{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,17]],"date-time":"2026-05-17T06:03:38Z","timestamp":1778997818667,"version":"3.51.4"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009256","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,8,24]],"date-time":"2021-08-24T00:00:00Z","timestamp":1629763200000}}],"reference-count":72,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T00:00:00Z","timestamp":1628726400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swiss Government"},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"crossref","award":["798\/10"],"award-info":[{"award-number":["798\/10"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Nehemia Levzion Scholarship"},{"name":"Bar-Ilan University President\u2019s Scholarship"},{"DOI":"10.13039\/501100002744","name":"Bar-Ilan University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002744","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Metazoan core promoters, which direct the initiation of transcription by RNA polymerase II (Pol II), may contain short sequence motifs termed core promoter elements\/motifs (\n                    <jats:italic>e<\/jats:italic>\n                    .\n                    <jats:italic>g<\/jats:italic>\n                    . the TATA box, initiator (Inr) and downstream core promoter element (DPE)), which recruit Pol II via the general transcription machinery. The DPE was discovered and extensively characterized in\n                    <jats:italic>Drosophila<\/jats:italic>\n                    , where it is strictly dependent on both the presence of an Inr and the precise spacing from it. Since the\n                    <jats:italic>Drosophila<\/jats:italic>\n                    DPE is recognized by the human transcription machinery, it is most likely that some human promoters contain a downstream element that is similar, though not necessarily identical, to the\n                    <jats:italic>Drosophila<\/jats:italic>\n                    DPE. However, only a couple of human promoters were shown to contain a functional DPE, and attempts to computationally detect human DPE-containing promoters have mostly been unsuccessful. Using a newly-designed motif discovery strategy based on Expectation-Maximization probabilistic partitioning algorithms, we discovered preferred downstream positions (PDP) in human promoters that resemble the\n                    <jats:italic>Drosophila<\/jats:italic>\n                    DPE. Available chromatin accessibility footprints revealed that\n                    <jats:italic>Drosophila<\/jats:italic>\n                    and human Inr+DPE promoter classes are not only highly structured, but also similar to each other, particularly in the proximal downstream region. Clustering of the corresponding sequence motifs using a neighbor-joining algorithm strongly suggests that canonical Inr+DPE promoters could be common to metazoan species. Using reporter assays we demonstrate the contribution of the identified downstream positions to the function of multiple human promoters. Furthermore, we show that alteration of the spacing between the Inr and PDP by two nucleotides results in reduced promoter activity, suggesting a spacing dependency of the newly discovered human PDP on the Inr. Taken together, our strategy identified novel functional downstream positions within human core promoters, supporting the existence of DPE-like motifs in human promoters.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009256","type":"journal-article","created":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T15:16:40Z","timestamp":1628781400000},"page":"e1009256","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Computational identification and experimental characterization of preferred downstream positions in human core promoters"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0816-7775","authenticated-orcid":true,"given":"Ren\u00e9","family":"Dreos","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2076-1141","authenticated-orcid":true,"given":"Anna","family":"Sloutskin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nati","family":"Malachi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diana","family":"Ideses","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4824-885X","authenticated-orcid":true,"given":"Philipp","family":"Bucher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2607-5476","authenticated-orcid":true,"given":"Tamar","family":"Juven-Gershon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,8,12]]},"reference":[{"issue":"8","key":"pcbi.1009256.ref001","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1016\/j.bbagrm.2015.04.003","article-title":"The