{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T01:43:29Z","timestamp":1772761409675,"version":"3.50.1"},"reference-count":37,"publisher":"American Association for the Advancement of Science (AAAS)","issue":"5831","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Science"],"published-print":{"date-parts":[[2007,6,15]]},"abstract":"<jats:p>\n            The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5\n            <jats:italic>Drosophila melanogaster<\/jats:italic>\n            genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs.\n            <jats:italic>Drosophila<\/jats:italic>\n            heterochromatin contains \u201cislands\u201d of highly conserved genes embedded in these \u201coceans\u201d of complex repeats, which may require special expression and splicing mechanisms.\n          <\/jats:p>","DOI":"10.1126\/science.1139815","type":"journal-article","created":{"date-parts":[[2007,6,14]],"date-time":"2007-06-14T20:53:32Z","timestamp":1181854412000},"page":"1586-1591","source":"Crossref","is-referenced-by-count":161,"title":["The Release 5.1 Annotation of\n            <i>Drosophila melanogaster<\/i>\n            Heterochromatin"],"prefix":"10.1126","volume":"316","author":[{"given":"Christopher D.","family":"Smith","sequence":"first","affiliation":[{"name":"Department of Biology, San Francisco State University, San Francisco, CA 94132, USA."},{"name":"Drosophila Heterochromatin Genome Project, Department of Genome and Computational Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA."},{"name":"National Center for Biomedical Ontology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA."},{"name":"Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA."}]},{"given":"ShengQiang","family":"Shu","sequence":"additional","affiliation":[{"name":"Department of Biology, San Francisco State University, San Francisco, CA 94132, USA."},{"name":"Drosophila Heterochromatin Genome Project, Department of Genome and Computational Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA."},{"name":"National Center for Biomedical Ontology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA."},{"name":"Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA."}]},{"given":"Christopher J.","family":"Mungall","sequence":"additional","affiliation":[{"name":"Department of Biology, San Francisco State University, San Francisco, CA 94132, USA."},{"name":"Drosophila Heterochromatin Genome Project, Department of Genome and Computational Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA."},{"name":"National Center for Biomedical Ontology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA."},{"name":"Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA."}]},{"given":"Gary H.","family":"Karpen","sequence":"additional","affiliation":[{"name":"Department of Biology, San Francisco State University, San Francisco, CA 94132, USA."},{"name":"Drosophila Heterochromatin Genome Project, Department of Genome and Computational Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA."},{"name":"National Center for Biomedical Ontology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA."},{"name":"Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA."}]}],"member":"221","reference":[{"key":"e_1_3_1_2_2","first-page":"RESEARCH0085","volume":"3","year":"2002","unstructured":"R. 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(www.fruitfly.org\/sequence\/release5genomic.shtml) (2006)."},{"key":"e_1_3_1_10_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1139816"},{"key":"e_1_3_1_11_2","unstructured":"Materials and methods are available as supporting material on Science Online."},{"key":"e_1_3_1_12_2","unstructured":"Supplemental data can be downloaded from ftp:\/\/ftp.dhgp.org\/pub\/DHGP\/Science_2007_Supplemental_Data. Future updates will be released through www.flybase.net."},{"key":"e_1_3_1_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2006.09.011"},{"key":"e_1_3_1_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/27.2.573"},{"key":"e_1_3_1_15_2","doi-asserted-by":"crossref","first-page":"R3","DOI":"10.1186\/gb-2003-5-1-r3","volume":"5","year":"2003","unstructured":"M. Hild et al., Genome Biol.5, R3 (2003).","journal-title":"Genome Biol."},{"key":"e_1_3_1_16_2","unstructured":"Berkeley Drosophila Genome Project www.fruitfly.org\/."},{"key":"e_1_3_1_17_2","unstructured":"C. Kopczynski et al . www.ncbi.nlm.nih.gov\/entrez\/viewer.fcgi?db=nucleotide&val=59874298."},{"key":"e_1_3_1_18_2","first-page":"D476","volume":"33","year":"2005","unstructured":"K. P. O'Brien, M. Remm, E. L. Sonnhammer, Nucleic Acids Res.33, D476 (2005).","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_1_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0401670101"},{"key":"e_1_3_1_20_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5075706"},{"key":"e_1_3_1_21_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5057506"},{"key":"e_1_3_1_22_2","unstructured":"Assembly Alignment and Annotation of Drosophilid Genomes http:\/\/rana.lbl.gov\/drosophila\/wiki\/index.php\/Main_Page."},{"key":"e_1_3_1_23_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/154.2.759"},{"key":"e_1_3_1_24_2","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.104.039701"},{"key":"e_1_3_1_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng1875"},{"key":"e_1_3_1_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg169"},{"key":"e_1_3_1_27_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1455503"},{"key":"e_1_3_1_28_2","first-page":"D390","volume":"33","year":"2005","unstructured":"R. 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Lewis et al., Genome Biol.3, RESEARCH0082 (2002).","journal-title":"Genome Biol."},{"key":"e_1_3_1_38_2","unstructured":"We thank E. Frise for maintaining the hardware and software used in these studies; M. Yandell for providing the specialized comparative genomics library\u2013based software used in our analyses; A. Dernburg D. Acevedo J. Carlson S. Celniker R. Hoskins and C. Kennedy for their helpful comments on the manuscript and input on annotations; and the members of the BDGP for cDNA sequencing. This work was supported by the National Human Genome Research Institute grant R01-HG000747 to C.D.S. and G.H.K. and NIH grant U54 HG004028-01 to S.S. and C.J.M."}],"container-title":["Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.science.org\/doi\/pdf\/10.1126\/science.1139815","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T08:49:19Z","timestamp":1704876559000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.science.org\/doi\/10.1126\/science.1139815"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,6,15]]},"references-count":37,"journal-issue":{"issue":"5831","published-print":{"date-parts":[[2007,6,15]]}},"alternative-id":["10.1126\/science.1139815"],"URL":"https:\/\/doi.org\/10.1126\/science.1139815","relation":{},"ISSN":["0036-8075","1095-9203"],"issn-type":[{"value":"0036-8075","type":"print"},{"value":"1095-9203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,6,15]]}}}