{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T20:46:23Z","timestamp":1782420383003,"version":"3.54.5"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Since packaging of DNA in the chromatin structure restricts the accessibility for regulatory factors, chromatin remodeling is required to facilitate nuclear processes such as gene transcription, replication, and genome recombination. Many conserved non-enzymatic protein domains have been identified that contribute to the activities of multiprotein remodeling complexes. Here we identified a novel conserved protein domain in Eukaryota whose putative function may be in regulating chromatin remodeling. Since this domain is associated with a known SANT domain in several vertebrate proteins, we named it the SANTA (SANT Associated) domain. Sequence analysis showed that the SANTA domain is approximately a 90 amino acid module and likely composed of four central \u03b2-sheets and three flanking \u03b1-helices. Many hydrophobic residues exhibited high conservation along the domain, implying a possible function in protein\u2013protein interactions. The SANTA domain was identified in mammals, chicken, frog, fish, sea squirt, sea urchin, worms and plants. Furthermore, a phylogenetic tree of SANTA domains showed that one plant-specific duplication event happened in the Viridiplantae lineage.<\/jats:p>\n               <jats:p>Contact: \u00a0trudeauv@uottawa.ca<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary Figure S1 for this paper is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl414","type":"journal-article","created":{"date-parts":[[2006,7,30]],"date-time":"2006-07-30T18:13:51Z","timestamp":1154283231000},"page":"2459-2462","source":"Crossref","is-referenced-by-count":32,"title":["SANTA domain: a novel conserved protein module in <i>Eukaryota<\/i> with potential involvement in chromatin regulation"],"prefix":"10.1093","volume":"22","author":[{"given":"Dapeng","family":"Zhang","sequence":"first","affiliation":[{"name":"Centre for Advanced Research in Environmental Genomics (CAREG), Department of Biology, University of Ottawa \u00a0 Ottawa, ON K1N 6N5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J.","family":"Martyniuk","sequence":"additional","affiliation":[{"name":"Centre for Advanced Research in Environmental Genomics (CAREG), Department of Biology, University of Ottawa \u00a0 Ottawa, ON K1N 6N5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vance L.","family":"Trudeau","sequence":"additional","affiliation":[{"name":"Centre for Advanced Research in Environmental Genomics (CAREG), Department of Biology, University of Ottawa \u00a0 Ottawa, ON K1N 6N5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2006,7,28]]},"reference":[{"key":"2023012409210585900_b1","first-page":"87","article-title":"The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB","volume":"21","author":"Aasland","year":"1996","journal-title":"Trends Biochem. Sci."},{"key":"2023012409210585900_b2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b3","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1126\/science.282.5394.1711","article-title":"Zebrafish hox clusters and vertebrate genome evolution","volume":"282","author":"Amores","year":"1998","journal-title":"Science"},{"key":"2023012409210585900_b4","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/gb-2002-3-8-research0039","article-title":"The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities","volume":"3","author":"Aravind","year":"2002","journal-title":"Genome Biol."},{"key":"2023012409210585900_b5","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.bbrc.2004.05.147","article-title":"In silico characterization of the INO80 subfamily of SWI2\/SNF2 chromatin remodeling proteins","volume":"320","author":"Bakshi","year":"2004","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2023012409210585900_b6","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b7","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.tibs.2005.11.001","article-title":"The PHD finger, a nuclear protein-interaction domain","volume":"31","author":"Bienz","year":"2005","journal-title":"Trends Biochem Sci, 2006"},{"key":"2023012409210585900_b8","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1038\/nrm1314","article-title":"The SANT domain: a unique histone-tail-binding module?","volume":"5","author":"Boyer","year":"2004","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023012409210585900_b9","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1002\/bies.10392","article-title":"The many colours of chromodomains","volume":"26","author":"Brehm","year":"2004","journal-title":"Bioessays"},{"key":"2023012409210585900_b10","first-page":"1007","article-title":"A subtracted cDNA library from the zebrafish (Danio rerio) embryonic inner ear","volume":"12","author":"Coimbra","year":"2000","journal-title":"Genome Res, 2002"},{"key":"2023012409210585900_b11","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/20974","article-title":"Structure and ligand of a histone acetyltransferase bromodomain","volume":"399","author":"Dhalluin","year":"1999","journal-title":"Nature"},{"key":"2023012409210585900_b12","doi-asserted-by":"crossref","first-page":"28009","DOI":"10.1074\/jbc.M403793200","article-title":"The SANT domain of human MI-ER1 interacts with Sp1 to interfere with GC box recognition and repress transcription from its own promoter","volume":"279","author":"Ding","year":"2004","journal-title":"J. Biol. Chem."},{"key":"2023012409210585900_b13","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b14","first-page":"164","article-title":"PHYLIP-Phylogeny Inference Package (Version 3.2)","volume":"5","author":"Felsenstein","year":"1989","journal-title":"Cladistics"},{"key":"2023012409210585900_b15","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.gde.2004.01.007","article-title":"Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer?","volume":"14","author":"Flaus","year":"2004","journal-title":"Curr. Opin. Genet. Dev"},{"key":"2023012409210585900_b16","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1093\/bioinformatics\/btg124","article-title":"3D-Jury: a simple approach to improve protein structure predictions","volume":"19","author":"Ginalski","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012409210585900_b17","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/bioinformatics\/17.9.845","article-title":"CHROMA: consensus-based colouring of multiple alignments for publication","volume":"17","author":"Goodstadt","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012409210585900_b18","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1023\/A:1007177623283","article-title":"A set of proteins interacting with transcription factor Sp1 identified in a two-hybrid screening","volume":"210","author":"Gunther","year":"2000","journal-title":"Mol. Cell Biochem."