and transfers soundly to mouse Ccnt1; the fault lies only in the term, which names DNA-templated elongation in general where the inherited biology is specifically RNA polymerase II elongation. UniProtKB:O60563 · human CCNT1 SUPPORTS TRANSFER The human orthologue, and the entry from which mouse Ccnt1's own UniProt function, complex and localization statements are propagated (ECO:0000250|UniProtKB:O60563). Its elongation evidence is RNA polymerase II elongation, which is why the Pol II-specific child term is the better fit for this row. UniProtKB:O60583 SUPPORTS TRANSFER A further human seed at this node, cited by identifier only because the local index does not resolve it; no claim is made here about which protein it is. SGD:S000003543 SUPPORTS TRANSFER Budding-yeast seed, cited by identifier because the local index does not resolve it. Its presence shows the node reaches fungi, where RNA polymerase II elongation control also operates, so the Pol II-specific replacement term is not a lineage-restricted over-reach. FB:FBgn0025455 SUPPORTS TRANSFER Drosophila seed, cited by identifier only; PTHR10026 is not in the local PAINT cache and the local index does not resolve it, so no claim is made here about which gene it is. It is the fly member whose presence in the WITH/FROM supports the seed span described at the node above. UniProtKB:O75909 SUPPORTS TRANSFER A third human seed at this node, cited by identifier only because the local index does not resolve it; no claim is made here about which protein it is. Listed so the enumeration matches the row's WITH/FROM in full rather than in part. Proposed replacements: positive regulation of transcription elongation by RNA polymerase II Supporting Evidence: file:mouse/Ccnt1/Ccnt1-deep-research-falcon.md Cyclin T1 functions as the CDK9 cyclin partner in P-TEFb, enabling RNAPII transcriptional elongation by supporting phosphorylation events required for RNAPII pause release and productive elongation. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: By activating CDK9 to release paused Pol II, cyclin-T1/P-TEFb positively regulates RNA Pol II transcription of most protein-coding genes. Reason: Accurate process for P-TEFb-mediated pause release. |
| GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity | IBA GO_REF:0000033 | ACCEPT | Summary: Cyclin-T1 binds and activates the CDK9 serine/threonine kinase, switching on P-TEFb catalysis; this activator activity is cyclin-T1's defining molecular function. Reason: Core defining MF of the regulatory cyclin subunit; strongly supported. Supporting Evidence: file:mouse/Ccnt1/Ccnt1-deep-research-falcon.md The core P-TEFb heterodimer is CDK9-Cyclin T1. CDK9 is the catalytic kinase; Cyclin T1 is the cyclin subunit that enables CDK9 activity within transcriptional complexes. |
| GO:0008024 cyclin/CDK positive transcription elongation factor complex | IBA GO_REF:0000033 | ACCEPT | Summary: Cyclin-T1 is the cyclin half of the cyclin/CDK positive transcription elongation factor (P-TEFb) complex; explicit, accurate complex assignment. Reason: Precise complex term matching cyclin-T1's defining assembly. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Cyclin-T1 carries an NLS and functions in the nucleus as the cyclin subunit of P-TEFb regulating Pol II transcription elongation; primary site of action. Reason: Core localization; IDA-supported and matches UniProt. |
| GO:0006357 regulation of transcription by RNA polymerase II | IEA GO_REF:0000002 | MODIFY | Summary: Cyclin-T1's effect on Pol II transcription is specifically positive (pause release into elongation); the positive-regulation child captures direction lost by the neutral parent. Reason: Neutral parent; positive-regulation child (GO:0045944) is more precise. Proposed replacements: positive regulation of transcription by RNA polymerase II |
| GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity | IEA GO_REF:0000002 | MODIFY | Summary: Cyclin-T1 does not merely regulate CDK9 but positively activates it; the specific activator-activity child term better captures cyclin-T1's role within P-TEFb. Reason: Parent regulator term; specific activator child (GO:0061575) is more precise. Proposed replacements: cyclin-dependent protein serine/threonine kinase activator activity |
| GO:0051301 cell division | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: Cyclin-T1 is a transcriptional cyclin (cyclin C subfamily), not a cell-cycle cyclin; it controls Pol II elongation rather than cell-cycle progression or division. Reason: IEA keyword-derived; transcriptional, not cell-cycle, cyclin function. |
| GO:0005515 protein binding | IPI PMID:20434984 c-Myc regulates transcriptional pause release. | MARK AS OVER ANNOTATED | Summary: Bare protein binding (IPI) conveys no specific function; cyclin-T1's informative interactions (CDK9 activation, 7SK, TF recruitment) are captured by specific terms. Reason: Uninformative generic binding term. Supporting Evidence: PMID:20434984 c-Myc regulates transcriptional pause release. |
| GO:0005515 protein binding | IPI PMID:22922464 Bromodomain-dependent stage-specific male genome programming... | MARK AS OVER ANNOTATED | Summary: Bare protein binding (IPI) conveys no specific function; cyclin-T1's informative interactions (CDK9 activation, 7SK, TF recruitment) are captured by specific terms. Reason: Uninformative generic binding term. Supporting Evidence: PMID:22922464 Bromodomain-dependent stage-specific male genome programming by Brdt. |
| GO:0005634 nucleus | ISO GO_REF:0000119 | ACCEPT | Summary: Cyclin-T1 carries an NLS and functions in the nucleus as the cyclin subunit of P-TEFb regulating Pol II transcription elongation; primary site of action. Reason: Core localization; IDA-supported and matches UniProt. |
| GO:0005654 nucleoplasm | ISO GO_REF:0000119 | ACCEPT | Summary: Cyclin-T1/P-TEFb acts in the nucleoplasm at transcription sites; consistent with its bipartite nuclear localization signal and nuclear function. Reason: Accurate nuclear sub-compartment for elongation function. |
| GO:0008024 cyclin/CDK positive transcription elongation factor complex | ISO GO_REF:0000119 | ACCEPT | Summary: Cyclin-T1 is the cyclin half of the cyclin/CDK positive transcription elongation factor (P-TEFb) complex; explicit, accurate complex assignment. Reason: Precise complex term matching cyclin-T1's defining assembly. |
| GO:0032968 positive regulation of transcription elongation by RNA polymerase II | ISO GO_REF:0000119 | ACCEPT | Summary: Cyclin-T1/P-TEFb phosphorylates the Pol II CTD Ser2 and DSIF/NELF to release promoter-proximal pausing into productive elongation; the core biological process. Reason: Core elongation process; defining role of P-TEFb. Supporting Evidence: file:mouse/Ccnt1/Ccnt1-deep-research-falcon.md Cyclin T1 functions as the CDK9 cyclin partner in P-TEFb, enabling RNAPII transcriptional elongation by supporting phosphorylation events required for RNAPII pause release and productive elongation. |
| GO:0043923 host-mediated activation of viral transcription | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: Cyclin-T1 is the host cofactor that HIV-1 Tat hijacks to recruit P-TEFb to TAR and drive proviral elongation; a downstream, pathogen-specific role, not core cellular function. Reason: Viral co-option of P-TEFb; pleiotropic downstream role. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | ISO GO_REF:0000119 | ACCEPT | Summary: By activating CDK9 to release paused Pol II, cyclin-T1/P-TEFb positively regulates RNA Pol II transcription of most protein-coding genes. Reason: Accurate process for P-TEFb-mediated pause release. |
| GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity | ISO GO_REF:0000119 | ACCEPT | Summary: Cyclin-T1 binds and activates the CDK9 serine/threonine kinase, switching on P-TEFb catalysis; this activator activity is cyclin-T1's defining molecular function. Reason: Core defining MF of the regulatory cyclin subunit; strongly supported. |
