Ontology: Molecular Function (GO:0001077)

Definition: Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.

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This table lists the methods used to annotate genes either directly to the term RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (43 genes) or to its variants containing one or more qualifiers (7 genes). Note that some genes may have been annotated by more than one method so the numbers in the table below may not add up to the totals given here.

Annotation Method	GO Term	# Yeast Genes Annotated
Manually curated (download data)	contributes_to: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	7
	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	43
High-throughput	none	none
Computational	none	none

Links to Additional Annotations:

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• Search for S. cerevisiae genes annotated, by the Manually curated or High-throughput methods, to this term or to any terms that are descended from this term, i.e., child terms representing more specific biology than this term.

Annotation details for genes that have been directly annotated to the term RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription or its variants containing one or more qualifiers (NOT, contributes to, or colocalizes with).

RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription      43 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
ABF1/YKL112W	IDA: Inferred from Direct Assay Assigned on 2012-02-15	manually curated	Yoo HY, et al.  (1995) Transcriptional control of the Saccharomyces cerevisiae ADH1 gene by autonomously replicating sequence binding factor 1. Curr Microbiol 31(3):163-8	SGD
ACA1/YER045C	IDA: Inferred from Direct Assay Assigned on 2011-08-04	manually curated	Garcia-Gimeno MA and Struhl K  (2000) Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon source utilization but not the response to stress. Mol Cell Biol 20(12):4340-9	SGD
AFT2/YPL202C	IC: Inferred By Curator from RNA polymerase II core promoter proximal region sequence-specific DNA binding, positive regulation of transcription from RNA polymerase II promoter Assigned on 2012-01-05	manually curated	GO Annotation Working Group  (2011) Manual annotations that require more than one source of functional data to support the assignment of the associated GO term.	SGD
ARR1/YPR199C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2011-12-13	manually curated	Ilina Y, et al.  (2008) Characterization of the DNA-binding motif of the arsenic-responsive transcription factor Yap8p. Biochem J 415(3):467-75	SGD
AZF1/YOR113W	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2012-02-23	manually curated	Newcomb LL, et al.  (2002) AZF1 is a glucose-dependent positive regulator of CLN3 transcription in Saccharomyces cerevisiae. Mol Cell Biol 22(5):1607-14	SGD
CAD1/YDR423C	IDA: Inferred from Direct Assay Assigned on 2012-02-26	manually curated	Fernandes L, et al.  (1997) Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol Cell Biol 17(12):6982-93	SGD
CAT8/YMR280C	IDA: Inferred from Direct Assay Assigned on 2011-06-28	manually curated	Roth S, et al.  (2004) Transcriptional activators Cat8 and Sip4 discriminate between sequence variants of the carbon source-responsive promoter element in the yeast Saccharomyces cerevisiae. Curr Genet 45(3):121-8	SGD
CBF1/YJR060W	IDA: Inferred from Direct Assay Assigned on 2011-08-22	manually curated	O'Connell KF, et al.  (1995) Role of the Saccharomyces cerevisiae general regulatory factor CP1 in methionine biosynthetic gene transcription. Mol Cell Biol 15(4):1879-88	SGD
CRZ1/YNL027W	IDA: Inferred from Direct Assay Assigned on 2011-09-19	manually curated	Mendizabal I, et al.  (2001) Promoter sequences regulated by the calcineurin-activated transcription factor Crz1 in the yeast ENA1 gene. Mol Genet Genomics 265(5):801-11	SGD
	IDA: Inferred from Direct Assay Assigned on 2011-09-19	manually curated	Casado C, et al.  (2010) Regulation of Trk-dependent potassium transport by the calcineurin pathway involves the Hal5 kinase. FEBS Lett 584(11):2415-2420	SGD
CST6/YIL036W	IDA: Inferred from Direct Assay Assigned on 2011-10-17	manually curated	Garcia-Gimeno MA and Struhl K  (2000) Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon source utilization but not the response to stress. Mol Cell Biol 20(12):4340-9	SGD
ECM22/YLR228C	IDA: Inferred from Direct Assay Assigned on 2011-06-28	manually curated	Vik A and Rine J  (2001) Upc2p and Ecm22p, dual regulators of sterol biosynthesis in Saccharomyces cerevisiae. Mol Cell Biol 21(19):6395-405	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-06-28	manually curated	Davies BS, et al.  (2005) Dual activators of the sterol biosynthetic pathway of Saccharomyces cerevisiae: similar activation/regulatory domains but different response mechanisms. Mol Cell Biol 25(16):7375-85	SGD
FKH1/YIL131C	IDA: Inferred from Direct Assay, IGI: Inferred from Genetic Interaction with SGD:FKH2 Assigned on 2011-12-15	manually curated	Zhu G, et al.  (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406(6791):90-4	SGD
	IDA: Inferred from Direct Assay, IGI: Inferred from Genetic Interaction with SGD:FKH2 Assigned on 2011-12-15	manually curated	Hollenhorst PC, et al.  (2001) Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation. Genes Dev 15(18):2445-56	SGD
FLO8/YER109C	IDA: Inferred from Direct Assay Assigned on 2011-07-12	manually curated	Gagiano M, et al.  (1999) Divergent regulation of the evolutionarily closely related promoters of the Saccharomyces cerevisiae STA2 and MUC1 genes. J Bacteriol 181(20):6497-508	SGD
FZF1/YGL254W	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2011-08-30	manually curated	Avram D, et al.  (1999) Fzf1p of Saccharomyces cerevisiae is a positive regulator of SSU1 transcription and its first zinc finger region is required for DNA binding. Yeast 15(6):473-80	SGD
GAL4/YPL248C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2011-06-23	manually curated	Keegan L, et al.  (1986) Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science 231(4739):699-704	SGD
GAT1/YFL021W	IMP: Inferred from Mutant Phenotype Assigned on 2011-12-22	manually curated	Soussi-Boudekou S, et al.  (1997) Gzf3p, a fourth GATA factor involved in nitrogen-regulated transcription in Saccharomyces cerevisiae. Mol Microbiol 23(6):1157-68	SGD
