Ontology: Biological Process (GO:0006357)

Definition: Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.

Synonyms: regulation of transcription from Pol II promoter; global transcription regulation from Pol II promoter; regulation of global transcription from Pol II promoter; regulation of gene-specific transcription from RNA polymerase II promoter; regulation of transcription from RNA polymerase II promoter, global

View Ontology: (graph) | (text)

This table lists the methods used to annotate genes either directly to the term regulation of transcription from RNA polymerase II promoter (115 genes) or to its variants containing one or more qualifiers (0 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)	regulation of transcription from RNA polymerase II promoter	67
High-throughput	none	none
Computational (download data)	regulation of transcription from RNA polymerase II promoter	50

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 regulation of transcription from RNA polymerase II promoter or its variants containing one or more qualifiers (NOT, contributes to, or colocalizes with).

regulation of transcription from RNA polymerase II promoter      115 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
ACT1/YFL039C	IDA: Inferred from Direct Assay Assigned on 2002-09-18	manually curated	Galarneau L, et al.  (2000) Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol Cell 5(6):927-37	SGD
ADA2/YDR448W	IMP: Inferred from Mutant Phenotype Assigned on 2009-10-13	manually curated	Hoke SM, et al.  (2008) A conserved central region of yeast ada2 regulates the histone acetyltransferase activity of gcn5 and interacts with phospholipids. J Mol Biol 384(4):743-55	SGD
ARG81/YML099C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
ARP4/YJL081C	IDA: Inferred from Direct Assay Assigned on 2002-09-18	manually curated	Galarneau L, et al.  (2000) Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol Cell 5(6):927-37	SGD
ASG1/YIL130W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
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
CAF120/YNL278W	IPI: Inferred from Physical Interaction Assigned on 2002-08-08	manually curated	Chen J, et al.  (2001) Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex. J Mol Biol 314(4):683-94	SGD
CAF130/YGR134W	IPI: Inferred from Physical Interaction Assigned on 2002-08-08	manually curated	Chen J, et al.  (2001) Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex. J Mol Biol 314(4):683-94	SGD
CAF16/YFL028C	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction with SGD:CCR4 Assigned on 2009-09-25	manually curated	Liu HY, et al.  (2001) Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme. J Biol Chem 276(10):7541-8	SGD
CAF4/YKR036C	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction with SGD:CCR4 Assigned on 2009-09-25	manually curated	Liu HY, et al.  (2001) Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme. J Biol Chem 276(10):7541-8	SGD
CAF40/YNL288W	IPI: Inferred from Physical Interaction Assigned on 2002-08-08	manually curated	Chen J, et al.  (2001) Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex. J Mol Biol 314(4):683-94	SGD
CCR4/YAL021C	IPI: Inferred from Physical Interaction Assigned on 2002-08-02	manually curated	Bai Y, et al.  (1999) The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4, and NOT5. Mol Cell Biol 19(10):6642-51	SGD
CDC36/YDL165W	IPI: Inferred from Physical Interaction Assigned on 2002-08-02	manually curated	Bai Y, et al.  (1999) The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4, and NOT5. Mol Cell Biol 19(10):6642-51	SGD
CDC39/YCR093W	IPI: Inferred from Physical Interaction Assigned on 2002-08-02	manually curated	Bai Y, et al.  (1999) The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4, and NOT5. Mol Cell Biol 19(10):6642-51	SGD
CEP3/YMR168C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
CHA4/YLR098C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
CIN5/YOR028C	ISA: Inferred from Sequence Alignment with SGD:YAP6 Assigned on 2012-02-02	manually curated	Furuchi T, et al.  (2001) Two nuclear proteins, Cin5 and Ydr259c, confer resistance to cisplatin in Saccharomyces cerevisiae. Mol Pharmacol 59(3):470-4	SGD
CRT10/YOL063C	IMP: Inferred from Mutant Phenotype Assigned on 2006-06-13	manually curated	Fu Y and Xiao W  (2006) Identification and characterization of CRT10 as a novel regulator of Saccharomyces cerevisiae ribonucleotide reductase genes. Nucleic Acids Res 34(6):1876-83	SGD
CSE2/YNR010W	IEA: Inferred from Electronic Annotation with EBI:IPR011425 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
CSR2/YPR030W	IGI: Inferred from Genetic Interaction, IMP: Inferred from Mutant Phenotype Assigned on 2003-01-07	manually curated	Khanday FA, et al.  (2002) Molecular characterization of MRG19 of Saccharomyces cerevisiae. Implication in the regulation of galactose and nonfermentable carbon source utilization. Eur J Biochem 269(23):5840-50	SGD
CUP2/YGL166W	IMP: Inferred from Mutant Phenotype Assigned on 2011-12-14	manually curated	Buchman C, et al.  (1989) The CUP2 gene product, regulator of yeast metallothionein expression, is a copper-activated DNA-binding protein. Mol Cell Biol 9(9):4091-5	SGD
DEP1/YAL013W	IMP: Inferred from Mutant Phenotype Assigned on 2002-11-01	manually curated	Lamping E, et al.  (1994) Isolation and characterization of a mutant of Saccharomyces cerevisiae with pleiotropic deficiencies in transcriptional activation and repression. Genetics 137(1):55-65	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-07-20	manually curated	Wang SS, et al.  (2011) Histone H3 lysine 4 hypermethylation prevents aberrant nucleosome remodeling at the PHO5 promoter. Mol Cell Biol 31(15):3171-81	SGD
DOT6/YER088C	IGI: Inferred from Genetic Interaction Assigned on 2002-08-08	manually curated	Lorenz MC and Heitman J  (1998) Regulators of pseudohyphal differentiation in Saccharomyces cerevisiae identified through multicopy suppressor analysis in ammonium permease mutant strains. Genetics 150(4):1443-57	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-02-03	manually curated	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
DST1/YGL043W	IEA: Inferred from Electronic Annotation with EBI:IPR016492 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
EAF3/YPR023C	IMP: Inferred from Mutant Phenotype Assigned on 2002-09-18	manually curated	Eisen A, et al.  (2001) The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J Biol Chem 276(5):3484-91	SGD
EAF7/YNL136W	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction with SGD:EAF7 Assigned on 2004-09-22	manually curated	Krogan NJ, et al.  (2004) Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc Natl Acad Sci U S A 101(37):13513-8	SGD
EDS1/YBR033W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
ELP2/YGR200C	IMP: Inferred from Mutant Phenotype Assigned on 2002-09-18	manually curated	Krogan NJ and Greenblatt JF  (2001) Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae. Mol Cell Biol 21(23):8203-12	SGD
ELP3/YPL086C	IMP: Inferred from Mutant Phenotype Assigned on 2002-09-18	manually curated	Krogan NJ and Greenblatt JF  (2001) Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae. Mol Cell Biol 21(23):8203-12	SGD
ELP4/YPL101W	IMP: Inferred from Mutant Phenotype Assigned on 2002-09-18	manually curated	Krogan NJ and Greenblatt JF  (2001) Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae. Mol Cell Biol 21(23):8203-12	SGD
	IEA: Inferred from Electronic Annotation with EBI:IPR008728 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro

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