},{"key":"2023012409210585900_b19","doi-asserted-by":"crossref","first-page":"D447","DOI":"10.1093\/nar\/gki138","article-title":"Ensembl 2005","volume":"33","author":"Hubbard","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b20","doi-asserted-by":"crossref","first-page":"14321","DOI":"10.1074\/jbc.M601702200","article-title":"Mapping the principal interaction site of the Brf1 and Bdp1 subunits of S. cerevisiae TFIIIB","volume":"281","author":"Kassavetis","year":"2006","journal-title":"J. Biol. Chem."},{"key":"2023012409210585900_b21","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1242\/dev.127.8.1737","article-title":"Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development","volume":"127","author":"Ko","year":"2000","journal-title":"Development"},{"key":"2023012409210585900_b22","doi-asserted-by":"crossref","first-page":"4229","DOI":"10.1093\/nar\/23.21.4229","article-title":"The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin","volume":"23","author":"Koonin","year":"1995","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b23","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1093\/bib\/5.2.150","article-title":"MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment","volume":"5","author":"Kumar","year":"2004","journal-title":"Brief Bioinform."},{"key":"2023012409210585900_b24","doi-asserted-by":"crossref","first-page":"3305","DOI":"10.1093\/nar\/gkg557","article-title":"GeneSilico protein structure prediction meta-server","volume":"31","author":"Kurowski","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b25","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/nar\/30.1.242","article-title":"Recent improvements to the SMART domain-based sequence annotation resource","volume":"30","author":"Letunic","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b26","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1093\/bioinformatics\/bth487","article-title":"A simple and fast secondary structure prediction method using hidden neural networks","volume":"21","author":"Lin","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409210585900_b27","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1093\/bioinformatics\/btl096","article-title":"Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion","volume":"22","author":"Makarova","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012409210585900_b28","doi-asserted-by":"crossref","first-page":"D192","DOI":"10.1093\/nar\/gki069","article-title":"CDD: a Conserved Domain Database for protein classification","volume":"33","author":"Marchler-Bauer","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b29","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1093\/bioinformatics\/16.4.404","article-title":"The PSIPRED protein structure prediction server","volume":"16","author":"McGuffin","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012409210585900_b30","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1093\/dnares\/8.4.179","article-title":"Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins","volume":"8","author":"Nagase","year":"2001","journal-title":"DNA Res"},{"key":"2023012409210585900_b31","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/S0092-8674(02)00654-2","article-title":"Cooperation between complexes that regulate chromatin structure and transcription","volume":"108","author":"Narliker","year":"2002","journal-title":"Cell"},{"key":"2023012409210585900_b32","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1471-2164-7-6","article-title":"The Epc-N domain: a predicted protein-protein interaction domain found in select chromatin associated proteins","volume":"7","author":"Perry","year":"2006","journal-title":"BMC Genomics"},{"key":"2023012409210585900_b33","doi-asserted-by":"crossref","first-page":"3503","DOI":"10.1093\/nar\/gkg522","article-title":"Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments","volume":"31","author":"Poirot","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b34","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1002\/prot.10082","article-title":"Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles","volume":"47","author":"Pollastri","year":"2002","journal-title":"Proteins"},{"key":"2023012409210585900_b35","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1104\/pp.105.065110","article-title":"Transcription factor families have much higher expansion rates in plants than in animals","volume":"139","author":"Shiu","year":"2005","journal-title":"Plant Physiol."},{"key":"2023012409210585900_b36","doi-asserted-by":"crossref","first-page":"W289","DOI":"10.1093\/nar\/gki390","article-title":"PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information","volume":"33","author":"Simossis","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409210585900_b37","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.1104\/pp.126.4.1480","article-title":"Isolation and characterization of kinase interacting protein 1, a pollen protein that interacts with the kinase domain of PRK1, a receptor-like kinase of petunia","volume":"126","author":"Skirpan","year":"2001","journal-title":"Plant Physiol."},{"key":"2023012409210585900_b38","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/47412","article-title":"The language of covalent histone modifications","volume":"403","author":"Strahl","year":"2000","journal-title":"Nature"},{"key":"2023012409210585900_b39","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1101\/gad.1393506","article-title":"Histone deacetylase-associating Atrophin proteins are nuclear receptor corepressors","volume":"20","author":"Wang","year":"2006","journal-title":"Genes Dev."},{"key":"2023012409210585900_b40","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1101\/gr.1097503","article-title":"Functional divergence of two zebrafish midkine growth factors following fish-specific gene duplication","volume":"13","author":"Winkler","year":"2003","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/20\/2459\/48841106\/bioinformatics_22_20_2459.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/20\/2459\/48841106\/bioinformatics_22_20_2459.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:59:30Z","timestamp":1674554370000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/20\/2459\/218247"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,7,28]]},"references-count":40,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2006,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl414","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,10,15]]},"published":{"date-parts":[[2006,7,28]]}}}