SWI4

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000082 G1/S transition of mitotic cell cycle	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference at the APSES-family node PTN000917496 (Swi4/Mbp1/Swi6 and their C. albicans and S. pombe counterparts), seeded in part by Swi4's own experimental G1/S rows (SGD:S000000913 in the WITH list is the target itself, which is expected). Every extant member of the node is a subunit of a G1/S transcription factor (SBF, MBF, pombe MBF), so the node placement is sound. Reason: Swi4 is the DNA-binding subunit of SBF, the transcription factor whose activation constitutes the Start transcriptional switch; swi4 swi6 double mutants are inviable because G1 cyclin transcription fails (PMID:1832338). The inherited function is the core function of the gene and the target-in-WITH pattern reflects experimental grounding on Swi4 itself, not circularity. Supporting Evidence: PMID:1832338 We show that the essential role of SWI4 and SWI6 is to ensure the activity of G1-specific cyclin genes. PMID:10490612 Swi4 and Mbp1 are the DNA binding components of SBF and MBF, respectively.
GO:0000082 G1/S transition of mitotic cell cycle	IDA PMID:10490612 Regulation of cell cycle transcription factor Swi4 through a...	ACCEPT	Summary: Baetz and Andrews 1999 (full text cached; annotation sourced via ComplexPortal for the SBF complex). The paper reconstitutes SBF from insect-cell Swi4 and Swi6, shows that Swi4 alone cannot bind SCBs, that the Swi4 C terminus auto-inhibits DNA binding, and that Swi6 relieves the inhibition, all in the explicit context of SBF-driven induction of G1 cyclin genes at the G1/S transition. Reason: The G1/S role of SBF is the framing and the biological readout of the paper (SCB::lacZ reporter activity in vivo), and the mechanistic finding, Swi6-relieved auto-inhibition of Swi4 DNA binding, is one of the regulatory layers that restricts SBF activity to late M/G1. Core function. Supporting Evidence: PMID:10490612 Maximal expression of the G 1 cyclin genes CLN1 , CLN2 , PCL1 , and PCL2 at Start requires the activity of a transcription factor, SBF (SCB binding factor) PMID:10490612 The interaction of the carboxy-terminal region of Swi4 with Swi6 alleviates this inhibition, allowing Swi4 to bind DNA.
GO:0000082 G1/S transition of mitotic cell cycle	IMP PMID:2649246 Identification of a DNA binding factor involved in cell-cycl...	ACCEPT	Summary: Andrews and Herskowitz 1989 (Cell; abstract-only cache): gel-retardation and footprinting identify the cell-cycle box factor (CCBF, later SBF) that binds the CCB repeats responsible for late-G1 expression of HO; swi4 and swi6 mutant extracts lack the CCBF-promoter complex, and SWI4 and SWI6 are the only SWI genes required for CCB-driven expression in vivo. Reason: Loss of Swi4 abolishes the factor that confers late-G1 (i.e. G1/S) periodicity on HO transcription; this is the founding IMP evidence that Swi4 acts in the G1/S transcriptional program. The paper predates the identification of the CLN targets, but the mutant phenotype is on the cell-cycle-regulated transcription that GO:0000082 describes, and SGD applies GO:0000082 uniformly to the Start transcription machinery. Supporting Evidence: PMID:2649246 We show that the SWI4 and SWI6 genes are required for formation of the CCBF-promoter complex in vitro, either as components of CCBF or as modulators of CCBF activity. PMID:2649246 These observations indicate that the CCBF is responsible for cell-cycle regulation of HO and lead to the view that two of the SWI genes, SWI4 and SWI6, are specifically involved in this regulatory event.
GO:0000082 G1/S transition of mitotic cell cycle	IMP PMID:3542227 Cell cycle control of the yeast HO gene: cis- and trans-acti...	ACCEPT	Summary: Breeden and Nasmyth 1987 (Cell; abstract-only cache): the CACGA4 repeat of the HO promoter confers cell-cycle-dependent transcription on a heterologous gene, and among the ten SWI genes SWI4 and SWI6 are specifically required for CACGA4-mediated activation. Reason: Defines the SCB element and shows by mutant analysis that Swi4 is required for the cell-cycle-regulated (late G1) activation it directs. The same convention as the companion 1989 row; core function. Supporting Evidence: PMID:3542227 SWI4 and SWI6 are specifically required for CACGA4-mediated activation of transcription. PMID:3542227 We show that this sequence activates transcription of a heterologous gene in a cell-cycle-dependent fashion indistinguishable from that of the wild-type HO promoter.