	ISA: Inferred from Sequence Alignment with SGD:GLN3 Assigned on 2011-12-22	manually curated	Stanbrough M, et al.  (1995) Role of the GATA factors Gln3p and Nil1p of Saccharomyces cerevisiae in the expression of nitrogen-regulated genes. Proc Natl Acad Sci U S A 92(21):9450-4	SGD
GCR1/YPL075W	IMP: Inferred from Mutant Phenotype Assigned on 2011-06-20	manually curated	Turkel S, et al.  (1997) GCR1-dependent transcriptional activation of yeast retrotransposon Ty2-917. Yeast 13(10):917-30	SGD
	IDA: Inferred from Direct Assay Assigned on 2011-06-20	manually curated	Uemura H, et al.  (1997) The role of Gcr1p in the transcriptional activation of glycolytic genes in yeast Saccharomyces cerevisiae. Genetics 147(2):521-32	SGD
GIS1/YDR096W	IC: Inferred By Curator from positive regulation of transcription from RNA polymerase II promoter Assigned on 2011-07-14	manually curated	Pedruzzi I, et al.  (2000) Saccharomyces cerevisiae Ras/cAMP pathway controls post-diauxic shift element-dependent transcription through the zinc finger protein Gis1. EMBO J 19(11):2569-79	SGD
	IC: Inferred By Curator from RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription Assigned on 2011-07-14	manually curated	Oshiro J, et al.  (2003) Regulation of the yeast DPP1-encoded diacylglycerol pyrophosphate phosphatase by transcription factor Gis1p. J Biol Chem 278(34):31495-503	SGD
HAP1/YLR256W	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2011-10-18	manually curated	Prezant T, et al.  (1987) Organization of the regulatory region of the yeast CYC7 gene: multiple factors are involved in regulation. Mol Cell Biol 7(9):3252-9	SGD
HAP5/YOR358W	ISA: Inferred from Sequence Alignment with EBI:Q5A1M2 Assigned on 2011-07-01	manually curated	Johnson DC, et al.  (2005) Novel regulatory function for the CCAAT-binding factor in Candida albicans. Eukaryot Cell 4(10):1662-76	SGD
LEU3/YLR451W	IDA: Inferred from Direct Assay Assigned on 2011-12-13	manually curated	Sze JY, et al.  (1992) In vitro transcriptional activation by a metabolic intermediate: activation by Leu3 depends on alpha-isopropylmalate. Science 258(5085):1143-5	SGD
LYS14/YDR034C	ISA: Inferred from Sequence Alignment with SGD:GAL4 Assigned on 2011-11-03	manually curated	Feller A, et al.  (1994) Repression of the genes for lysine biosynthesis in Saccharomyces cerevisiae is caused by limitation of Lys14-dependent transcriptional activation. Mol Cell Biol 14(10):6411-8	SGD
MAC1/YMR021C	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	manually curated	Keller G, et al.  (2000) Functional independence of the two cysteine-rich activation domains in the yeast Mac1 transcription factor. J Biol Chem 275(38):29193-9	SGD
MBP1/YDL056W	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction Assigned on 2012-02-10	manually curated	Koch C, et al.  (1993) A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 261(5128):1551-7	SGD
MCM1/YMR043W	IMP: Inferred from Mutant Phenotype Assigned on 2012-01-30	manually curated	Acton TB, et al.  (2000) Scanning mutagenesis of Mcm1: residues required for DNA binding, DNA bending, and transcriptional activation by a MADS-box protein. Mol Cell Biol 20(1):1-11	SGD
	IDA: Inferred from Direct Assay Assigned on 2012-01-30	manually curated	Acton TB, et al.  (1997) DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein. Mol Cell Biol 17(4):1881-9	SGD
	IDA: Inferred from Direct Assay Assigned on 2012-01-30	manually curated	Mead J, et al.  (2002) Interactions of the Mcm1 MADS box protein with cofactors that regulate mating in yeast. Mol Cell Biol 22(13):4607-21	SGD
MSS11/YMR164C	IDA: Inferred from Direct Assay Assigned on 2011-07-12	manually curated	Gagiano M, et al.  (1999) Divergent regulation of the evolutionarily closely related promoters of the Saccharomyces cerevisiae STA2 and MUC1 genes. J Bacteriol 181(20):6497-508	SGD
OAF1/YAL051W	IDA: Inferred from Direct Assay Assigned on 2011-10-25	manually curated	Baumgartner U, et al.  (1999) Functional analysis of the Zn(2)Cys(6) transcription factors Oaf1p and Pip2p. Different roles in fatty acid induction of beta-oxidation in Saccharomyces cerevisiae. J Biol Chem 274(32):22208-16	SGD
PDR1/YGL013C	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction Assigned on 2011-09-22	manually curated	Katzmann DJ, et al.  (1996) Multiple Pdr1p/Pdr3p binding sites are essential for normal expression of the ATP binding cassette transporter protein-encoding gene PDR5. J Biol Chem 271(38):23049-54	SGD
	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction Assigned on 2011-09-22	manually curated	Wolfger H, et al.  (1997) The yeast ATP binding cassette (ABC) protein genes PDR10 and PDR15 are novel targets for the Pdr1 and Pdr3 transcriptional regulators. FEBS Lett 418(3):269-74	SGD
PDR3/YBL005W	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction Assigned on 2011-09-22	manually curated	Katzmann DJ, et al.  (1996) Multiple Pdr1p/Pdr3p binding sites are essential for normal expression of the ATP binding cassette transporter protein-encoding gene PDR5. J Biol Chem 271(38):23049-54	SGD
	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction Assigned on 2011-09-22	manually curated	Wolfger H, et al.  (1997) The yeast ATP binding cassette (ABC) protein genes PDR10 and PDR15 are novel targets for the Pdr1 and Pdr3 transcriptional regulators. FEBS Lett 418(3):269-74	SGD
PHO2/YDL106C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2011-06-23	manually curated	Arndt KT, et al.  (1987) Multiple global regulators control HIS4 transcription in yeast. Science 237(4817):874-80	SGD
	IDA: Inferred from Direct Assay, IGI: Inferred from Genetic Interaction with SGD:PHO4, IMP: Inferred from Mutant Phenotype Assigned on 2011-06-23	manually curated	Barbaric S, et al.  (1998) Cooperative Pho2-Pho4 interactions at the PHO5 promoter are critical for binding of Pho4 to UASp1 and for efficient transactivation by Pho4 at UASp2. Mol Cell Biol 18(5):2629-39	SGD
	IDA: Inferred from Direct Assay, IGI: Inferred from Genetic Interaction with SGD:SWI5, IMP: Inferred from Mutant Phenotype Assigned on 2011-06-23	manually curated	Brazas RM and Stillman DJ  (1993) The Swi5 zinc-finger and Grf10 homeodomain proteins bind DNA cooperatively at the yeast HO promoter. Proc Natl Acad Sci U S A 90(23):11237-41	SGD

