GO term: nuclear chromatin 
Ontology: Cellular Component (GO:0000790)
Definition: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
View Ontology:
(graph) | 
(text)
Definition: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
View Ontology:
(graph) | (text)
This table lists the methods used to annotate genes either directly to the term
nuclear chromatin (42 genes)
or to its variants containing one or more
qualifiers (14 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.
Links to Additional Annotations:
| Annotation Method | GO Term | # Yeast Genes Annotated |
|---|---|---|
| Manually curated (download data) | colocalizes_with: nuclear chromatin | 14 |
| nuclear chromatin | 40 | |
| High-throughput | none | none |
| Computational (download data) | nuclear chromatin | 3 |
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
nuclear chromatin or its variants containing one or more
qualifiers (NOT, contributes to, or colocalizes with).
| nuclear chromatin 42 genes directly annotated to this term |
||||
|---|---|---|---|---|
| Locus | Evidence | Annotation Method | Reference | Assigned By |
| ARP4/YJL081C | IDA: Inferred from Direct Assay Assigned on 2001-01-18 |
manually curated | Harata M, et al. (1999) The nuclear actin-related protein of Saccharomyces cerevisiae, Act3p/Arp4, interacts with core histones. Mol Biol Cell 10(8):2595-605 |
SGD |
| BDF1/YLR399C | IDA: Inferred from Direct Assay Assigned on 2005-04-15 |
manually curated | Chua P and Roeder GS (1995) Bdf1, a yeast chromosomal protein required for sporulation. Mol Cell Biol 15(7):3685-96 |
SGD |
| CHD1/YER164W | IDA: Inferred from Direct Assay Assigned on 2011-10-07 |
manually curated | Alen C, et al. (2002) A role for chromatin remodeling in transcriptional termination by RNA polymerase II. Mol Cell 10(6):1441-52 |
SGD |
| IDA: Inferred from Direct Assay Assigned on 2011-10-07 |
manually curated | Simic R, et al. (2003) Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J 22(8):1846-56 |
SGD | |
| CMR1/YDL156W | IDA: Inferred from Direct Assay Assigned on 2012-03-15 |
manually curated | Choi DH, et al. (2012) Saccharomyces cerevisiae Cmr1 protein preferentially binds to UV-damaged DNA in vitro. J Microbiol 50(1):112-8 |
SGD |
| CRF1/YDR223W | IDA: Inferred from Direct Assay Assigned on 2010-02-09 |
manually curated | Martin DE, et al. (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119(7):969-79 |
SGD |
| ECO1/YFR027W | IPI: Inferred from Physical Interaction Assigned on 2003-04-03 |
manually curated | Toth A, et al. (1999) Yeast cohesin complex requires a conserved protein, Eco1p(Ctf7), to establish cohesion between sister chromatids during DNA replication. Genes Dev 13(3):320-33 |
SGD |
| FHL1/YPR104C | IDA: Inferred from Direct Assay Assigned on 2010-02-09 |
manually curated | Martin DE, et al. (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119(7):969-79 |
SGD |
| IDA: Inferred from Direct Assay Assigned on 2007-08-28 |
manually curated | Rudra D, et al. (2005) Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J 24(3):533-42 |
SGD | |
| FKH1/YIL131C | IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN1262 Assigned on 2010-05-03 |
computational | Gaudet P, et al. (2011) Annotation inferences using phylogenetic trees. |
RefGenome |
| FKH2/YNL068C | IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN1262 Assigned on 2010-05-03 |
computational | Gaudet P, et al. (2011) Annotation inferences using phylogenetic trees. |
RefGenome |
| GTR2/YGR163W | IDA: Inferred from Direct Assay Assigned on 2008-04-16 |
manually curated | Sekiguchi T, et al. (2008) Genetic evidence that Ras-like GTPases, Gtr1p, and Gtr2p, are involved in epigenetic control of gene expression in Saccharomyces cerevisiae. Biochem Biophys Res Commun 368(3):748-54 |
SGD |
| HCM1/YCR065W | IDA: Inferred from Direct Assay Assigned on 2008-11-18 |
manually curated | Horak CE, et al. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16(23):3017-33 |
SGD |
| HTZ1/YOL012C | IDA: Inferred from Direct Assay, IPI: Inferred from Physical Interaction Assigned on 2001-01-18 |
manually curated | Santisteban MS, et al. (2000) Histone H2A.Z regulats transcription and is partially redundant with nucleosome remodeling complexes. Cell 103(3):411-22 |
SGD |
| IDA: Inferred from Direct Assay, IPI: Inferred from Physical Interaction Assigned on 2001-01-18 |
