# HISTORY 23 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.12 # molecular_function # cellular_component 20130318: Eukaryota_PTN000001217 is found in nucleus (GO:0005634) 20130318: Dikarya_PTN000797509 is found in RSC complex (GO:0016586) 20130318: Eumetazoa_PTN000797502 is found in BAF-type complex (GO:0090544) # biological_process 20130318: Eukaryota_PTN000001217 participates in regulation of transcription from RNA polymerase II promoter (GO:0006357) 20130318: Eukaryota_PTN000001217 participates in nucleosome disassembly (GO:0006337) 20130318: Eukaryota_PTN000001217 participates in DNA repair (GO:0006281) 20130318: Eukaryota_PTN000001217 participates in ATP-dependent chromatin remodeling (GO:0043044) 20130318: Eumetazoa_PTN000797502 participates in cell differentiation (GO:0030154) 20130318: Eumetazoa_PTN000797502 participates in negative regulation of cell proliferation (GO:0008285) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES Members of this family encodes a component of the SWI/SNF or RSC chromatin remodeling complex. Chromatin-remodeling complexes carry out key enzymatic activities, changing chromatin structure by altering DNA�histone contacts within a nucleosome in an ATP-dependent manner (PMID12672490). There is a duplication in the fungi clade. BP: 1) Propagate 'ATP-dependent chromatin remodeling' to the root (Eukaryota_PTN000001217). 2) Proteins in this family are annotated to both 'positive' and 'negative' regulation of transcription. Propagate the parent term 'regulation of transcription from RNA polymerase II promoter' to the root. 3) 'Cell differentiation': Mouse Smarcb1 is annotated to 'cell differentiation', fly Snr1 is annotated to two child terms of 'cell differentiation': dendrite morphogenesis and dendrite guidance. Propagate 'cell differentiation' to the root of the Eumetazoa clade (PTN000797502). 4) 'DNA repair': yeast_SFH1 and SNF5 are annotated to 'double-strand DNA repair' and 'double-strand DNA repair via homologous recombination' respectively. No annotations to DNA repair related terms exist for the animal clade. I found the following article (http://www.ncbi.nlm.nih.gov/pubmed/19805520) which shows that human_SMARCB1 is involved in the nuclear excision repair pathway. Propagate 'DNA repair' (the parent term of 'double-strand DNA repair) to the root (Eukaryota_PTN000001217). 5) 'mitotic cell cycle phase transition': two yeast proteins (yeast_SFH1 and SCHPO_snf5) are annotated to G2/M transition of mitotic cell cycle (pombe gene is annotated to negative regulation of this process). No annotations to cell cycle phase transition related terms exist yet for genes in the animal clade. I found one article (http://www.nature.com/onc/journal/v29/n28/abs/onc2010159a) which shows that human SNF5 (SMARCB1) has a cell-cycle arrest in G1 mutant phenotype (SNF5, a core component of the SWI/SNF chromatin remodeling complex, is expressed as two isoforms, SNF5a and SNF5b. SNF5 is a tumor suppressor, as mutation of SNF5 leads to tumor formation and cooperates with p53 deficiency to enhance cancer susceptibility. Interestingly, lack of SNF5 inhibits cell survival and embryonic development, potentially through abnormal activation of p53. To further examine this, we generated cell lines in which SNF5a, SNF5b or both can be inducibly knocked down. We found that SNF5 knockdown leads to cell-cycle arrest in G1, and SNF5a and SNF5b are functionally redundant). Propagate 'mitotic cell cycle phase transition' to the root. 6) 'nucleosome disassembly': propagate to the root (both human and yeast SFH1 are annotated to this term). 7) 'negative regulation of cell proliferation': propagate to the root of the Eumetazoa clade (PTN000797502) based on annotations to mouse_Smarcb1 and fly_Snr1 orthologs. CC: 1) In the Eumetazoa clade (PTN000797502), human and mouse orthologs are annotated to 'SWI/SNF complex' while fly Snr1 is annotated to 'brahma complex' which is a counterpart of the S. cerevisiae SWI/SNF ATP-dependent chromatin remodeling complex (PMID12482982). The immediate parent of these two terms is 'BAF-type complex'. Propagate 'BAF-type complex' to the Eumetazoa clade. 2) In the fungi clade, SFH1 (S. cerevisiae) and Sfh1 (S. pombe) are annotated to 'RSC complex'; S. cerevisiae SNF5 and S. pombe SNF5 are annotated to 'SWI/SNF complex'; propagate these two terms to the yeast SFH1 and SNF5 clade respectively. 3) Propagate 'nucleus' to the root Eukaryota_PTN000001217. MF: reviewed existing annotations, no terms propagated. Yeast_SFH1 is annotated to DNA translocase activity with a 'contributes to' qualifier. As of today, PAINT lack the functionality to label a propagated annotation with the 'contributes to' qualifier. This term is not propagated. References: http://www.ncbi.nlm.nih.gov/pubmed/12672490 http://www.ncbi.nlm.nih.gov/pubmed/12482982 http://www.nature.com/onc/journal/v29/n28/abs/onc2010159a Annotation issues: 1) UniProt: Suggest updating the annotation for human SMARCB1: a) involved in nuclear excision repair, http://www.ncbi.nlm.nih.gov/pubmed/19805520; b) SNF5 knockdown leads to cell-cycle arrest in G1 http://www.nature.com/onc/journal/v29/n28/abs/onc2010159a.html # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).