snf5 null mutants are viable, but display reduced growth on glucose and sucrose, are unable to grow on raffinose, galactose, or glycerol, and are hypersensitive to lithium and calcium ions (1, 11, 35). snf5 null mutations are synthetically lethal in combination with dst1 null mutations (37, 38), and expression of an active Moloney murine leukemia virus (M-MuLV) integrase (IN) is lethal in rad52 null mutants, but not in rad52 snf5 double null mutants (41). Snf5p is similar to Sfh1p, Drosophila SNR1, Schizosaccharomyces pombe Snf5p, and Arabidopsis thaliana BSH, which can partially complement the defects seen in snf5 null mutants (42, 45, 46, 49). Snf5p also has a region of similarity to zebrafish SMARCB1 and Caenorhabditis elegans R07E5.3 (24). The human homolog of Snf5p (SMARCB1) is a tumor suppressor, mutation of which is associated with oncogenesis (24, 51). SMARCB1 binds to Epstein-Barr virus (EBV) nuclear protein 2 (EBNA2), which is expressed in latently-infected B lymphocytes and is essential to the immortalization of B cells by EBV (53). Human SMARCB1 also binds to human papillomavirus (HPV) E1 protein in two-hybrid assays and stimulates HPV DNA replication in vitro (55). By regulating the structure of chromatin, chromatin remodeling complexes, all of which contain an ATPase as a central motor subunit, perform critical functions in the maintenance, transmission, and expression of eukaryotic genomes. The SWI/SNF chromatin remodeling complex is involved in DNA replication, stress response, and transcription, and binds DNA nonspecifically, altering nucleosome structure to facilitate binding of transcription factors. For some genes, transcriptional activators are able to target the SWI/SNF complex to upstream activation sequences (UAS) in the promoter. The SWI/SNF chromatin remodeling complex family contains two evolutionary conserved subclasses of chromatin remodeling factors, one subfamily includes yeast SWI/SNF, fly BAP, and mammalian BAF, and the other subfamily includes yeast RSC (Remodel the Structure of Chromatin), fly PBAP, and mammalian PBAF (7, 9, 2, 12, 13, 8, 17, 6, 20, 22, 23, 26, 27, 30, 32, 33, 34, 36, 39, 40, 43, 44, 47, 48, 50, 39, 52, 54, 56, 57, 35). It appears that some human SWI/SNF subunits act as tumor suppressors and there is also evidence that human SWI/SNF subunits are involved in controlling cell growth via their interaction with other tumor suppressors (58). Expression of adenovirus E1A oncoproteins, which are regulators of cellular and viral transcription, in Saccharomyces cerevisiae requires the function of the SWI/SNF complex, and expression of E1A in wild-type cells leads to a specific loss of SWI/SNF dependent transcription. These results suggest that the SWI/SNF complex is a target of these oncoproteins in mammalian cells and that the disruption of normal cell cycle control by E1A may be due in part to altered activity of the SWI/SNF complex (59).", "date_edited": "2006-03-27"}, "literature_overview": {"primary_count": 91, "additional_count": 123, "review_count": 59, "go_count": 14, "phenotype_count": 12, "disease_count": 0, "interaction_count": 110, "regulation_count": 5, "ptm_count": 8, "funComplement_count": 0, "htp_count": 53, "total_count": 389}, "disease_overview": {"manual_disease_terms": [], "htp_disease_terms": [], "computational_annotation_count": 0, "date_last_reviewed": null}, "ecnumbers": [], "URS_ID": null, "main_strain": "S288C", "regulation_overview": {"regulator_count": 4, "target_count": 1, "paragraph": {"text": "SNF5 promoter is bound by Fkh1p; SNF5 promoter is bound by Xbp1p in response to heat; SNF5 transcription is regulated by Spt10p; SNF5 transcription is downregulated by Ixr1p in response to hypoxia", "date_edited": "2023-08-31", "references": [{"id": 371969, "display_name": "Ostrow AZ, et al. (2014)", "citation": "Ostrow AZ, et al. (2014) Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics. PLoS One 9(2):e87647", "pubmed_id": 24504085, "link": "/reference/S000156933", "year": 2014, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1371/journal.pone.0087647"}, {"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913637/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/24504085"}]}, {"id": 414327, "display_name": "Venters BJ, et al. (2011)", "citation": "Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92", "pubmed_id": 21329885, "link": "/reference/S000145602", "year": 2011, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1016/j.molcel.2011.01.015"}, {"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057419/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/21329885"}]}, {"id": 524734, "display_name": "Mendiratta G, et al. (2006)", "citation": "Mendiratta G, et al. (2006) The DNA-binding domain of the yeast Spt10p activator includes a zinc finger that is homologous to foamy virus integrase. J Biol Chem 281(11):7040-8", "pubmed_id": 16415340, "link": "/reference/S000114259", "year": 2006, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1074/jbc.M511416200"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/16415340"}]}, {"id": 407966, "display_name": "Vizoso-V\u00e1zquez A, et al. (2012)", "citation": "Vizoso-V\u00e1zquez A, et al. (2012) Ixr1p and the control of the Saccharomyces cerevisiae hypoxic response. Appl Microbiol Biotechnol 94(1):173-84", "pubmed_id": 22189861, "link": "/reference/S000147832", "year": 