GO:0000785 chromatin	IDA PMID:12464632 Complex transcriptional circuitry at the G1/S transition in ...	ACCEPT	Summary: Horak et al. 2002 (full text cached): chromatin immunoprecipitation of Swi4-HA confirms occupancy of 22 of 26 candidate promoters (including CLN2 and twelve transcription-factor genes such as HCM1, TOS4, YOX1 and the SWI4 promoter itself), building on the 183 Swi4-bound promoters found by ChIP-chip. Reason: Direct in vivo demonstration that Swi4 is bound to promoter chromatin at its target genes; this is where the core function is exerted. Supporting Evidence: PMID:12464632 Swi4, the DNA-binding component of SBF, was determined to bind upstream of 183 genes by chIp–chip analysis PMID:12464632 Twenty-two of the 26 promoters tested were enriched in Swi4–HA immunoprecipitates over immunoprecipitated DNA from the untagged strain.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference at the APSES-family node, seeded by the S. pombe MBF subunits. In budding yeast Swi4 is the subunit of SBF that carries the APSES DNA-binding domain and recognises the SCB element (CRCGAAA) in target promoters. Reason: Swi4 is the sequence-specific DNA-binding subunit of SBF: its N-terminal 197 residues bind SCBs in vitro, and C-terminally truncated Swi4 binds SCB DNA without Swi6 (PMID:8423776, PMID:1465410, PMID:10490612). If anything the qualifier understates the case, since Swi4 supplies the DNA-binding activity outright rather than merely contributing to it; the term is exactly right. Supporting Evidence: PMID:1465410 we propose that Swi4 is responsible for binding to the SCB sequence while Swi6, through its association with Swi4, regulates activity of the complex. PMID:10490612 Biochemical studies have revealed that Swi4 is the component of SBF that specifically binds SCB sequences
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference at the APSES-family node, seeded by Swi4's own IMP rows, by Mbp1 and by the pombe MBF subunit. All extant members are the DNA-binding subunits of G1/S transcriptional activators. Reason: Swi4 binds SCBs and, as part of SBF, activates Pol II transcription of CLN1, CLN2, PCL1, HO and cell-wall genes; C-terminal Swi4 mutants activate an SCB::lacZ reporter even without Swi6 (PMID:10490612). The activator term is the correct MF and the target-in-WITH pattern reflects experimental grounding on Swi4 itself. Supporting Evidence: PMID:8423776 Overproduction of SWI4 eliminates the SWI6 dependency of HO transcription in vivo and results in a new SWI6-independent, SCB-specific complex in vitro, which is heterogeneous and reacts with SWI4 antibodies.
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific	IEA GO_REF:0000117	ACCEPT	Summary: ARBA machine-learned rule assigning the Pol II activator MF; it reproduces the experimentally established function. Reason: Matches the IMP and IBA rows for the same term; correct level of specificity for an electronic annotation. Supporting Evidence: PMID:3542227 SWI4 and SWI6 are specifically required for CACGA4-mediated activation of transcription.
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific	IMP PMID:2649246 Identification of a DNA binding factor involved in cell-cycl...	ACCEPT	Summary: Andrews and Herskowitz 1989 (abstract-only cache): swi4 mutants lack the CCBF-DNA complex in vitro and lose CCB-driven expression in vivo, identifying Swi4 as a component (or essential modulator) of the DNA-binding activator of HO. Reason: The mutant phenotype is loss of a sequence-specific activator of Pol II transcription; together with the 1989 Nature paper showing Swi4 protein in the CCBF-DNA complex (PMID:2689885) this establishes the activator MF. Core function. Supporting Evidence: PMID:2649246 We also show that SWI4 and SWI6 are the only SWI genes required for expression in vivo from the CCB sequences. PMID:2689885 We demonstrate by using antibodies to the SWI4 protein in gel-shift assays that the protein is present in the CCBF-DNA complex.