| GO:0070063 RNA polymerase binding | ISO GO_REF:0000119 | ACCEPT | Summary: Within P-TEFb, cyclin-T1 contributes to engagement of RNA Pol II so CDK9 can phosphorylate the CTD; HRD-driven LLPS enhances P-TEFb binding to the Pol II CTD. Reason: Supported by mechanistic role of cyclin-T1 in targeting P-TEFb to Pol II. |
| GO:0070691 P-TEFb complex | ISO GO_REF:0000119 | ACCEPT | Summary: Cyclin-T1 is an obligate component of P-TEFb, the CDK9/cyclin-T1 heterodimer; complex membership is its defining cellular role. Reason: Core complex membership; directly supported by SUBUNIT evidence. Supporting Evidence: file:mouse/Ccnt1/Ccnt1-deep-research-falcon.md Mouse Ccnt1 encodes Cyclin T1, a nuclear cyclin-family regulatory subunit that forms P-TEFb with CDK9. |
| GO:0097322 7SK snRNA binding | ISO GO_REF:0000119 | ACCEPT | Summary: Cyclin-T1 binds the 7SK snRNA scaffold to assemble the inactive 7SK snRNP that sequesters P-TEFb, a defining feature of CDK9/cyclin-T1 regulation. Reason: Direct, well-supported molecular function central to P-TEFb availability control. |
| GO:0140297 DNA-binding transcription factor binding | ISO GO_REF:0000119 | ACCEPT | Summary: Cyclin-T1/P-TEFb is recruited to genes by sequence-specific transcription factors (e.g. TBX21/T-bet), and binds DNA-binding TFs to deliver CDK9 to target promoters. Reason: Consistent with TF-directed P-TEFb recruitment documented for cyclin-T1. |
| GO:0140693 molecular condensate scaffold activity | ISO GO_REF:0000119 | ACCEPT | Summary: The intrinsically disordered histidine-rich domain of cyclin-T1 drives liquid-liquid phase separation that scaffolds condensates enhancing P-TEFb binding to the Pol II CTD. Reason: Supported by HRD/LLPS DOMAIN evidence; mechanistically central. |
| GO:0003677 DNA binding | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Cyclin-T1 is a transcription-elongation cofactor recruited to chromatin via P-TEFb partners (BRD4, SEC); it is not a sequence-specific DNA-binding protein. Reason: Generic electronic DNA-binding term; cyclin-T1 acts via protein partners, not direct DNA contact. |
| GO:0005654 nucleoplasm | IEA GO_REF:0000107 | ACCEPT | Summary: Cyclin-T1/P-TEFb acts in the nucleoplasm at transcription sites; consistent with its bipartite nuclear localization signal and nuclear function. Reason: Accurate nuclear sub-compartment for elongation function. |
| GO:0008024 cyclin/CDK positive transcription elongation factor complex | IEA GO_REF:0000107 | ACCEPT | Summary: Cyclin-T1 is the cyclin half of the cyclin/CDK positive transcription elongation factor (P-TEFb) complex; explicit, accurate complex assignment. Reason: Precise complex term matching cyclin-T1's defining assembly. |
| GO:0032968 positive regulation of transcription elongation by RNA polymerase II | IEA GO_REF:0000107 | ACCEPT | Summary: Cyclin-T1/P-TEFb phosphorylates the Pol II CTD Ser2 and DSIF/NELF to release promoter-proximal pausing into productive elongation; the core biological process. Reason: Core elongation process; defining role of P-TEFb. |
| GO:0043923 host-mediated activation of viral transcription | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Cyclin-T1 is the host cofactor that HIV-1 Tat hijacks to recruit P-TEFb to TAR and drive proviral elongation; a downstream, pathogen-specific role, not core cellular function. Reason: Viral co-option of P-TEFb; pleiotropic downstream role. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IEA GO_REF:0000107 | ACCEPT | Summary: By activating CDK9 to release paused Pol II, cyclin-T1/P-TEFb positively regulates RNA Pol II transcription of most protein-coding genes. Reason: Accurate process for P-TEFb-mediated pause release. |
| GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity | IEA GO_REF:0000107 | ACCEPT | Summary: Cyclin-T1 binds and activates the CDK9 serine/threonine kinase, switching on P-TEFb catalysis; this activator activity is cyclin-T1's defining molecular function. Reason: Core defining MF of the regulatory cyclin subunit; strongly supported. |