core promoter: At the heart of gene expression","volume":"1849","author":"Y.M. Danino","year":"2015","journal-title":"Biochim Biophys Acta"},{"issue":"10","key":"pcbi.1009256.ref002","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/s41580-018-0028-8","article-title":"Eukaryotic core promoters and the functional basis of transcription initiation","volume":"19","author":"V. Haberle","year":"2018","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"4","key":"pcbi.1009256.ref003","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nrg3163","article-title":"Metazoan promoters: emerging characteristics and insights into transcriptional regulation","volume":"13","author":"B. Lenhard","year":"2012","journal-title":"Nat Rev Genet"},{"issue":"3","key":"pcbi.1009256.ref004","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1080\/10409230600648736","article-title":"The general transcription machinery and general cofactors","volume":"41","author":"M.C. 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Burke","year":"1996","journal-title":"Genes Dev"},{"issue":"22","key":"pcbi.1009256.ref020","doi-asserted-by":"crossref","first-page":"3020","DOI":"10.1101\/gad.11.22.3020","article-title":"The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila","volume":"11","author":"T.W. Burke","year":"1997","journal-title":"Genes Dev"},{"issue":"13","key":"pcbi.1009256.ref021","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1101\/gad.1193404","article-title":"The MTE, a new core promoter element for transcription by RNA polymerase II","volume":"18","author":"C.Y. Lim","year":"2004","journal-title":"Genes Dev"},{"issue":"14","key":"pcbi.1009256.ref022","doi-asserted-by":"crossref","first-page":"3471","DOI":"10.1128\/MCB.00053-10","article-title":"Three key subregions contribute to the function of the downstream RNA polymerase II core promoter","volume":"30","author":"J.W. 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Kedmi","year":"2014","journal-title":"Genes Dev"},{"issue":"13","key":"pcbi.1009256.ref026","doi-asserted-by":"crossref","first-page":"4754","DOI":"10.1128\/MCB.20.13.4754-4764.2000","article-title":"The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters","volume":"20","author":"A.K. Kutach","year":"2000","journal-title":"Mol Cell Biol"},{"issue":"20","key":"pcbi.1009256.ref027","doi-asserted-by":"crossref","first-page":"5943","DOI":"10.1093\/nar\/gkl608","article-title":"Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction","volume":"34","author":"U. Ohler","year":"2006","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"pcbi.1009256.ref028","doi-asserted-by":"crossref","first-page":"RESEARCH0087","DOI":"10.1186\/gb-2002-3-12-research0087","article-title":"Computational analysis of core promoters in the Drosophila genome","volume":"3","author":"U. Ohler","year":"2002","journal-title":"Genome Biol"},{"issue":"7","key":"pcbi.1009256.ref029","doi-asserted-by":"crossref","first-page":"R73","DOI":"10.1186\/gb-2009-10-7-r73","article-title":"Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome","volume":"10","author":"E.A. Rach","year":"2009","journal-title":"Genome Biol"},{"issue":"4","key":"pcbi.1009256.ref030","doi-asserted-by":"crossref","first-page":"e0215695","DOI":"10.1371\/journal.pone.0215695","article-title":"Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes","volume":"14","author":"H. Shir-Shapira","year":"2019","journal-title":"PLoS One"},{"issue":"5493","key":"pcbi.1009256.ref031","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1126\/science.290.5493.982","article-title":"A basal transcription factor that activates or represses transcription","volume":"290","author":"P.J. Willy","year":"2000","journal-title":"Science"},{"issue":"17","key":"pcbi.1009256.ref032","doi-asserted-by":"crossref","first-page":"11993","DOI":"10.1074\/jbc.M114.550251","article-title":"Core promoter functions in the regulation of gene expression of Drosophila dorsal target genes","volume":"289","author":"Y. Zehavi","year":"2014","journal-title":"J Biol Chem"},{"issue":"29","key":"pcbi.1009256.ref033","doi-asserted-by":"crossref","first-page":"20396","DOI":"10.1074\/jbc.M114.563254","article-title":"RNA