This page displays GO annotations in different sections according to the annotation method used to add that annotation to SGD.

Last Reviewed on: 2011-10-12    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin DNA binding	IDA: Inferred from Direct Assay Assigned on 2011-10-07	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
DNA binding	IDA: Inferred from Direct Assay Assigned on 2011-06-14	Ryan DP, et al.  (2011) The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains. EMBO J ()	SGD
DNA-dependent ATPase activity	IDA: Inferred from Direct Assay Assigned on 2011-10-03	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
methylated histone residue binding	IDA: Inferred from Direct Assay Assigned on 2011-10-07	Pray-Grant MG, et al.  (2005) Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433(7024):434-8	SGD
rDNA binding	IDA: Inferred from Direct Assay Assigned on 2011-10-07	Jones HS, et al.  (2007) RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. Nat Struct Mol Biol 14(2):123-30	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
ATP-dependent chromatin remodeling	IDA: Inferred from Direct Assay Assigned on 2011-10-03	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
histone H2B conserved C-terminal lysine ubiquitination	IMP: Inferred from Mutant Phenotype Assigned on 2013-02-13	Lee JS, et al.  (2012) Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1. Genes Dev 26(9):914-9	SGD
negative regulation of DNA-dependent DNA replication	IGI: Inferred from Genetic Interaction with SGD:ORC2, SGD:SPT16, SGD:SET2, SGD:POB3, SGD:RAD53, SGD:MEC1 Assigned on 2011-10-07	Biswas D, et al.  (2008) A Role for Chd1 and Set2 in Negatively Regulating DNA Replication in Saccharomyces cerevisiae. Genetics 178(2):649-59	SGD
negative regulation of histone H3-K14 acetylation	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-11	Quan TK and Hartzog GA  (2010) Histone H3K4 and K36 Methylation, Chd1 and Rpd3S Oppose the Functions of Saccharomyces cerevisiae Spt4-Spt5 in Transcription. Genetics 184(2):321-34	SGD
negative regulation of histone H3-K9 acetylation	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-11	Quan TK and Hartzog GA  (2010) Histone H3K4 and K36 Methylation, Chd1 and Rpd3S Oppose the Functions of Saccharomyces cerevisiae Spt4-Spt5 in Transcription. Genetics 184(2):321-34	SGD
nucleosome mobilization	IDA: Inferred from Direct Assay Assigned on 2011-10-07	Stockdale C, et al.  (2006) Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J Biol Chem 281(24):16279-88	SGD
nucleosome positioning	IGI: Inferred from Genetic Interaction with SGD:ISW1, SGD:ISW2 Assigned on 2011-10-07	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
	IDA: Inferred from Direct Assay Assigned on 2008-08-21	Ferreira H, et al.  (2007) Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms. J Mol Biol 374(3):563-79	SGD
regulation of transcription by chromatin organization	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-07	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
	IGI: Inferred from Genetic Interaction with SGD:SNF2 Assigned on 2011-10-03	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
regulation of transcriptional start site selection at RNA polymerase II promoter	IGI: Inferred from Genetic Interaction with SGD:ISW1 Assigned on 2011-10-11	Quan TK and Hartzog GA  (2010) Histone H3K4 and K36 Methylation, Chd1 and Rpd3S Oppose the Functions of Saccharomyces cerevisiae Spt4-Spt5 in Transcription. Genetics 184(2):321-34	SGD
termination of RNA polymerase I transcription	IGI: Inferred from Genetic Interaction with SGD:ISW1, SGD:ISW2 Assigned on 2011-10-07	Jones HS, et al.  (2007) RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. Nat Struct Mol Biol 14(2):123-30	SGD
termination of RNA polymerase II transcription	IGI: Inferred from Genetic Interaction with SGD:ISW1, SGD:ISW2 Assigned on 2011-10-07 IMP: Inferred from Mutant Phenotype Assigned on 2011-10-07	Alen C, et al.  (2002) A role for chromatin remodeling in transcriptional termination by RNA polymerase II. Mol Cell 10(6):1441-52	SGD
transcription elongation from RNA polymerase II promoter	IGI: Inferred from Genetic Interaction with SGD:SPT5 Assigned on 2011-10-07 IPI: Inferred from Physical Interaction with SGD:RTF1, SGD:SPT5, SGD:POB3 Assigned on 2011-10-07	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