| GO:0070063 RNA polymerase binding | IEA GO_REF:0000107 | ACCEPT | Summary: Within P-TEFb, cyclin-T1 contributes to engagement of RNA Pol II so CDK9 can phosphorylate the CTD; HRD-driven LLPS enhances P-TEFb binding to the Pol II CTD. Reason: Supported by mechanistic role of cyclin-T1 in targeting P-TEFb to Pol II. |
| GO:0070691 P-TEFb complex | IEA GO_REF:0000107 | ACCEPT | Summary: Cyclin-T1 is an obligate component of P-TEFb, the CDK9/cyclin-T1 heterodimer; complex membership is its defining cellular role. Reason: Core complex membership; directly supported by SUBUNIT evidence. |
| GO:0097322 7SK snRNA binding | IEA GO_REF:0000107 | ACCEPT | Summary: Cyclin-T1 binds the 7SK snRNA scaffold to assemble the inactive 7SK snRNP that sequesters P-TEFb, a defining feature of CDK9/cyclin-T1 regulation. Reason: Direct, well-supported molecular function central to P-TEFb availability control. |
| GO:0140297 DNA-binding transcription factor binding | IEA GO_REF:0000107 | ACCEPT | Summary: Cyclin-T1/P-TEFb is recruited to genes by sequence-specific transcription factors (e.g. TBX21/T-bet), and binds DNA-binding TFs to deliver CDK9 to target promoters. Reason: Consistent with TF-directed P-TEFb recruitment documented for cyclin-T1. |
| GO:0140693 molecular condensate scaffold activity | IEA GO_REF:0000107 | ACCEPT | Summary: The intrinsically disordered histidine-rich domain of cyclin-T1 drives liquid-liquid phase separation that scaffolds condensates enhancing P-TEFb binding to the Pol II CTD. Reason: Supported by HRD/LLPS DOMAIN evidence; mechanistically central. |
| GO:0005829 cytosol | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: A minor cytosolic pool may exist (e.g. monomeric CDK9/cyclin-T1 between 7SK release and chromatin reassembly), but cyclin-T1 functions in the nucleus. Reason: Secondary localization; function is nuclear, ISO-supported only. |
| GO:0032968 positive regulation of transcription elongation by RNA polymerase II | ISS GO_REF:0000024 | ACCEPT | Summary: Cyclin-T1/P-TEFb phosphorylates the Pol II CTD Ser2 and DSIF/NELF to release promoter-proximal pausing into productive elongation; the core biological process. Reason: Core elongation process; defining role of P-TEFb. |
| GO:0070691 P-TEFb complex | ISS GO_REF:0000024 | ACCEPT | Summary: Cyclin-T1 is an obligate component of P-TEFb, the CDK9/cyclin-T1 heterodimer; complex membership is its defining cellular role. Reason: Core complex membership; directly supported by SUBUNIT evidence. |
| GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity | ISS GO_REF:0000024 | ACCEPT | Summary: Cyclin-T1 binds and activates the CDK9 serine/threonine kinase, switching on P-TEFb catalysis; this activator activity is cyclin-T1's defining molecular function. Reason: Core defining MF of the regulatory cyclin subunit; strongly supported. |
| GO:0140693 molecular condensate scaffold activity | ISS GO_REF:0000024 | ACCEPT | Summary: The intrinsically disordered histidine-rich domain of cyclin-T1 drives liquid-liquid phase separation that scaffolds condensates enhancing P-TEFb binding to the Pol II CTD. Reason: Supported by HRD/LLPS DOMAIN evidence; mechanistically central. |
| GO:0019901 protein kinase binding | IDA PMID:22547058 Cyclin K-containing kinase complexes maintain self-renewal i... | MARK AS OVER ANNOTATED | Summary: This reflects cyclin-T1 binding the CDK9 protein kinase, but the specific functional consequence is already captured by the CDK9 activator-activity annotation. Reason: Generic binding redundant with the specific CDK9 activator-activity term. Supporting Evidence: PMID:22547058 Cyclin K-containing kinase complexes maintain self-renewal in murine embryonic stem cells. |
| GO:0097322 7SK snRNA binding | ISS GO_REF:0000024 | ACCEPT | Summary: Cyclin-T1 binds the 7SK snRNA scaffold to assemble the inactive 7SK snRNP that sequesters P-TEFb, a defining feature of CDK9/cyclin-T1 regulation. Reason: Direct, well-supported molecular function central to P-TEFb availability control. |