polymerase III accurately initiates transcription from RNA polymerase II promoters in vitro","volume":"289","author":"S.H. Duttke","year":"2014","journal-title":"J Biol Chem"},{"issue":"27","key":"pcbi.1009256.ref034","doi-asserted-by":"crossref","first-page":"25503","DOI":"10.1074\/jbc.M102875200","article-title":"The intronless and TATA-less human TAF(II)55 gene contains a functional initiator and a downstream promoter element","volume":"276","author":"T. Zhou","year":"2001","journal-title":"J Biol Chem"},{"issue":"9","key":"pcbi.1009256.ref035","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1016\/j.tcb.2019.06.004","article-title":"Promoter Recognition: Putting TFIID on the Spot","volume":"29","author":"T. Bhuiyan","year":"2019","journal-title":"Trends Cell Biol"},{"issue":"7772","key":"pcbi.1009256.ref036","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/s41586-019-1517-4","article-title":"Organization and regulation of gene transcription","volume":"573","author":"P. Cramer","year":"2019","journal-title":"Nature"},{"key":"pcbi.1009256.ref037","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.sbi.2019.10.001","article-title":"Recent insights into the structure of TFIID, its assembly, and its binding to core promoter","volume":"61","author":"A.B. Patel","year":"2019","journal-title":"Curr Opin Struct Biol"},{"issue":"9","key":"pcbi.1009256.ref038","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1038\/s41594-019-0287-x","article-title":"50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms","volume":"26","author":"R.G. Roeder","year":"2019","journal-title":"Nat Struct Mol Biol"},{"issue":"7","key":"pcbi.1009256.ref039","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1016\/S0092-8674(05)80016-9","article-title":"Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II","volume":"81","author":"C.P. Verrijzer","year":"1995","journal-title":"Cell"},{"issue":"2","key":"pcbi.1009256.ref040","doi-asserted-by":"crossref","first-page":"e0148918","DOI":"10.1371\/journal.pone.0148918","article-title":"Engineered Promoters for Potent Transient Overexpression","volume":"11","author":"D.Y. Even","year":"2016","journal-title":"PLoS One"},{"issue":"1-2","key":"pcbi.1009256.ref041","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.cell.2012.12.005","article-title":"Human TFIID binds to core promoter DNA in a reorganized structural state","volume":"152","author":"M.A. Cianfrocco","year":"2013","journal-title":"Cell"},{"issue":"7596","key":"pcbi.1009256.ref042","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1038\/nature17394","article-title":"Structure of promoter-bound TFIID and model of human pre-initiation complex assembly","volume":"531","author":"R.K. Louder","year":"2016","journal-title":"Nature"},{"issue":"1","key":"pcbi.1009256.ref043","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.6831208","article-title":"A code for transcription initiation in mammalian genomes","volume":"18","author":"M.C. Frith","year":"2008","journal-title":"Genome Res"},{"issue":"18","key":"pcbi.1009256.ref044","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1101\/gad.1951110","article-title":"The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery","volume":"24","author":"T.J. Parry","year":"2010","journal-title":"Genes Dev"},{"issue":"D1","key":"pcbi.1009256.ref045","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gky1038","article-title":"PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools","volume":"47","author":"H. Mi","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pcbi.1009256.ref046","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/nmeth.1313","article-title":"Global mapping of protein-DNA interactions in vivo by digital genomic footprinting","volume":"6","author":"J.R. Hesselberth","year":"2009","journal-title":"Nat Methods"},{"issue":"1","key":"pcbi.1009256.ref047","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13059-019-1654-y","article-title":"Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling","volume":"20","author":"A. Karabacak Calviello","year":"2019","journal-title":"Genome Biol"},{"issue":"6","key":"pcbi.1009256.ref048","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1101\/gr.5754707","article-title":"Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1","volume":"17","author":"H. Xi","year":"2007","journal-title":"Genome