GO term: chromatin silencing at rDNA

Ontology: Biological Process (GO:0000183)

Definition: Repression of transcription of ribosomal DNA by altering the structure of chromatin.

Synonyms: chromatin silencing at ribosomal DNA; heterochromatic silencing at rDNA; rDNA chromatin silencing

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Annotation Summary

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This table lists the methods used to annotate genes either directly to the term chromatin silencing at rDNA (23 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)	chromatin silencing at rDNA	23
High-throughput	none	none
Computational	none	none

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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.

Genes Annotated with this Term

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Annotation details for genes that have been directly annotated to the term chromatin silencing at rDNA or its variants containing one or more qualifiers (NOT, contributes to, or colocalizes with).

chromatin silencing at rDNA 23 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
ADA2/YDR448W	IMP: Inferred from Mutant Phenotype Assigned on 2009-11-13	manually curated	Jacobson S and Pillus L (2009) The SAGA subunit Ada2 functions in transcriptional silencing. Mol Cell Biol 29(22):6033-45	SGD
DOT6/YER088C	IGI: Inferred from Genetic Interaction Assigned on 2002-08-08	manually curated	Singer MS, et al. (1998) Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150(2):613-32	SGD
ESA1/YOR244W	IGI: Inferred from Genetic Interaction with SGD:SIR2, IMP: Inferred from Mutant Phenotype Assigned on 2009-03-11	manually curated	Clarke AS, et al. (2006) Distinct roles for the essential MYST family HAT Esa1p in transcriptional silencing. Mol Biol Cell 17(4):1744-57	SGD
FOB1/YDR110W	IDA: Inferred from Direct Assay Assigned on 2003-10-10	manually curated	Huang J and Moazed D (2003) Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing. Genes Dev 17(17):2162-76	SGD
FPR4/YLR449W	IMP: Inferred from Mutant Phenotype Assigned on 2006-09-22	manually curated	Kuzuhara T and Horikoshi M (2004) A nuclear FK506-binding protein is a histone chaperone regulating rDNA silencing. Nat Struct Mol Biol 11(3):275-83	SGD
FUN30/YAL019W	IMP: Inferred from Mutant Phenotype Assigned on 2009-12-15	manually curated	Neves-Costa A, et al. (2009) The SNF2-family member Fun30 promotes gene silencing in heterochromatic loci. PLoS One 4(12):e8111	SGD
HST2/YPL015C	IMP: Inferred from Mutant Phenotype Assigned on 2007-02-15	manually curated	Perrod S, et al. (2001) A cytosolic NAD-dependent deacetylase, Hst2p, can modulate nucleolar and telomeric silencing in yeast. EMBO J 20(1-2):197-209	SGD
HST2/YPL015C	IMP: Inferred from Mutant Phenotype Assigned on 2007-02-15	manually curated	Lamming DW, et al. (2005) HST2 mediates SIR2-independent life-span extension by calorie restriction. Science 309(5742):1861-4	SGD
IRS4/YKR019C	IMP: Inferred from Mutant Phenotype Assigned on 2002-12-11	manually curated	Smith JS, et al. (1999) A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol 19(4):3184-97	SGD
ISW2/YOR304W	IMP: Inferred from Mutant Phenotype Assigned on 2007-08-17	manually curated	Mueller JE, et al. (2007) Isw2 regulates gene silencing at the ribosomal DNA locus in Saccharomyces cerevisiae. Biochem Biophys Res Commun 361(4):1017-21	SGD
LRS4/YDR439W	IDA: Inferred from Direct Assay Assigned on 2002-10-01	manually curated	Smith JS, et al. (1999) A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol 19(4):3184-97	SGD
NET1/YJL076W	IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction Assigned on 2001-01-18	manually curated	Straight AF, et al. (1999) Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97(2):245-56	SGD
NNT1/YLR285W	IMP: Inferred from Mutant Phenotype Assigned on 2003-05-09	manually curated	Anderson RM, et al. (2003) Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae. Nature 423(6936):181-5	SGD
NPT1/YOR209C	IMP: Inferred from Mutant Phenotype Assigned on 2002-07-08	manually curated	Sandmeier JJ, et al. (2002) Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway. Genetics 160(3):877-89	SGD
NSI1/YDR026C	IMP: Inferred from Mutant Phenotype Assigned on 2012-03-15	manually curated	Ha CW, et al. (2012) Nsi1 plays a significant role in the silencing of ribosomal DNA in Saccharomyces cerevisiae. Nucleic Acids Res 40(11):4892-903	SGD
PAF1/YBR279W	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	manually curated	Mueller JE, et al. (2006) The requirements for COMPASS and Paf1 in transcriptional silencing and methylation of histone H3 in Saccharomyces cerevisiae. Genetics 173(2):557-67	SGD
PNC1/YGL037C	IMP: Inferred from Mutant Phenotype Assigned on 2002-07-08	manually curated	Sandmeier JJ, et al. (2002) Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway. Genetics 160(3):877-89	SGD
SET1/YHR119W	TAS: Traceable Author Statement Assigned on 2004-12-06	manually curated	Dror V and Winston F (2004) The Swi/Snf chromatin remodeling complex is required for ribosomal DNA and telomeric silencing in Saccharomyces cerevisiae. Mol Cell Biol 24(18):8227-35	SGD
SIR2/YDL042C	IMP: Inferred from Mutant Phenotype Assigned on 2003-08-14	manually curated	Gottlieb S and Esposito RE (1989) A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56(5):771-6	SGD
SPT10/YJL127C	IMP: Inferred from Mutant Phenotype Assigned on 2010-11-18	manually curated	Chang JS and Winston F (2011) Spt10 and Spt21 Are Required for Transcriptional Silencing in Saccharomyces cerevisiae. Eukaryot Cell 10(1):118-29	SGD
SPT21/YMR179W	IMP: Inferred from Mutant Phenotype Assigned on 2010-11-18	manually curated	Chang JS and Winston F (2011) Spt10 and Spt21 Are Required for Transcriptional Silencing in Saccharomyces cerevisiae. Eukaryot Cell 10(1):118-29	SGD
TOF2/YKR010C	IMP: Inferred from Mutant Phenotype Assigned on 2008-07-28	manually curated	Huang J, et al. (2006) Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer. Genes Dev 20(20):2887-901	SGD
TOP1/YOL006C	IMP: Inferred from Mutant Phenotype Assigned on 2006-09-08	manually curated	Smith JS, et al. (1999) A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol 19(4):3184-97	SGD
ZDS2/YML109W	IMP: Inferred from Mutant Phenotype Assigned on 2002-10-18	manually curated	Roy N and Runge KW (2000) Two paralogs involved in transcriptional silencing that antagonistically control yeast life span. Curr Biol 10(2):111-4	SGD

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