contributes_to: RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription      7 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
HAP2/YGL237C	IDA: Inferred from Direct Assay Assigned on 2011-07-01	manually curated	Hahn S and Guarente L  (1988) Yeast HAP2 and HAP3: transcriptional activators in a heteromeric complex. Science 240(4850):317-21	SGD
HAP3/YBL021C	IDA: Inferred from Direct Assay Assigned on 2011-07-01	manually curated	Hahn S and Guarente L  (1988) Yeast HAP2 and HAP3: transcriptional activators in a heteromeric complex. Science 240(4850):317-21	SGD
HAP4/YKL109W	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2011-07-01	manually curated	Forsburg SL and Guarente L  (1989) Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes Dev 3(8):1166-78	SGD
HAP5/YOR358W	IC: Inferred By Curator from CCAAT-binding factor complex, RNA polymerase II core promoter proximal region sequence-specific DNA binding Assigned on 2011-07-01	manually curated	McNabb DS, et al.  (1995) Cloning of yeast HAP5: a novel subunit of a heterotrimeric complex required for CCAAT binding. Genes Dev 9(1):47-58	SGD
INO2/YDR123C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction with SGD:INO4 Assigned on 2011-06-09	manually curated	Ambroziak J and Henry SA  (1994) INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem 269(21):15344-9	SGD
INO4/YOL108C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction with SGD:INO2 Assigned on 2011-06-09	manually curated	Ambroziak J and Henry SA  (1994) INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem 269(21):15344-9	SGD
MET28/YIR017C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2011-07-22	manually curated	Kuras L, et al.  (1996) A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediates the transcription activation of yeast sulfur metabolism. EMBO J 15(10):2519-29	SGD

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