{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T18:28:44Z","timestamp":1783103324035,"version":"3.54.6"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Endogenous retrovirus (ERV) elements have been shown to contribute promoter sequences that can initiate transcription of adjacent human genes. However, the extent to which retroviral sequences initiate transcription within the human genome is currently unknown. We analyzed genome sequence and high-throughput expression data to systematically evaluate the presence of retroviral promoters in the human genome.<\/jats:p>\n               <jats:p>Results: We report the existence of 51 197 ERV-derived promoter sequences that initiate transcription within the human genome, including 1743 cases where transcription is initiated from ERV sequences that are located in gene proximal promoter or 5\u2032 untranslated regions (UTRs). A total of 114 of the ERV-derived transcription start sites can be demonstrated to drive transcription of 97 human genes, producing chimeric transcripts that are initiated within ERV long terminal repeat (LTR) sequences and read-through into known gene sequences. ERV promoters drive tissue-specific and lineage-specific patterns of gene expression and contribute to expression divergence between paralogs. These data illustrate the potential of retroviral sequences to regulate human transcription on a large scale consistent with a substantial effect of ERVs on the function and evolution of the human genome.<\/jats:p>\n               <jats:p>Contact: \u00a0king.jordan@biology.gatech.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn243","type":"journal-article","created":{"date-parts":[[2008,6,6]],"date-time":"2008-06-06T00:45:31Z","timestamp":1212713131000},"page":"1563-1567","source":"Crossref","is-referenced-by-count":112,"title":["Retroviral promoters in the human genome"],"prefix":"10.1093","volume":"24","author":[{"given":"Andrew B.","family":"Conley","sequence":"first","affiliation":[{"name":"School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jittima","family":"Piriyapongsa","sequence":"additional","affiliation":[{"name":"School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I. King","family":"Jordan","sequence":"additional","affiliation":[{"name":"School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30306, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,6,5]]},"reference":[{"key":"2023020210384166100_B1","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":"2023020210384166100_B2","doi-asserted-by":"crossref","first-page":"14572","DOI":"10.1073\/pnas.0404838101","article-title":"Retroelements and the human genome: new perspectives on an old relation","volume":"101","author":"Bannert","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020210384166100_B3","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gr.1933104","article-title":"Aligning multiple genomic sequences with the threaded blockset aligner","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res"},{"key":"2023020210384166100_B4","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1016\/S0959-437X(00)00138-6","article-title":"Endogenous retroviruses and the human germline","volume":"10","author":"Bock","year":"2000","journal-title":"Curr. Opin. Genet. Dev"},{"key":"2023020210384166100_B5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S0169-5347(01)02394-1","article-title":"The human zoo: endogenous retroviruses in the human genome","volume":"17","author":"Bromham","year":"2002","journal-title":"Trends Ecol. Evol"},{"key":"2023020210384166100_B6","doi-asserted-by":"crossref","first-page":"12841","DOI":"10.1073\/pnas.2134464100","article-title":"An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon","volume":"100","author":"Dunn","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020210384166100_B7","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.gene.2005.09.003","article-title":"Transcription of two human genes from a bidirectional endogenous retrovirus promoter","volume":"366","author":"Dunn","year":"2006","journal-title":"Gene"},{"key":"2023020210384166100_B8","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE project","volume":"447","author":"ENCODE Project Consortium","year":"2007","journal-title":"Nature"},{"key":"2023020210384166100_B9","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1101\/gr.4086505","article-title":"Galaxy: a platform for interactive large-scale genome analysis","volume":"15","author":"Giardine","year":"2005","journal-title":"Genome Res"},{"key":"2023020210384166100_B10","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/S0168-9525(02)00006-9","article-title":"Origin of a substantial fraction of human regulatory sequences from transposable elements","volume":"19","author":"Jordan","year":"2003","journal-title":"Trends Genet"},{"key":"2023020210384166100_B11","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1093\/nar\/gkg129","article-title":"The UCSC genome browser