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

Last Reviewed on: 2012-01-13    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin binding	IDA: Inferred from Direct Assay Assigned on 2011-10-21	Pokholok DK, et al.  (2002) Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell 9(4):799-809	SGD
RNA polymerase II core binding	IPI: Inferred from Physical Interaction with SGD:RPO21 Assigned on 2011-10-28	Qiu H, et al.  (2006) The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Mol Cell Biol 26(8):3135-48	SGD
RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity	IDA: Inferred from Direct Assay Assigned on 2011-10-28	Qiu H, et al.  (2006) The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Mol Cell Biol 26(8):3135-48	SGD
RNA polymerase II transcription factor binding transcription factor activity	IPI: Inferred from Physical Interaction with SGD:SPT5 Assigned on 2011-10-19	Squazzo SL, et al.  (2002) The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J 21(7):1764-74	SGD
	IPI: Inferred from Physical Interaction with SGD:SPT5, SGD:SPT4 Assigned on 2011-10-28	Qiu H, et al.  (2006) The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Mol Cell Biol 26(8):3135-48	SGD
TFIIF-class binding transcription factor activity	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-21 IPI: Inferred from Physical Interaction with SGD:TFG2 Assigned on 2011-10-21	Shi X, et al.  (1997) Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Mol Cell Biol 17(3):1160-9	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin silencing at rDNA	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	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
global genome nucleotide-excision repair	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-11	Tatum D, et al.  (2011) Diverse roles of RNA polymerase II-associated factor 1 complex in different subpathways of nucleotide excision repair. J Biol Chem 286(35):30304-13	SGD
mRNA 3'-end processing	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-20	Mueller CL, et al.  (2004) The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol Cell 14(4):447-56	SGD
negative regulation of DNA recombination	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-21	Chang M, et al.  (1999) A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol Cell Biol 19(2):1056-67	SGD
negative regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	Carvin CD and Kladde MP  (2004) Effectors of lysine 4 methylation of histone H3 in Saccharomyces cerevisiae are negative regulators of PHO5 and GAL1-10. J Biol Chem 279(32):33057-62	SGD
positive regulation of histone H3-K36 trimethylation	IMP: Inferred from Mutant Phenotype Assigned on 2012-01-13	Chu Y, et al.  (2007) Regulation of histone modification and cryptic transcription by the Bur1 and Paf1 complexes. EMBO J 26(22):4646-56	SGD
positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-10	Nordick K, et al.  (2008) Direct interactions between the Paf1 complex and a cleavage and polyadenylation factor are revealed by dissociation of Paf1 from RNA polymerase II. Eukaryot Cell 7(7):1158-67	SGD
positive regulation of transcription elongation from RNA polymerase I promoter	IDA: Inferred from Direct Assay Assigned on 2011-11-30	Zhang Y, et al.  (2010) The RNA polymerase-associated factor 1 complex (Paf1C) directly increases the elongation rate of RNA polymerase I and is required for efficient regulation of rRNA synthesis. J Biol Chem 285(19):14152-9	SGD
positive regulation of transcription elongation from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-20	Rondon AG, et al.  (2004) Molecular evidence indicating that the yeast PAF complex is required for transcription elongation. EMBO Rep 5(1):47-53	SGD
regulation of chromatin silencing at telomere	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-11	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
	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-20	Krogan NJ, et al.  (2003) The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell 11(3):721-9	SGD
regulation of histone H2B conserved C-terminal lysine ubiquitination	IDA: Inferred from Direct Assay Assigned on 2011-11-11	Kim J and Roeder RG  (2009) Direct Bre1-Paf1 Complex Interactions and RING Finger-independent Bre1-Rad6 Interactions Mediate Histone H2B Ubiquitylation in Yeast. J Biol Chem 284(31):20582-92	SGD
regulation of histone H2B ubiquitination	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	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
regulation of histone H3-K4 methylation	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	Carvin CD and Kladde MP  (2004) Effectors of lysine 4 methylation of histone H3 in Saccharomyces cerevisiae are negative regulators of PHO5 and GAL1-10. J Biol Chem 279(32):33057-62	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-20	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