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific	IMP PMID:8423776 Analysis of the SWI4/SWI6 protein complex, which directs G1/...	ACCEPT	Summary: Sidorova and Breeden 1993 (abstract-only cache): SWI4 overproduction bypasses the SWI6 requirement for HO transcription and yields a Swi6-independent SCB-specific complex; the C terminus of Swi4 is dispensable for SCB binding but necessary and sufficient for Swi6 association, placing the sequence-specific DNA-binding domain in Swi4 and the accessibility control in Swi6. Reason: Gain-of-function and truncation data show that Swi4 is the DNA-binding, activating subunit of SBF; Swi6 controls access of that domain to DNA. Core function. Supporting Evidence: PMID:8423776 From these data, we propose that the sequence-specific DNA-binding domain resides in SWI4 but that SWI6 controls the accessibility of this domain in the SWI4/6 complex. PMID:8423776 The C terminus of SWI4 is not required for SWI6-independent binding of SWI4 to SCB sequences, but it is necessary and sufficient for association with SWI6.
GO:0003677 DNA binding	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO mapping from the APSES-type HTH DNA-binding domain superfamily (IPR036887), which is the Swi4 N-terminal SCB-recognition domain (UniProt DOMAIN 37-147, H-T-H motif 71-92). Reason: Correct but generic; the specific activity (GO:0000978, sequence-specific binding of SCB cis-regulatory elements) is carried by the IBA and HDA rows. Acceptable as a domain-level electronic annotation. Supporting Evidence: PMID:10490612 Swi4 contains an N-terminal DNA binding domain that is sufficient for the specific recognition of SCB sequences in vitro
GO:0005515 protein binding	IPI PMID:10490612 Regulation of cell cycle transcription factor Swi4 through a...	MODIFY	Summary: Interaction with Swi6 (UniProtKB:P09959) from Baetz and Andrews 1999 (full text cached): insect-cell Swi4 and Swi6 reconstitute SBF that sediments as a 180 kDa heterodimer, GST-Swi4 C-terminal region pulls down Swi6, and Swi6 binding relieves the intramolecular auto-inhibition of the Swi4 DNA-binding domain. Reason: Generic protein binding is uninformative. The paper characterises the obligate Swi4-Swi6 heterodimer (SBF), so GO:0046982 protein heterodimerization activity is the informative MF term, following the treatment of the E2F1-DP1 partner rows in the human E2F1 review; complex membership is separately captured by the GO:0033309 rows. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:10490612 SBF ran at 180 kDa, a size which is close to the predicted size of a heterodimer of Swi4 (123 kDa) and Swi6 (91 kDa). PMID:10490612 The interaction of the carboxy-terminal region of Swi4 with Swi6 alleviates this inhibition, allowing Swi4 to bind DNA.
GO:0005515 protein binding	IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine...	REMOVE	Summary: Swi4-Swi6 pair recovered in the Gavin et al. 2006 genome-wide TAP-MS complex survey (abstract-only cache; Swi4 is not named in the cached text). The interaction is the well-established SBF heterodimer. Reason: Generic protein binding derived from a high-throughput survey adds no functional information; the Swi4-Swi6 association it recovers is already represented by five experimental GO:0033309 SBF transcription complex rows and by the heterodimerization MODIFY proposed on the Baetz and Andrews row. Removal does not assert that the interaction is false, only that this row is uninformative and redundant. Supporting Evidence: PMID:16429126 Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry.