manually curated | Dhillon N and Kamakaka RT (2000) A histone variant, Htz1p, and a Sir1p-like protein, Esc2p, mediate silencing at HMR. Mol Cell 6(4):769-80 |
SGD | |
| IFH1/YLR223C | IDA: Inferred from Direct Assay Assigned on 2010-02-09 |
manually curated | Martin DE, et al. (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119(7):969-79 |
SGD |
| MCM1/YMR043W | IDA: Inferred from Direct Assay Assigned on 2003-03-04 |
manually curated | Chang VK, et al. (2003) Mcm1 binds replication origins. J Biol Chem 278(8):6093-100 |
SGD |
| NFI1/YOR156C | IDA: Inferred from Direct Assay Assigned on 2006-12-15 |
manually curated | Takahashi Y, et al. (2006) SIZ1/SIZ2 control of chromosome transmission fidelity is mediated by the sumoylation of topoisomerase II. Genetics 172(2):783-94 |
SGD |
| PLM2/YDR501W | IDA: Inferred from Direct Assay Assigned on 2008-11-18 |
manually curated | Horak CE, et al. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16(23):3017-33 |
SGD |
| POB3/YML069W | IDA: Inferred from Direct Assay Assigned on 2006-09-14 |
manually curated | Wittmeyer J, et al. (1999) Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. Biochemistry 38(28):8961-71 |
SGD |
| POG1/YIL122W | IDA: Inferred from Direct Assay Assigned on 2008-11-18 |
manually curated | Horak CE, et al. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16(23):3017-33 |
SGD |
| RAD18/YCR066W | IDA: Inferred from Direct Assay Assigned on 2002-08-06 |
manually curated | Ulrich HD and Jentsch S (2000) Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair. EMBO J 19(13):3388-97 |
SGD |
| RAD5/YLR032W | IDA: Inferred from Direct Assay Assigned on 2002-08-06 |
manually curated | Ulrich HD and Jentsch S (2000) Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair. EMBO J 19(13):3388-97 |
SGD |
| RGM1/YMR182C | IDA: Inferred from Direct Assay Assigned on 2012-03-29 |
manually curated | Mak HC, et al. (2009) Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Res 19(6):1014-25 |
SGD |
| IDA: Inferred from Direct Assay Assigned on 2012-03-29 |
manually curated | Smith JJ, et al. (2011) Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Mol Syst Biol 7():455 |
SGD | |
| ROX1/YPR065W | IC: Inferred By Curator from DNA binding, bending, sequence-specific DNA binding Assigned on 2010-02-10 |
manually curated | Deckert J, et al. (1999) Characterization of the DNA binding and bending HMG domain of the yeast hypoxic repressor Rox1. Nucleic Acids Res 27(17):3518-26 |
SGD |
| IC: Inferred By Curator from sequence-specific DNA binding Assigned on 2010-02-10 |
manually curated | Fujiwara D, et al. (1999) Molecular mechanism of the multiple regulation of the Saccharomyces cerevisiae ATF1 gene encoding alcohol acetyltransferase. Yeast 15(12):1183-97 |
SGD | |
| IC: Inferred By Curator from sequence-specific DNA binding Assigned on 2010-02-10 |
manually curated | Balasubramanian B, et al. (1993) The Rox1 repressor of the Saccharomyces cerevisiae hypoxic genes is a specific DNA-binding protein with a high-mobility-group motif. Mol Cell Biol 13(10):6071-8 |
SGD | |
| IC: Inferred By Curator from DNA binding, bending Assigned on 2010-02-10 |
manually curated | Deckert J, et al. (1995) Mutational analysis of Rox1, a DNA-bending repressor of hypoxic genes in Saccharomyces cerevisiae. Mol Cell Biol 15(11):6109-17 |
SGD | |
| IEA: Inferred from Electronic Annotation with EBI:IPR027142 Last Updated 2013-03-02 |
computational | DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms. |
InterPro | |
| RTT103/YDR289C | IDA: Inferred from Direct Assay Assigned on 2012-03-26 |
manually curated | Kim M, et al. (2004) The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432(7016):517-22 |
SGD |
| SAS2/YMR127C | IDA: Inferred from Direct Assay Assigned on 2002-06-01 |
manually curated | Osada S, et al. (2001) The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev 15(23):3155-68 |
SGD |
| SAS4/YDR181C | IDA: Inferred from Direct Assay Assigned on 2002-06-01 |
manually curated | Osada S, et al. (2001) The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev 15(23):3155-68 |
SGD |
| SAS5/YOR213C | IDA: Inferred from Direct Assay Assigned on 2002-06-01 |
manually curated | Osada S, et al. (2001) The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev 15(23):3155-68 |
SGD |
| SCC2/YDR180W | IDA: Inferred from Direct Assay Assigned on 2010-02-24 |
manually curated | Toth A, et al. (1999) Yeast cohesin complex requires a conserved protein, Eco1p(Ctf7), to establish cohesion between sister chromatids during DNA replication. Genes Dev 13(3):320-33 |