database","volume":"31","author":"Karolchik","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023020210384166100_B12","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkh103","article-title":"The UCSC table browser data retrieval tool","volume":"32","author":"Karolchik","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023020210384166100_B13","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1126\/science.1090005","article-title":"Evolution at two levels in humans and chimpanzees","volume":"188","author":"King","year":"1975","journal-title":"Science"},{"key":"2023020210384166100_B14","doi-asserted-by":"crossref","first-page":"5131","DOI":"10.1074\/jbc.274.8.5131","article-title":"The cloning and characterization of a new stress response protein. A mammalian member of a family of theta class glutathione s-transferase-like proteins","volume":"274","author":"Kodym","year":"1999","journal-title":"J. Biol. Chem"},{"key":"2023020210384166100_B15","doi-asserted-by":"crossref","first-page":"2255","DOI":"10.1212\/01.WNL.0000147294.29309.47","article-title":"Polymorphisms in glutathione S-transferase omega-1 and AD, vascular dementia, and stroke","volume":"63","author":"Kolsch","year":"2004","journal-title":"Neurology"},{"key":"2023020210384166100_B16","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"2023020210384166100_B17","doi-asserted-by":"crossref","first-page":"3259","DOI":"10.1093\/hmg\/ddg357","article-title":"Glutathione S-transferase omega-1 modifies age-at-onset of Alzheimer disease and Parkinson disease","volume":"12","author":"Li","year":"2003","journal-title":"Hum. Mol. Genet"},{"key":"2023020210384166100_B18","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1159\/000084966","article-title":"Impact of transposable elements on the evolution of mammalian gene regulation","volume":"110","author":"Medstrand","year":"2005","journal-title":"Cytogenet. Genome Res"},{"key":"2023020210384166100_B19","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nmeth733","article-title":"Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation","volume":"2","author":"Ng","year":"2005","journal-title":"Nat. Methods"},{"key":"2023020210384166100_B20","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins","volume":"35","author":"Pruitt","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020210384166100_B21","doi-asserted-by":"crossref","first-page":"e10","DOI":"10.1371\/journal.pgen.0030010","article-title":"Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution","volume":"3","author":"Romanish","year":"2007","journal-title":"PLoS Genet"},{"key":"2023020210384166100_B22","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1093\/bioinformatics\/18.11.1542","article-title":"GeneCards 2002: towards a complete, object-oriented, human gene compendium","volume":"18","author":"Safran","year":"2002","journal-title":"Bioinformatics"},{"key":"2023020210384166100_B23","first-page":"2513","article-title":"Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution","volume":"10","author":"Samuelson","year":"1990","journal-title":"Mol. Cell. Biol"},{"key":"2023020210384166100_B24","doi-asserted-by":"crossref","first-page":"15776","DOI":"10.1073\/pnas.2136655100","article-title":"Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage","volume":"100","author":"Shiraki","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020210384166100_B25","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes","volume":"15","author":"Siepel","year":"2005","journal-title":"Genome Res"},{"key":"2023020210384166100_B26","article-title":"RepeatMasker Open-3.0","author":"Smit","year":"1996"},{"key":"2023020210384166100_B27","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1073\/pnas.0400782101","article-title":"A gene atlas of the mouse and human protein-encoding transcriptomes","volume":"101","author":"Su","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020210384166100_B28","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1002\/(SICI)1521-1878(200002)22:2<161::AID-BIES7>3.0.CO;2-X","article-title":"Retroviruses and primate evolution","volume":"22","author":"Sverdlov","year":"2000","journal-title":"Bioessays"},{"key":"2023020210384166100_B29","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/j.tig.2003.08.004","article-title":"Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions","volume":"19","author":"van de Lagemaat","year":"2003","journal-title":"Trends Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/14\/1563\/49046914\/bioinformatics_24_14_1563.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/14\/1563\/49046914\/bioinformatics_24_14_1563.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T12:20:23Z","timestamp":1675340423000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/14\/1563\/182042"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,6,5]]},"references-count":29,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2008,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn243","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,7,15]]},"published":{"date-parts":[[2008,6,5]]}}}