GO:0005515 protein binding	IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome.	MODIFY	Summary: Lambert et al. 2010 (full text cached): modified chromatin immunopurification (mChIP) coupled to MS of Swi4-TAP, Swi6-TAP and Mbp1-TAP recovers the SBF/MBF partners and chromatin-associated regulators such as Stb1, Whi5, Nrm1 and Msa1. Reason: Generic protein binding is uninformative; the recovered Swi4-Swi6 interaction is the SBF heterodimer, so GO:0046982 protein heterodimerization activity is proposed for consistency with the Baetz and Andrews row (complex membership is already captured by the GO:0033309 rows). Note that the paper's text misdescribes MBF as Swi4-Mbp1; MBF is Mbp1-Swi6 and does not contain Swi4. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:21179020 mChIP-MS analyses of Swi4-TAP, Swi6-TAP and Mbp1-TAP successfully identified known interaction partners (such as Stb1) for both MBF and SBF
GO:0005515 protein binding	IPI PMID:25112483 3,6-Epidioxy-1,10-bisaboladiene inhibits G1 -specific transc...	MODIFY	Summary: Imamura et al. 2014 (abstract-only cache): the sesquiterpene EDBD inhibits SBF- and MBF-dependent G1 transcription via Hog1 and Cln3; the structured digital abstract records Swi4-Swi6 co-immunoprecipitation with tagged proteins. Reason: Generic protein binding is uninformative; the co-IP documents the SBF heterodimer, so GO:0046982 protein heterodimerization activity is the informative term (as for the other Swi6 rows). The drug-response findings themselves do not warrant any additional process annotation for Swi4. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:25112483 Swi4 physically interacts with Swi6 by anti tag coimmunoprecipitation
GO:0005515 protein binding	IPI PMID:37968396 The social and structural architecture of the yeast protein ...	REMOVE	Summary: Swi4-Swi6 pair recovered in the Michaelis et al. 2023 proteome-wide AP-MS interactome (full text cached; Swi4 is not discussed in the text, the pair is a dataset entry). Reason: Generic protein binding from a proteome-wide survey adds no functional information beyond the five experimental GO:0033309 SBF complex rows and the heterodimerization MODIFY on the targeted studies. Removal does not question the interaction, which is one of the best-established heterodimers in yeast. Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome.
GO:0005634 nucleus	NAS PMID:10490612 Regulation of cell cycle transcription factor Swi4 through a...	ACCEPT	Summary: ComplexPortal-sourced statement of nuclear localization citing Baetz and Andrews 1999. The cited paper in fact contains direct evidence: indirect immunofluorescence with affinity-purified anti-Swi4 antibody shows nuclear staining at all cell-cycle stages in wild-type but not swi4 null cells. Reason: Swi4 is a nuclear transcription factor and, unlike Swi6, stays nuclear throughout the cycle; the evidence in the cited paper would support IDA. Site of the core function. Supporting Evidence: PMID:10490612 We conclude that, unlike Swi6, whose localization changes throughout the cell cycle, Swi4 remains nuclear throughout the cell cycle.
GO:0005737 cytoplasm	IBA GO_REF:0000033	REMOVE	Summary: PAINT inference of a cytoplasmic site of activity at the APSES-family node, seeded by a single donor, Swi6 (SGD:S000004172). Swi6 genuinely cycles between nucleus and cytoplasm (largely cytoplasmic in S, G2 and early M through phosphorylation of Ser160 next to its NLS), but Swi4 does not: immunofluorescence shows Swi4 nuclear at every cell-cycle stage, and no cytoplasmic activity of Swi4 has been described. Reason: Over-propagated IBA argued against on target-specific grounds. The cytoplasmic localization is a Swi6-specific regulatory property (cell-cycle-controlled nuclear import of the shared activator subunit), not a property of the DNA-binding subunits Swi4 and Mbp1, and Baetz and Andrews 1999 directly contrast Swi4 (constitutively nuclear) with Swi6. Even for Swi6 the cytoplasm is where the inactive, exported pool resides, so "is_active_in cytoplasm" is not the right claim for any member of the node; for Swi4 it is contradicted. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000917496 SUPPORTS SOURCE BUT NOT TARGET Family node grouping the DNA-binding subunits (Swi4, Mbp1) with the regulatory subunit Swi6; the cytoplasm evidence belongs only to the Swi6 branch. SGD:S000004172 · SWI6 SUPPORTS SOURCE BUT NOT TARGET Swi6 is cytoplasmic in S/G2/M because of Ser160-regulated nuclear import; Swi4 is nuclear throughout the cycle (PMID:10490612). Supporting Evidence: PMID:10490612 We show that in contrast to Swi6, Swi4 remains nuclear throughout the cell cycle. PMID:10490612 Indeed, Swi6 localization studies have confirmed that the majority of Swi6 is nuclear throughout the late M and G 1 phases but is largely cytoplasmic during the rest of the cell cycle file:yeast/SWI4/SWI4-deep-research-falcon.md Swi4 is predominantly nuclear and was reported to remain nuclear throughout the mitotic cell cycle.