2012, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1007/s00253-011-3785-2"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/22189861"}]}]}}, "reference_mapping": {"638930": 1, "636694": 2, "595387": 3, "617905": 4, "397497": 5, "616820": 6, "611245": 7, "600257": 8, "572435": 9, "553639": 10, "627050": 11, "591652": 12, "589270": 13, "622573": 14, "641072": 15, "646971": 16, "636210": 17, "628984": 18, "639439": 19, "615870": 20, "623641": 21, "635012": 22, "613366": 23, "586406": 24, "544367": 25, "619148": 26, "604412": 27, "531990": 28, "641962": 29, "593591": 30, "628236": 31, "584881": 32, "584872": 33, "580378": 34, "643583": 35, "547947": 36, "619652": 37, "631343": 38, "546954": 39, "546548": 40, "528249": 41, "614034": 42, "536087": 43, "529681": 44, "607071": 45, "601566": 46, "584878": 47, "584875": 48, "610689": 49, "584863": 50, "528240": 51, "639568": 52, "626727": 53, "584884": 54, "525675": 55, "636189": 56, "601809": 57, "556456": 58, "611554": 59, "599335": 60, "624823": 61, "601740": 62}, "history": [{"category": "Name", "history_type": "LSP", "note": "Name: HAF4", "date_created": "2010-02-16", "references": [{"id": 599335, "display_name": "Kuchin SV, et al. (1993)", "citation": "Kuchin SV, et al. (1993) Genes required for derepression of an extracellular glucoamylase gene, STA2, in the yeast Saccharomyces. Yeast 9(5):533-41", "pubmed_id": 8322516, "link": "/reference/S000056109", "year": 1993, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1002/yea.320090510"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/8322516"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: SNF5", "date_created": "2000-05-19", "references": [{"id": 638930, "display_name": "Neigeborn L and Carlson M (1984)", "citation": "Neigeborn L and Carlson M (1984) Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae. Genetics 108(4):845-58", "pubmed_id": 6392017, "link": "/reference/S000042746", "year": 1984, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1093/genetics/108.4.845"}, {"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1224269/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/6392017"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: SWI10", "date_created": "2010-02-16", "references": [{"id": 622573, "display_name": "Breeden L and Nasmyth K (1987)", "citation": "Breeden L and Nasmyth K (1987) Cell cycle control of the yeast HO gene: cis- and trans-acting regulators. Cell 48(3):389-97", "pubmed_id": 3542227, "link": "/reference/S000048261", "year": 1987, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1016/0092-8674(87)90190-5"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/3542227"}]}]}, {"category": "Name", "history_type": "LSP", "note": "Name: TYE4", "date_created": "2010-02-16", "references": [{"id": 601740, "display_name": "Ciriacy M and Williamson VM (1981)", "citation": "Ciriacy M and Williamson VM (1981) Analysis of mutations affecting Ty-mediated gene expression in Saccharomyces cerevisiae. Mol Gen Genet 182(1):159-63", "pubmed_id": 6267430, "link": "/reference/S000055296", "year": 1981, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1007/BF00422784"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/6267430"}]}, {"id": 624823, "display_name": "Ciriacy M, et al. (1991)", "citation": "Ciriacy M, et al. (1991) Characterization of trans-acting mutations affecting Ty and Ty-mediated transcription in Saccharomyces cerevisiae. Curr Genet 20(6):441-8", "pubmed_id": 1664298, "link": "/reference/S000047501", "year": 1991, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1007/BF00334769"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/1664298"}]}]}, {"category": "Sequence change", "history_type": "SEQUENCE", "note": "Sequence change: Two nucleotide substitutions within the coding region of SNF5/YBR289W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 564 is now Aspartic Acid rather than Glutamic Acid.
Transcriptional regulation information for a gene, including any predicted DNA binding site
motifs
(YeTFaSCo) for the gene's protein product, as well as any of its targets (genes it regulates) or
regulators (genes that regulate it), based on experimental evidence. For genes with regulatory
targets, shared GO Biological Process terms for these targets are listed.
Collection of domains associated with the protein based on various sources, including the
protein coordinates for the domain, a domain Description, a Source and corresponding
accession ID, and the number of S. cerevisiae genes that share the same domain.
Increase the total number of rows showing on this page by using the pull-down located below the table, or use the
page scroll at the table's top right to browse through its pages; use the arrows to the right of a column header to
sort by that column; filter the table using the "Filter" box at the top of the table.
Binding sites motifs as predicted by YeTFaSCo.
This table lists putative transcriptional regulatory targets for the central gene represented
on this page. These targets were identified based on the presence of predicted regulator
binding sites or experimental regulator binding in the target promoter, and/or changes in
the target gene’s transcript levels in regulator mutant strains. Data includes
high-throughput techniques such as microarray, RNA-seq, and ChIP assays; information about
the experiment and assay type, constructs, conditions, and strains, as well as a reference,
are provided for each Regulator annotation.