Res"},{"issue":"3","key":"pcbi.1009256.ref049","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1080\/21541264.2015.1067286","article-title":"ElemeNT: a computational tool for detecting core promoter elements","volume":"6","author":"A. Sloutskin","year":"2015","journal-title":"Transcription"},{"issue":"7","key":"pcbi.1009256.ref050","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1101\/gr.188193.114","article-title":"Core promoter sequence in yeast is a major determinant of expression level","volume":"25","author":"S. Lubliner","year":"2015","journal-title":"Genome Res"},{"issue":"19","key":"pcbi.1009256.ref051","doi-asserted-by":"crossref","first-page":"4145","DOI":"10.1093\/nar\/gkf537","article-title":"Sp1 and AP2 regulate but do not constitute TATA-less human TAF(II)55 core promoter activity","volume":"30","author":"T. Zhou","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"pcbi.1009256.ref052","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1093\/bioinformatics\/bti172","article-title":"Synergy of human Pol II core promoter elements revealed by statistical sequence analysis","volume":"21","author":"N.I. Gershenzon","year":"2005","journal-title":"Bioinformatics"},{"issue":"6421","key":"pcbi.1009256.ref053","doi-asserted-by":"crossref","DOI":"10.1126\/science.aau8872","article-title":"Structure of human TFIID and mechanism of TBP loading onto promoter DNA","volume":"362","author":"A.B. Patel","year":"2018","journal-title":"Science"},{"issue":"7","key":"pcbi.1009256.ref054","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/ng.3867","article-title":"Paused RNA polymerase II inhibits new transcriptional initiation","volume":"49","author":"W. Shao","year":"2017","journal-title":"Nat Genet"},{"issue":"1","key":"pcbi.1009256.ref055","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1534\/genetics.119.302021","article-title":"The RNA Polymerase II Core Promoter in Drosophila","volume":"212","author":"L. Vo Ngoc","year":"2019","journal-title":"Genetics"},{"issue":"43","key":"pcbi.1009256.ref056","doi-asserted-by":"crossref","first-page":"12316","DOI":"10.1073\/pnas.1603217113","article-title":"Nascent RNA sequencing reveals distinct features in plant transcription","volume":"113","author":"J. Hetzel","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7825","key":"pcbi.1009256.ref057","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/s41586-020-2689-7","article-title":"Identification of the human DPR core promoter element using machine learning","volume":"585","author":"L. Vo Ngoc","year":"2020","journal-title":"Nature"},{"issue":"D1","key":"pcbi.1009256.ref058","doi-asserted-by":"crossref","first-page":"D51","DOI":"10.1093\/nar\/gkw1069","article-title":"The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms","volume":"45","author":"R. Dreos","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"17","key":"pcbi.1009256.ref059","doi-asserted-by":"crossref","first-page":"2406","DOI":"10.1093\/bioinformatics\/btu318","article-title":"Probabilistic partitioning methods to find significant patterns in ChIP-Seq data","volume":"30","author":"N.U. Nair","year":"2014","journal-title":"Bioinformatics"},{"issue":"2","key":"pcbi.1009256.ref060","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/s40484-013-0012-4","article-title":"Modeling the specificity of protein-DNA interactions","volume":"1","author":"G.D. Stormo","year":"2013","journal-title":"Quant Biol"},{"issue":"4","key":"pcbi.1009256.ref061","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1016\/0022-2836(88)90482-2","article-title":"Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites","volume":"200","author":"O.G. Berg","year":"1988","journal-title":"J Mol Biol"},{"issue":"12","key":"pcbi.1009256.ref062","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"J.D. Buenrostro","year":"2013","journal-title":"Nat Methods"},{"issue":"2","key":"pcbi.1009256.ref063","doi-asserted-by":"crossref","first-page":"e1004994","DOI":"10.1371\/journal.pgen.1004994","article-title":"Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling","volume":"11","author":"K. Davie","year":"2015","journal-title":"PLoS Genet"},{"issue":"D1","key":"pcbi.1009256.ref064","doi-asserted-by":"crossref","first-page":"D175","DOI":"10.1093\/nar\/gkx995","article-title":"MGA repository: a curated data resource for ChIP-seq and other genome annotated data","volume":"46","author":"R. 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