GO:0006355 regulation of DNA-templated transcription	IMP PMID:18268013 Yeast Mpk1 mitogen-activated protein kinase activates transc...	MODIFY	Summary: Kim, Truman and Levin 2008 (abstract-only cache; ComplexPortal-sourced IMP): cell-wall stress induction of FKS2 requires SBF and an activating signal to Mpk1 but not Mpk1 catalytic activity; phosphorylated Mpk1 (or Mlp1) is found with Swi4 and Swi6 at the FKS2 promoter, Mpk1 and Swi4 promoter association are codependent and Swi6-independent, and Swi6 is then recruited to activate transcription. Reason: The assertion is sound but the term is the direction-neutral root of transcription regulation. The evidence is specifically for Swi4-dependent activation of Pol II transcription of FKS2, so the direction- and polymerase-specific child GO:0045944, which Swi4 already carries from the companion 2010 paper and the HO/CLN work, describes the finding; a granularity refinement, not a challenge to the annotation. Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:18268013 Transcriptional activation of FKS2 was dependent on the Swi4/Swi6 (SBF) transcription factor and on an activating signal to Mpk1 but not on protein kinase activity. PMID:18268013 Promoter association of Mpk1 and the Swi4 DNA-binding subunit of SBF were codependent but did not require Swi6, indicating that the MAPK confers DNA-binding ability to Swi4.
GO:0030907 MBF transcription complex	IBA GO_REF:0000033	REMOVE	Summary: PAINT inference of MBF membership at the APSES-family node, seeded by the two genuine S. cerevisiae MBF subunits Mbp1 (SGD:S000002214) and Swi6 (SGD:S000004172) and by the S. pombe MBF subunits. GO:0030907 is defined as the MCB-binding Mbp1-Swi6 heterodimer; Swi4 is the paralogous DNA-binding subunit of the sister complex SBF (GO:0033309), and the two DNA-binding subunits are mutually exclusive within a complex. Reason: Over-propagated IBA: the family node conflates the two paralogous G1/S complexes. Swi4 forms SBF with Swi6 and never MBF; SBF reconstituted from Swi4 and Swi6 alone comigrates with the yeast complex, and Swi4 and Mbp1 are explicitly the alternative DNA-binding components of SBF and MBF respectively (PMID:10490612). Swi4 already carries six experimental GO:0033309 rows for the correct complex, so this is a paralog/complex mismatch rather than a missing annotation. Note that in S. pombe MBF is the only such complex, so the PomBase donors are correct for themselves but the complex-specific term cannot transfer to the SBF-specific paralog in S. cerevisiae. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000917496 SUPPORTS SOURCE BUT NOT TARGET Node groups both DNA-binding paralogs (Swi4, Mbp1) with Swi6; a complex-identity term that distinguishes SBF from MBF cannot be placed at this node. SGD:S000002214 · MBP1 SUPPORTS SOURCE BUT NOT TARGET Mbp1 is the DNA-binding subunit of MBF; Swi4 is its paralog in SBF. SGD:S000004172 · SWI6 SUPPORTS SOURCE BUT NOT TARGET Swi6 is the shared subunit of both SBF and MBF; Swi4 is not. PomBase:SPAC22F3.09c SUPPORTS SOURCE BUT NOT TARGET S. pombe MBF subunit; pombe has a single MBF and no SBF/MBF split. PomBase:SPBC336.12c SUPPORTS SOURCE BUT NOT TARGET S. pombe MBF subunit; pombe has a single MBF and no SBF/MBF split. PomBase:SPBC725.16 SUPPORTS SOURCE BUT NOT TARGET S. pombe MBF subunit; pombe has a single MBF and no SBF/MBF split. Supporting Evidence: PMID:10490612 Swi4 and Mbp1 are the DNA binding components of SBF and MBF, respectively. PMID:10490612 Since the SBF complex formed from insect cells and yeast extracts migrated at the same position, SBF is likely composed of only Swi4 and Swi6 proteins. file:yeast/SWI4/SWI4-deep-research-falcon.md SBF contains Swi4 plus Swi6, whereas the related MBF complex substitutes Mbp1 for Swi4 while retaining Swi6.