Increase the total number of rows displayed on this page using the pull-down located below the table, or use the
page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column
header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box
(for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to
further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.
Increase the total number of rows displayed on this page using the pull-down located below the table, or use the
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Increase the total number of rows displayed on this page using the pull-down located below the table, or use the
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The shared GO processes listed in this table are based on the data presented in the Targets section above; shared GO terms,
the number of target genes that share them, and the P-value are all indicated in the table.
Increase the total number of rows displayed on this page using the pull-down located below the table, or use the
page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column
header to sort by that column; filter the table using the "Filter" box at the top of the table; download this table
as a .txt file using the Download button; after filtering the above table, the option to ”Recalculate With New
Filter” will appear next to the Download button in this Shared GO Processes table.
This table lists genes that are putative regulators of the central gene represented on this
page, based primarily on experiments showing that a regulator binds to the gene’s promoter
or affects the gene’s transcription when the regulator is mutated. This includes data
generated by high-throughput techniques such as microarray, RNA-seq, and ChIP assays;
information about the experiment and assay type, constructs, conditions, and strains, as
well as a reference, are provided for each Regulator annotation.
Increase the total number of rows displayed on this page using the pull-down located below the table, or use the
page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column
header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box
(for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to
further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.
Increase the total number of rows displayed on this page using the pull-down located below the table, or use the
page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column
header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box
(for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to
further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.
Increase the total number of rows displayed on this page using the pull-down located below the table, or use the
page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column
header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box
(for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to
further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, or SPELL.
This diagram displays targets (purple) and regulators (green) of the given gene (blue)
based on the data presented in the Targets and Regulators tables and therefore includes
high-throughput data generated by techniques such as microarray, RNA-seq, and ChIP assays.
The arrows move in the direction of Regulator -> Target and include any regulatory
relationships between genes other than the given gene.
\r\nNew 780521 ACAACCTCCCACCAATGTTCAGCCAACTATTGGCCAACTTCCTCAACTTCCAAAATTAAA 780580\r\n |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||\r\nOld 780517 ACAACCTCCCACCAATGTTCAGCCCACTATTGGCCAACTTCCTCAACTTCCAAAATTAAA 780576\r\n\r\nNew 781311 GATATTGTCGTGGGACAAAACCAGTTAATCGATCAATTTGAGTGGGACATCTCTAATAGT 781370\r\n ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||\r\nOld 781307 GATATTGTCGTGGGACAAAACCAGTTAATCGATCAATTTGAGTGGGAGATCTCTAATAGT 781366", "date_created": "2011-02-03", "references": [{"id": 374815, "display_name": "Engel SR, et al. (2014)", "citation": "Engel SR, et al. (2014) The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (Bethesda) 4(3):389-98", "pubmed_id": 24374639, "link": "/reference/S000156273", "year": 2014, "urls": [{"display_name": "DOI full text", "link": "http://dx.doi.org/10.1534/g3.113.008995"}, {"display_name": "PMC full text", "link": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962479/"}, {"display_name": "PubMed", "link": "http://www.ncbi.nlm.nih.gov/pubmed/24374639"}]}]}], "complexes": [{"format_name": "CPX-1150", "display_name": "SWI/SNF chromatin remodelling complex"}]};
SNF5 / YBR289W Regulation
Domains and Classification
Evidence ID
Analyze ID
Gene
Gene Systematic Name
Protein Coordinates
Accession ID
Description
Source
No. of Genes with Domain
DNA Binding Site Motifs
Targets
Manually Curated
Evidence ID
Analyze ID
Regulator
Regulator Systematic Name
Target
Target Systematic Name
Direction
Regulation of
Happens During
Regulator Type
Direction
Regulation Of
Happens During
Method
Evidence
Strain Background
Reference
High-throughput
Evidence ID
Analyze ID
Regulator
Regulator Systematic Name
Target
Target Systematic Name
Direction
Regulation of
Happens During
Regulator Type
Direction
Regulation Of
Happens During
Method
Evidence
Strain Background
Reference
Evidence ID
Analyze ID
Regulator
Regulator Systematic Name
Target
Target Systematic Name
Direction
Regulation of
Happens During
Regulator Type
Direction
Regulation Of
Happens During
Method
Evidence
Strain Background
Reference
Shared GO Processes Among Targets
GO Term ID
GO Term
Number of genes
P-Value
Regulators
Manually Curated
Evidence ID
Analyze ID
Regulator
Regulator Systematic Name
Target
Target Systematic Name
Direction
Regulation of
Happens During
Regulator Type
Direction
Regulation Of
Happens During
Method
Evidence
Strain Background
Reference
High-throughput
Evidence ID
Analyze ID
Regulator
Regulator Systematic Name
Target
Target Systematic Name
Direction
Regulation of
Happens During
Regulator Type
Direction
Regulation Of
Happens During
Method
Evidence
Strain Background
Reference
Evidence ID
Analyze ID
Regulator
Regulator Systematic Name
Target
Target Systematic Name
Direction
Regulation of
Happens During
Regulator Type
Direction
Regulation Of
Happens During
Method
Evidence
Strain Background
Reference
Regulation Network