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nuclear chromatin	IDA: Inferred from Direct Assay Assigned on 2011-10-07	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
	IDA: Inferred from Direct Assay Assigned on 2011-10-07	Alen C, et al.  (2002) A role for chromatin remodeling in transcriptional termination by RNA polymerase II. Mol Cell 10(6):1441-52	SGD
nucleolar chromatin	IDA: Inferred from Direct Assay Assigned on 2011-10-07	Jones HS, et al.  (2007) RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. Nat Struct Mol Biol 14(2):123-30	SGD
SAGA complex	IDA: Inferred from Direct Assay Assigned on 2005-08-04	Pray-Grant MG, et al.  (2005) Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433(7024):434-8	SGD
SLIK (SAGA-like) complex	IDA: Inferred from Direct Assay Assigned on 2005-08-04	Pray-Grant MG, et al.  (2005) Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433(7024):434-8	SGD

* Manually curated GO annotations reflect our best understanding of the basic molecular function, biological process, and cellular component for this gene product. Manually curated annotations are assigned by SGD curators based on published papers when available, or by curatorial statements if necessary. Curators periodically review all Manually curated GO annotations for accuracy and completeness. The "Last Reviewed on:" date at the top of this section indicates when these annotations were last reviewed.

Cellular Component

High-throughput Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
mitochondrion	IDA: Inferred from Direct Assay Assigned on 2006-12-12	Reinders J, et al.  (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5(7):1543-54	SGD
	IDA: Inferred from Direct Assay Assigned on 2004-09-28	Sickmann A, et al.  (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207-12	SGD

** GO annotations from High-throughput experiments are made based on a variety of large scale high-throughput experiments, including genome-wide experiments. Many of these annotations are made based on GO annotations (or mappings to GO annotations) assigned by the authors, rather than SGD curators. While SGD curators read these publications and often work closely with authors to incorporate the information, each individual annotation may not necessarily be reviewed by a curator. GO Annotations from high-throughput experiments will be assigned only when this type of data is available, and thus may not be assigned in all three aspects of the Gene Ontologies.

Molecular Function | Biological Process | Cellular Component

Computational Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
ATP binding	IEA: Inferred from Electronic Annotation with EBI:IPR001650, EBI:IPR000330 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	IEA: Inferred from Electronic Annotation with EBI:KW-0067 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
DNA binding	IEA: Inferred from Electronic Annotation with EBI:IPR009057, EBI:IPR000330 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	IEA: Inferred from Electronic Annotation with EBI:KW-0238 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
helicase activity	IEA: Inferred from Electronic Annotation with EBI:IPR001650 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	IEA: Inferred from Electronic Annotation with EBI:KW-0347 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
hydrolase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0378 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleic acid binding	IEA: Inferred from Electronic Annotation with EBI:IPR001650 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nucleotide binding	IEA: Inferred from Electronic Annotation with EBI:KW-0547 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin modification	IEA: Inferred from Electronic Annotation with EBI:KW-0156 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:KW-0805 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:KW-0804 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

Computational Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleus	IEA: Inferred from Electronic Annotation with EBI:IPR000953 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	IEA: Inferred from Electronic Annotation with EBI:SL-0191 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.	UniProtKB
	IEA: Inferred from Electronic Annotation with EBI:KW-0539 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

*** Computational GO Annotations are predictions. These annotations are NOT reviewed by a curator. Currently, all computational GO annotations for S. cerevisiae are assigned by an external source (for example, the Gene Ontology Annotation (GOA) project of the European Bioinformatics Institute (EBI)).