GO:0033309 SBF transcription complex	IDA PMID:1832338 The role of SWI4 and SWI6 in the activity of G1 cyclins in y...	ACCEPT	Summary: Nasmyth and Dirick 1991 (Cell; abstract-only cache): SWI4 and SWI6 are required for CLN1 and CLN2 transcription and the swi4 swi6 double deletion is inviable; the complex-formation evidence the SGD curator used is in the full text, which is not cached. Reason: Swi4 is one of the two subunits of SBF by every subsequent biochemical study (PMID:2689885, PMID:1465410, PMID:8423776, PMID:10490612); the specific gel-shift data in this paper cannot be quoted from the abstract, but the assertion is beyond doubt and is deferred to the SGD curator. Core complex. Supporting Evidence: PMID:1832338 SWI4 and SWI6 appear necessary for the transcription of CLN1 and CLN2, but not for that of CLN3. PMID:10490612 Since the SBF complex formed from insect cells and yeast extracts migrated at the same position, SBF is likely composed of only Swi4 and Swi6 proteins.
GO:0033309 SBF transcription complex	IDA PMID:2689885 The yeast SWI4 protein contains a motif present in developme...	ACCEPT	Summary: Andrews and Herskowitz 1989 (Nature; abstract-only cache): cloning and sequencing of SWI4 reveals the Swi6/cdc10 (ankyrin) motifs, and anti-Swi4 antibodies supershift the CCBF-DNA complex, showing that Swi4 protein is a physical component of the SCB-binding complex. Reason: Direct antibody evidence that Swi4 is in the complex that binds the cell-cycle box; this is the discovery of Swi4 as an SBF subunit. Core complex. Supporting Evidence: PMID:2689885 We demonstrate by using antibodies to the SWI4 protein in gel-shift assays that the protein is present in the CCBF-DNA complex.
GO:0033309 SBF transcription complex	IDA PMID:8423776 Analysis of the SWI4/SWI6 protein complex, which directs G1/...	ACCEPT	Summary: Sidorova and Breeden 1993 (abstract-only cache): Swi4 and Swi6 form a specific complex on SCB sequences; the Swi4 C terminus is necessary and sufficient for Swi6 association and the TPLH (ankyrin) repeats are dispensable for it. Reason: Direct biochemical characterisation of the Swi4-Swi6 complex on DNA and mapping of the interaction surfaces. Core complex. Supporting Evidence: PMID:8423776 SWI4 and SWI6 form a specific complex on the SCB (SWI4/6-dependent cell cycle box) sequences which have been found in the promoters of HO and G1 cyclin genes.
GO:0033309 SBF transcription complex	IMP PMID:8423776 Analysis of the SWI4/SWI6 protein complex, which directs G1/...	ACCEPT	Summary: Same paper, mutant-based evidence: C-terminal truncation of Swi4 abolishes Swi6 association while preserving SCB binding, and SWI6 mutations in the TPLH repeats or leucine zipper leave complex formation intact but abolish DNA binding of the complex. Reason: Structure-function mapping of the two subunits within SBF; the same complex membership as the IDA row from a different evidence angle. Core complex. Supporting Evidence: PMID:8423776 The C terminus of SWI4 is not required for SWI6-independent binding of SWI4 to SCB sequences, but it is necessary and sufficient for association with SWI6.
GO:0033309 SBF transcription complex	IPI PMID:10490612 Regulation of cell cycle transcription factor Swi4 through a...	ACCEPT	Summary: Baetz and Andrews 1999 (full text cached): SBF reconstituted in insect cells from Swi4 and Swi6 comigrates with the yeast complex in gel shifts, sediments at 180 kDa as a 1:1 heterodimer, and the Swi4 C-terminal 144 residues bind Swi6 in GST pull-downs. Reason: Definitive reconstitution showing that SBF is the Swi4-Swi6 heterodimer, with Swi4 supplying the DNA-binding domain whose access is gated by Swi6. Core complex. Supporting Evidence: PMID:10490612 SBF ran at 180 kDa, a size which is close to the predicted size of a heterodimer of Swi4 (123 kDa) and Swi6 (91 kDa). PMID:10490612 We conclude that SBF can be functionally reconstituted by the expression of Swi4 and Swi6 in insect cells.