	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-20	Krogan NJ, et al.  (2003) The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell 11(3):721-9	SGD
regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	Mueller CL, et al.  (2004) The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol Cell 14(4):447-56	SGD
regulation of transcription by chromatin organization	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-11	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
regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-20	Mueller CL and Jaehning JA  (2002) Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol Cell Biol 22(7):1971-80	SGD
regulation of transcription involved in G1 phase of mitotic cell cycle	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-21	Koch C, et al.  (1999) A role for Ctr9p and Paf1p in the regulation G1 cyclin expression in yeast. Nucleic Acids Res 27(10):2126-34	SGD
regulation of transcription-coupled nucleotide-excision repair	IGI: Inferred from Genetic Interaction with SGD:RAD16 Assigned on 2011-11-11	Tatum D, et al.  (2011) Diverse roles of RNA polymerase II-associated factor 1 complex in different subpathways of nucleotide excision repair. J Biol Chem 286(35):30304-13	SGD
rRNA processing	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-11	Zhang Y, et al.  (2010) The RNA polymerase-associated factor 1 complex (Paf1C) directly increases the elongation rate of RNA polymerase I and is required for efficient regulation of rRNA synthesis. J Biol Chem 285(19):14152-9	SGD
snoRNA 3'-end processing	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	Sheldon KE, et al.  (2005) A Requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' end formation. Mol Cell 20(2):225-36	SGD
snoRNA transcription from an RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28 IDA: Inferred from Direct Assay Assigned on 2011-10-28	Sheldon KE, et al.  (2005) A Requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' end formation. Mol Cell 20(2):225-36	SGD
transcription elongation from RNA polymerase I promoter	IMP: Inferred from Mutant Phenotype Assigned on 2009-10-14	Zhang Y, et al.  (2009) The Paf1 complex is required for efficient transcription elongation by RNA polymerase I. Proc Natl Acad Sci U S A 106(7):2153-8	SGD
transcription elongation from RNA polymerase II promoter	IGI: Inferred from Genetic Interaction with SGD:SPT16, SGD:SPT5, SGD:DST1, SGD:SPT4 Assigned on 2011-10-19 IMP: Inferred from Mutant Phenotype Assigned on 2011-10-19	Squazzo SL, et al.  (2002) The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J 21(7):1764-74	SGD
transcription from RNA polymerase I promoter	IGI: Inferred from Genetic Interaction with SGD:RPA49 Assigned on 2011-11-11 IMP: Inferred from Mutant Phenotype Assigned on 2011-11-11	Zhang Y, et al.  (2010) The RNA polymerase-associated factor 1 complex (Paf1C) directly increases the elongation rate of RNA polymerase I and is required for efficient regulation of rRNA synthesis. J Biol Chem 285(19):14152-9	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
Cdc73/Paf1 complex	IPI: Inferred from Physical Interaction with SGD:RTF1 Assigned on 2011-10-19	Squazzo SL, et al.  (2002) The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J 21(7):1764-74	SGD
	IPI: Inferred from Physical Interaction with SGD:CDC73 Assigned on 2005-11-08	Shi X, et al.  (1997) Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Mol Cell Biol 17(3):1160-9	SGD
	IPI: Inferred from Physical Interaction with SGD:CDC73, SGD:CTR9 Assigned on 2011-10-20	Mueller CL and Jaehning JA  (2002) Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol Cell Biol 22(7):1971-80	SGD
nucleus	IDA: Inferred from Direct Assay Assigned on 2004-08-04	Mueller CL, et al.  (2004) The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol Cell 14(4):447-56	SGD
	IDA: Inferred from Direct Assay Assigned on 2005-02-28	Porter SE, et al.  (2005) Separation of the Saccharomyces cerevisiae Paf1 complex from RNA polymerase II results in changes in its subnuclear localization. Eukaryot Cell 4(1):209-20	SGD
transcriptionally active chromatin	IDA: Inferred from Direct Assay Assigned on 2011-10-21	Pokholok DK, et al.  (2002) Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell 9(4):799-809	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.

There are no High-throughput annotations for PAF1

** 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.

Biological Process | Cellular Component

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
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
nucleoplasm	IEA: Inferred from Electronic Annotation with EBI:SL-0190 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
nucleus	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)).