SGD |
| SCC4/YER147C | IDA: Inferred from Direct Assay Assigned on 2002-10-18 |
manually curated | Ciosk R, et al. (2000) Cohesin's binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins. Mol Cell 5(2):243-54 |
SGD |
| SET5/YHR207C | IDA: Inferred from Direct Assay Assigned on 2012-03-08 |
manually curated | Green EM, et al. (2012) Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses.LID - 10.1038/nsmb.2252 [doi] Nat Struct Mol Biol () |
SGD |
| SIZ1/YDR409W | IDA: Inferred from Direct Assay Assigned on 2006-12-15 |
manually curated | Takahashi Y, et al. (2006) SIZ1/SIZ2 control of chromosome transmission fidelity is mediated by the sumoylation of topoisomerase II. Genetics 172(2):783-94 |
SGD |
| colocalizes_with: nuclear chromatin 14 genes directly annotated to this term |
||||
|---|---|---|---|---|
| Locus | Evidence | Annotation Method | Reference | Assigned By |
| BRE1/YDL074C | IDA: Inferred from Direct Assay Assigned on 2009-11-11 |
manually curated | Wood A, et al. (2003) The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. J Biol Chem 278(37):34739-42 |
SGD |
| DNL4/YOR005C | IPI: Inferred from Physical Interaction with SGD:LIF1 Assigned on 2007-04-25 |
manually curated | Teo SH and Jackson SP (2000) Lif1p targets the DNA ligase Lig4p to sites of DNA double-strand breaks. Curr Biol 10(3):165-8 |
SGD |
| GON7/YJL184W | IDA: Inferred from Direct Assay Assigned on 2006-09-21 |
manually curated | Kisseleva-Romanova E, et al. (2006) Yeast homolog of a cancer-testis antigen defines a new transcription complex. EMBO J 25(15):3576-85 |
SGD |
| HMO1/YDR174W | IDA: Inferred from Direct Assay Assigned on 2010-03-17 |
manually curated | Hall DB, et al. (2006) An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol Cell Biol 26(9):3672-9 |
SGD |
| IDA: Inferred from Direct Assay Assigned on 2010-03-17 |
manually curated | Kasahara K, et al. (2007) Assembly of Regulatory Factors on rRNA and Ribosomal Protein Genes in Saccharomyces cerevisiae. Mol Cell Biol 27(19):6686-6705 |
SGD | |
| IXR1/YKL032C | IDA: Inferred from Direct Assay Assigned on 2010-02-24 |
manually curated | Castro-Prego R, et al. (2010) Regulatory factors controlling transcription of Saccharomyces cerevisiae IXR1 by oxygen levels: a model of transcriptional adaptation from aerobiosis to hypoxia implicating ROX1 and IXR1 cross-regulation. Biochem J 425(1):235-43 |
SGD |
| KAE1/YKR038C | IDA: Inferred from Direct Assay Assigned on 2006-09-21 |
manually curated | Kisseleva-Romanova E, et al. (2006) Yeast homolog of a cancer-testis antigen defines a new transcription complex. EMBO J 25(15):3576-85 |
SGD |
| LIF1/YGL090W | IDA: Inferred from Direct Assay Assigned on 2007-04-25 |
manually curated | Teo SH and Jackson SP (2000) Lif1p targets the DNA ligase Lig4p to sites of DNA double-strand breaks. Curr Biol 10(3):165-8 |
SGD |
| MIG3/YER028C | IDA: Inferred from Direct Assay Assigned on 2011-08-05 |
manually curated | Wade SL, et al. (2009) The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression. EMBO J 28(19):2919-31 |
SGD |
| PCC1/YKR095W-A | IDA: Inferred from Direct Assay Assigned on 2006-09-21 |
manually curated | Kisseleva-Romanova E, et al. (2006) Yeast homolog of a cancer-testis antigen defines a new transcription complex. EMBO J 25(15):3576-85 |
SGD |
| RAD6/YGL058W | IDA: Inferred from Direct Assay Assigned on 2009-11-11 |
manually curated | Kao CF, et al. (2004) Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B. Genes Dev 18(2):184-95 |
SGD |
| REV1/YOR346W | IDA: Inferred from Direct Assay Assigned on 2010-02-02 |
manually curated | Hirano Y and Sugimoto K (2006) ATR homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break. Curr Biol 16(6):586-90 |
SGD |
| REV3/YPL167C | IPI: Inferred from Physical Interaction with SGD:REV7 Assigned on 2010-02-02 |
manually curated | Hirano Y and Sugimoto K (2006) ATR homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break. Curr Biol 16(6):586-90 |
SGD |
| REV7/YIL139C | IDA: Inferred from Direct Assay Assigned on 2010-02-02 |
manually curated | Hirano Y and Sugimoto K (2006) ATR homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break. Curr Biol 16(6):586-90 |
SGD |
| RRD1/YIL153W | IDA: Inferred from Direct Assay Assigned on 2011-03-09 |
manually curated | Jouvet N, et al. (2010) Rrd1 isomerizes RNA polymerase II in response to rapamycin. BMC Mol Biol 11():92 |
SGD |