GO:0033309 SBF transcription complex	IPI PMID:1465410 Interaction of the yeast Swi4 and Swi6 cell cycle regulatory...	ACCEPT	Summary: Andrews and Moore 1992 (PNAS; abstract-only cache): in vitro-translated Swi4 and Swi6 associate directly through regions near their C termini, independently of the ankyrin motifs, and Swi6 is not needed for Swi4 to recognise the SCB sequence specifically. Reason: Direct pairwise interaction with Swi6 (SGD:S000004172) that constitutes SBF; the paper also assigns the SCB-recognition function to Swi4. Core complex. Supporting Evidence: PMID:1465410 We show, by using proteins synthesized in vitro, a direct association between Swi4 and Swi6. PMID:1465410 The cdc10-Swi6 or ankyrin motifs present in both Swi4 and Swi6 are dispensable for their association, which is mediated instead by a region near the C terminus of each protein.
GO:0034605 cellular response to heat	IMP PMID:20641022 Transcriptional reporters for genes activated by cell wall s...	KEEP AS NON CORE	Summary: Kim and Levin 2010 (full text cached): lacZ reporters for FKS2, CHA1, YKR013w and YLR042c are induced by cell-wall stress (growth at 39 degrees C, Congo Red, calcofluor white, Zymolyase) through the non-catalytic Mpk1-Swi4 mechanism, and induction is strictly dependent on SWI4 and SWI6; elevated temperature was the strongest inducer. Reason: Swi4 genuinely executes the transcriptional output of a heat-triggered response, so the term is not wrong, but heat here is one of several stimuli that engage the cell-wall-integrity MAPK pathway, and the process Swi4 serves is the CWI transcriptional response (Rlm1-independent, Mpk1-docking-dependent activation of cell-wall genes) rather than a heat-shock program. This is a secondary, stress-context role of the transcription factor, distinct from its core G1/S function; graded the same way as other pleiotropic outputs of SBF. Supporting Evidence: PMID:20641022 Transcriptional induction of all of these reporters by cell wall stress was strictly dependent on both SWI4 and SWI6 PMID:20641022 Cell wall stress was induced by increasing the growth temperature from 23°C to 39°C, or by treatment with Congo Red PMID:20641022 in general, elevated growth temperature was the strongest inducer for all of the reporters
GO:0042802 identical protein binding	IPI PMID:10490612 Regulation of cell cycle transcription factor Swi4 through a...	REMOVE	Summary: IntAct-derived self-interaction from Baetz and Andrews 1999 (full text cached). The underlying experiment is a GST pull-down in which the C-terminal 144 residues of Swi4 bind full-length Swi4 and its N-terminal 197 residues in trans; the authors show by glycerol-gradient sedimentation that full-length Swi4 is monomeric in solution and interpret the C-to-N contact as an intramolecular auto-inhibitory interaction. Reason: The annotation asserts homomeric binding, which the paper's own conclusion argues against: Swi4 is monomeric, SBF is a 1:1 Swi4-Swi6 heterodimer, and the fragment interaction is the intramolecular fold-back that masks the DNA-binding domain. Recording it as identical protein binding misrepresents an auto-inhibition mechanism as oligomerisation. The fragment-level in vitro contact is real; the biological claim is not supported. Supporting Evidence: PMID:10490612 Full-length Swi4 was determined to be monomeric in solution, suggesting an intramolecular mechanism for auto-inhibition of binding to DNA by Swi4. PMID:10490612 showing that the C-terminal 144 amino acids of Swi4 can interact in vitro with the first 949 amino acids of Swi4 file:yeast/SWI4/SWI4-deep-research-falcon.md Evidence that full-length Swi4 is monomeric favors intramolecular masking rather than inhibition through Swi4 oligomerization.
GO:0042802 identical protein binding	IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome.	REMOVE	Summary: IntAct-derived self-interaction from the Lambert et al. 2010 mChIP-MS survey (full text cached). Swi4-TAP was a bait; the text does not discuss any Swi4 homo-oligomer, and recovery of the bait protein in its own purification does not evidence self-association. Reason: Uninformative and unsupported by the paper's text; a Swi4 homodimer is contradicted by the monomeric behaviour of full-length Swi4 and the heterodimeric stoichiometry of SBF (PMID:10490612). Removal does not exclude that Swi4 molecules co-purify via shared chromatin in mChIP, which is a property of the method rather than a molecular function. Supporting Evidence: PMID:10490612 Full-length Swi4 was determined to be monomeric in solution, suggesting an intramolecular mechanism for auto-inhibition of binding to DNA by Swi4.