| GO:0008024 cyclin/CDK positive transcription elongation factor complex | ISS GO_REF:0000024 | ACCEPT | Summary: Cyclin-T1 is the cyclin half of the cyclin/CDK positive transcription elongation factor (P-TEFb) complex; explicit, accurate complex assignment. Reason: Precise complex term matching cyclin-T1's defining assembly. |
| GO:0003682 chromatin binding | IDA PMID:18662700 The positive transcription elongation factor b is an essenti... | ACCEPT | Summary: Active P-TEFb engages chromatin at paused genes; cyclin-T1 chromatin association (IDA) reflects recruitment of the elongation machinery to template chromatin. Reason: Experimental IDA consistent with chromatin-associated active P-TEFb. Supporting Evidence: PMID:18662700 The positive transcription elongation factor b is an essential cofactor for the activation of transcription by myocyte enhancer factor 2. |
| GO:0000976 transcription cis-regulatory region binding | IDA PMID:20570862 Multiple functions of Ldb1 required for beta-globin activati... | MARK AS OVER ANNOTATED | Summary: Cyclin-T1 occupies cis-regulatory regions only indirectly via P-TEFb recruitment by DNA-binding factors; it has no intrinsic sequence-specific cis-element binding. Reason: Indirect occupancy via partners; not an intrinsic cyclin-T1 binding activity. Supporting Evidence: PMID:20570862 Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation. |
| GO:0008024 cyclin/CDK positive transcription elongation factor complex | TAS PMID:20570862 Multiple functions of Ldb1 required for beta-globin activati... | ACCEPT | Summary: Cyclin-T1 is the cyclin half of the cyclin/CDK positive transcription elongation factor (P-TEFb) complex; explicit, accurate complex assignment. Reason: Precise complex term matching cyclin-T1's defining assembly. Supporting Evidence: PMID:20570862 Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation. |
| GO:0003677 DNA binding | ISO PMID:16109376 The bromodomain protein Brd4 is a positive regulatory compon... | MARK AS OVER ANNOTATED | Summary: Cyclin-T1 is a transcription-elongation cofactor recruited to chromatin via P-TEFb partners (BRD4, SEC); it is not a sequence-specific DNA-binding protein. Reason: Generic electronic DNA-binding term; cyclin-T1 acts via protein partners, not direct DNA contact. Supporting Evidence: PMID:16109376 The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. |
| GO:0005634 nucleus | IDA PMID:16109376 The bromodomain protein Brd4 is a positive regulatory compon... | ACCEPT | Summary: Cyclin-T1 carries an NLS and functions in the nucleus as the cyclin subunit of P-TEFb regulating Pol II transcription elongation; primary site of action. Reason: Core localization; IDA-supported and matches UniProt. Supporting Evidence: PMID:16109376 The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. |
| GO:0006468 protein phosphorylation | ISO PMID:16109376 The bromodomain protein Brd4 is a positive regulatory compon... | MODIFY | Summary: Cyclin-T1 is the non-catalytic regulatory subunit; it does not itself phosphorylate substrates. Its role is positively regulating CDK9's kinase activity. Reason: Catalytic process belongs to CDK9; cyclin-T1 regulates that activity (GO:0033674). Proposed replacements: positive regulation of kinase activity Supporting Evidence: PMID:16109376 The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. |
| GO:0017069 snRNA binding | IDA PMID:16109376 The bromodomain protein Brd4 is a positive regulatory compon... | ACCEPT | Summary: Cyclin-T1 binds snRNA, consistent with its IDA-supported association with the 7SK snRNA scaffold of the inactive 7SK snRNP reservoir of P-TEFb. Reason: Experimental IDA; underlies 7SK snRNP regulatory function. Supporting Evidence: PMID:16109376 The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. file:mouse/Ccnt1/Ccnt1-deep-research-falcon.md A substantial fraction of P-TEFb is sequestered in an inactive ribonucleoprotein complex organized around 7SK snRNA, with protein components including HEXIM1/2, LARP7, and MePCE. |
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