Ontology: Biological Process (GO:0034401)

Definition: Any cellular process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin that modulates the rate, frequency or extent of DNA-dependent transcription.

Synonyms: establishment or maintenance of chromatin architecture during transcription; regulation of transcription by chromatin organisation

View Ontology: (graph) | (text)

This table lists the methods used to annotate genes either directly to the term regulation of transcription by chromatin organization (18 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 by chromatin organization	18
High-throughput	none	none
Computational	none	none

Links to Additional Annotations:

• View annotations in multiple organisms using
• 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 by chromatin organization or its variants containing one or more qualifiers (NOT, contributes to, or colocalizes with).

regulation of transcription by chromatin organization      18 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
ADR1/YDR216W	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-04	manually curated	Agricola E, et al.  (2004) Common chromatin architecture, common chromatin remodeling, and common transcription kinetics of Adr1-dependent genes in Saccharomyces cerevisiae. Biochemistry 43(27):8878-84	SGD
	IGI: Inferred from Genetic Interaction with SGD:GCN5, SGD:ADA2, IPI: Inferred from Physical Interaction with SGD:GCN5, SGD:ADA2 Assigned on 2011-10-04	manually curated	Chiang YC, et al.  (1996) ADR1 activation domains contact the histone acetyltransferase GCN5 and the core transcriptional factor TFIIB. J Biol Chem 271(50):32359-65	SGD
BDF1/YLR399C	IMP: Inferred from Mutant Phenotype Assigned on 2012-01-19	manually curated	Ladurner AG, et al.  (2003) Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol Cell 11(2):365-76	SGD
CHD1/YER164W	IGI: Inferred from Genetic Interaction with SGD:SNF2 Assigned on 2011-10-03	manually curated	Tran HG, et al.  (2000) The chromo domain protein chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J 19(10):2323-31	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-07	manually curated	Xella B, et al.  (2006) The ISWI and CHD1 chromatin remodelling activities influence ADH2 expression and chromatin organization. Mol Microbiol 59(5):1531-41	SGD
CTR9/YOL145C	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-11	manually curated	Marton HA and Desiderio S  (2008) The Paf1 complex promotes displacement of histones upon rapid induction of transcription by RNA polymerase II. BMC Mol Biol 9():4	SGD
ELF1/YKL160W	IGI: Inferred from Genetic Interaction with SGD:HIR1, IMP: Inferred from Mutant Phenotype Assigned on 2011-06-28	manually curated	Prather D, et al.  (2005) Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae. Mol Cell Biol 25(22):10122-35	SGD
ESA1/YOR244W	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	manually curated	Verdone L, et al.  (2002) Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions. EMBO J 21(5):1101-11	SGD
FPR4/YLR449W	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-09	manually curated	Nelson CJ, et al.  (2006) Proline isomerization of histone h3 regulates lysine methylation and gene expression. Cell 126(5):905-16	SGD
GCN5/YGR252W	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	manually curated	Verdone L, et al.  (2002) Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions. EMBO J 21(5):1101-11	SGD
HDA1/YNL021W	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	manually curated	Verdone L, et al.  (2002) Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions. EMBO J 21(5):1101-11	SGD
HMO1/YDR174W	IDA: Inferred from Direct Assay Assigned on 2010-03-17	manually curated	Merz K, et al.  (2008) Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules. Genes Dev 22(9):1190-204	SGD
ISW1/YBR245C	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-07	manually curated	Xella B, et al.  (2006) The ISWI and CHD1 chromatin remodelling activities influence ADH2 expression and chromatin organization. Mol Microbiol 59(5):1531-41	SGD
PAF1/YBR279W	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-11	manually curated	Marton HA and Desiderio S  (2008) The Paf1 complex promotes displacement of histones upon rapid induction of transcription by RNA polymerase II. BMC Mol Biol 9():4	SGD
POB3/YML069W	IC: Inferred By Curator from FACT complex Assigned on 2010-03-05	manually curated	Jamai A, et al.  (2009) Histone chaperone spt16 promotes redeposition of the original h3-h4 histones evicted by elongating RNA polymerase. Mol Cell 35(3):377-83	SGD
RAP1/YNL216W	IDA: Inferred from Direct Assay Assigned on 2012-05-02	manually curated	Yu L and Morse RH  (1999) Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol Cell Biol 19(8):5279-88	SGD
RPD3/YNL330C	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	manually curated	Verdone L, et al.  (2002) Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions. EMBO J 21(5):1101-11	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	manually curated	Kadosh D and Struhl K  (1998) Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol Cell Biol 18(9):5121-7	SGD
SPN1/YPR133C	IMP: Inferred from Mutant Phenotype Assigned on 2011-08-26	manually curated	Hainer SJ, et al.  (2011) Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev 25(1):29-40	SGD
	IPI: Inferred from Physical Interaction with SGD:SPT6 Assigned on 2011-08-26	manually curated	McDonald SM, et al.  (2010) Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. Mol Cell 40(5):725-35	SGD
SPT16/YGL207W	IMP: Inferred from Mutant Phenotype Assigned on 2010-03-05	manually curated	Jamai A, et al.  (2009) Histone chaperone spt16 promotes redeposition of the original h3-h4 histones evicted by elongating RNA polymerase. Mol Cell 35(3):377-83	SGD
SPT6/YGR116W	IGI: Inferred from Genetic Interaction with SGD:SNF5, IMP: Inferred from Mutant Phenotype Assigned on 2011-10-13	manually curated	Bortvin A and Winston F  (1996) Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272(5267):1473-6	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-05-05	manually curated	Kaplan CD, et al.  (2003) Transcription elongation factors repress transcription initiation from cryptic sites. Science 301(5636):1096-9	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-08-26	manually curated	Hainer SJ, et al.  (2011) Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev 25(1):29-40	SGD

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