GO:0043565 sequence-specific DNA binding	HDA PMID:19111667 A library of yeast transcription factor motifs reveals a wid...	ACCEPT	Summary: Badis et al. 2008 (abstract-only cache): protein-binding microarray determination of DNA-binding specificities for 112 yeast DNA-binding proteins, including the Swi4 APSES domain, which yields the SCB-type CRCGAAA motif. Reason: Correct in vitro demonstration of sequence-specific binding; the more specific in vivo term GO:0000978 is already carried by IBA, and the high-throughput assay supports the parent at the appropriate level. Core MF. Supporting Evidence: PMID:19111667 We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes. PMID:20641022 Swi4 is the sequence-specific DNA-binding subunit (CA/GCGAAA; Taylor et al., 2000), but Swi6 is required for binding to cell cycle-regulated promoters
GO:0045944 positive regulation of transcription by RNA polymerase II	IBA GO_REF:0000033	ACCEPT	Summary: PAINT inference at the APSES-family node, seeded by experimental rows on Swi4 itself, Mbp1, Swi6, the C. albicans, S. pombe and A. nidulans family members. All are subunits of G1/S transcriptional activators. Reason: Swi4 activates Pol II transcription of HO, CLN1, CLN2 and the cell-wall regulon as the DNA-binding subunit of SBF; the inherited function is the core function of the gene, and Swi4 in its own WITH list reflects experimental grounding on the target. Supporting Evidence: PMID:1832338 SWI4 and SWI6 appear necessary for the transcription of CLN1 and CLN2, but not for that of CLN3.
GO:0045944 positive regulation of transcription by RNA polymerase II	IMP PMID:20641022 Transcriptional reporters for genes activated by cell wall s...	ACCEPT	Summary: Kim and Levin 2010 (full text cached): cell-wall-stress induction of FKS2-, CHA1-, YKR013w- and YLR042c-lacZ reporters is abolished in swi4 mutants, reflecting the Mpk1-Swi4 non-catalytic activation mechanism at Swi4-binding sites in these promoters. Reason: Direct mutant evidence that Swi4 is required to activate Pol II transcription of a defined set of target genes. Although the context is the cell-wall-stress rather than the G1/S regulon, the molecular role (sequence-specific activator) is the same core function; the stimulus-specific process is graded separately on the GO:0034605 row. Supporting Evidence: PMID:20641022 Transcriptional induction of all of these reporters by cell wall stress was strictly dependent on both SWI4 and SWI6 PMID:20641022 This dimer binds to the FKS2 promoter, but requires the further binding of the Swi6 transcriptional activator for transcriptional initiation.
GO:0045944 positive regulation of transcription by RNA polymerase II	IMP PMID:2649246 Identification of a DNA binding factor involved in cell-cycl...	ACCEPT	Summary: Andrews and Herskowitz 1989 (abstract-only cache): SWI4 and SWI6 are the only SWI genes required for expression in vivo from the cell-cycle-box sequences of the HO promoter. Reason: Loss-of-function evidence for activation of Pol II transcription from SCB elements; core function. Supporting Evidence: PMID:2649246 We also show that SWI4 and SWI6 are the only SWI genes required for expression in vivo from the CCB sequences.
GO:0045944 positive regulation of transcription by RNA polymerase II	IMP PMID:3542227 Cell cycle control of the yeast HO gene: cis- and trans-acti...	ACCEPT	Summary: Breeden and Nasmyth 1987 (abstract-only cache): SWI4 and SWI6 are specifically required for CACGA4-mediated activation of HO transcription, whereas SWI1, SWI2 and SWI5 act on separate promoter elements. Reason: The founding genetic evidence that Swi4 activates transcription through the SCB element. Core function. Supporting Evidence: PMID:3542227 SWI4 and SWI6 are specifically required for CACGA4-mediated activation of transcription.
GO:0090575 RNA polymerase II transcription regulator complex	IEA GO_REF:0000117	ACCEPT	Summary: ARBA rule placing Swi4 in a Pol II transcription regulator complex. GO:0033309 SBF transcription complex is a descendant of this term, so the electronic annotation is a correct generalisation of the experimentally established complex membership. Reason: True and consistent with the SBF rows; a generic electronic parent of the specific complex term is acceptable. Supporting Evidence: PMID:10490612 SBF is a complex composed of at least two proteins, Swi4 and Swi6, which bind the repeated upstream regulatory sequence CACGAAA

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