Einzeltreffer — DigiBib

Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.

Titel:	Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Autor/in / Beteiligte Person:	Stark, A ; Lin, MF ; Kheradpour, P ; Pedersen, JS ; Parts, L ; Carlson, JW ; Crosby, MA ; Rasmussen, MD ; Roy, S ; Deoras, AN ; Ruby, JG ; Brennecke, J ; Hodges, E ; Hinrichs, AS ; Caspi, A ; Paten, B ; Park, SW ; Han, MV ; Maeder, ML ; Polansky, BJ ; Robson, BE ; Aerts, S ; van Helden J ; Hassan, B ; Gilbert, DG ; Eastman, DA ; Rice, M ; Weir, M ; Hahn, MW ; Park, Y ; Dewey, CN ; Pachter, L ; Kent, WJ ; Haussler, D ; Lai, EC ; Bartel, DP ; Hannon, GJ ; Kaufman, TC ; Eisen, MB ; Clark, AG ; Smith, D ; Celniker, SE ; Gelbart, WM ; Kellis, M
Link:	Full Text Finder (Volltext)
Zeitschrift:	Nature, Jg. 450 (2007-11-08), Heft 7167, S. 219-32
Veröffentlichung:	Basingstoke : Nature Publishing Group ; <i>Original Publication</i>: London, Macmillan Journals ltd., 2007
Medientyp:	academicJournal
ISSN:	1476-4687 (electronic)
DOI:	10.1038/nature06340
Schlagwort:	Animals Base Sequence Binding Sites Conserved Sequence Drosophila Proteins genetics Exons genetics Gene Expression Regulation genetics Genes, Insect genetics MicroRNAs genetics Molecular Sequence Data Organ Specificity Phylogeny Untranslated Regions genetics Drosophila classification Drosophila genetics Evolution, Molecular Genome, Insect genetics Genomics
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Corporate Authors: Harvard FlyBase curators ; Berkeley Drosophila Genome Project Publication Type: Comparative Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. Language: English [Nature] 2007 Nov 08; Vol. 450 (7167), pp. 219-32. MeSH Terms: Evolution, Molecular* ; Genomics* ; Drosophila / classification ; Drosophila / genetics ; Genome, Insect / *genetics ; Animals ; Base Sequence ; Binding Sites ; Conserved Sequence ; Drosophila Proteins / genetics ; Exons / genetics ; Gene Expression Regulation / genetics ; Genes, Insect / genetics ; MicroRNAs / genetics ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Untranslated Regions / genetics Comments: Comment in: Nature. 2007 Nov 8;450(7167):184-5. (PMID: 17994082) References: Genetics. 1996 Aug;143(4):1699-711. (PMID: 8844157) ; Nat Rev Genet. 2001 Dec;2(12):919-29. (PMID: 11733745) ; Nucleic Acids Res. 2003 Aug 1;31(15):4639-45. (PMID: 12888525) ; Nat Rev Genet. 2002 Mar;3(3):176-88. (PMID: 11972155) ; Genome Biol. 2002;3(12):RESEARCH0083. (PMID: 12537572) ; Bioinformatics. 2000 Jan;16(1):16-23. (PMID: 10812473) ; Dev Genet. 1998;22(3):187-200. (PMID: 9621427) ; Theory Biosci. 2005 Apr;123(4):301-69. (PMID: 18202870) ; Science. 2006 Dec 15;314(5806):1747-51. (PMID: 17138868) ; PLoS Biol. 2004 Sep;2(9):E271. (PMID: 15340490) ; Trends Genet. 2006 Apr;22(4):187-93. (PMID: 16499991) ; Genome Res. 2007 Dec;17(12):1919-31. (PMID: 17989251) ; Genome Biol. 2002;3(12):RESEARCH0080. (PMID: 12537569) ; Genes Dev. 2003 Apr 15;17(8):991-1008. (PMID: 12672692) ; Annu Rev Genomics Hum Genet. 2003;4:89-117. (PMID: 14527298) ; Science. 2000 Mar 24;287(5461):2222-4. (PMID: 10731138) ; Genes Dev. 2007 Feb 15;21(4):385-90. (PMID: 17322397) ; Genome Biol. 2005;6(12):R104. (PMID: 16356267) ; Nat Genet. 2006 Jun;38 Suppl:S2-7. (PMID: 16736019) ; Nature. 2007 Jun 14;447(7146):799-816. (PMID: 17571346) ; Mol Cell. 2007 Jul 6;27(1):91-105. (PMID: 17612493) ; Nature. 2007 Jul 12;448(7150):151-6. (PMID: 17625558) ; Genetics. 1999 Sep;153(1):135-77. (PMID: 10471706) ; Annu Rev Biochem. 2002;71:817-46. (PMID: 12045112) ; Genetics. 2007 Nov;177(3):1377-94. (PMID: 18039873) ; EMBO Rep. 2001 Aug;2(8):697-702. (PMID: 11493597) ; PLoS Genet. 2007 Nov;3(11):e197. (PMID: 17997610) ; Nucleic Acids Res. 2005 Jan 1;33(Database issue):D141-6. (PMID: 15608165) ; J Virol. 1995 Dec;69(12):7593-600. (PMID: 7494266) ; RNA. 2005 Jul;11(7):1017-29. (PMID: 15987813) ; Nature. 2007 Jul 5;448(7149):83-6. (PMID: 17589500) ; Nucleic Acids Res. 2003 May 15;31(10):2495-507. (PMID: 12736298) ; Cell. 2005 Sep 23;122(6):947-56. (PMID: 16153702) ; Nature. 2003 May 15;423(6937):241-54. (PMID: 12748633) ; Genome Res. 2005 Aug;15(8):1034-50. (PMID: 16024819) ; Development. 2005 Jun;132(12):2743-58. (PMID: 15901661) ; Nucleic Acids Res. 2006 Jan 1;34(Database issue):D158-62. (PMID: 16381836) ; Dev Biol. 2005 Feb 15;278(2):576-86. (PMID: 15680371) ; Genome Res. 2005 Dec;15(12):1777-86. (PMID: 16339376) ; Nature. 2003 Aug 14;424(6950):788-93. (PMID: 12917688) ; Development. 2004 May;131(10):2387-94. (PMID: 15128669) ; Cell. 2006 Apr 21;125(2):301-13. (PMID: 16630818) ; Genes Dev. 2007 Feb 15;21(4):436-49. (PMID: 17322403) ; Nucleic Acids Res. 2005 Dec 02;33(21):e185. (PMID: 16326860) ; Genes Dev. 1998 Apr 1;12(7):956-67. (PMID: 9531534) ; Nat Genet. 2006 Jun;38 Suppl:S8-13. (PMID: 16736023) ; Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4795-800. (PMID: 15778292) ; Nat Genet. 2000 May;25(1):25-9. (PMID: 10802651) ; Genome Biol. 2003;4(7):R42. (PMID: 12844358) ; Science. 2000 Mar 24;287(5461):2216-8. (PMID: 10731135) ; Mol Cell Biol. 1995 Apr;15(4):2219-30. (PMID: 7891716) ; Nat Genet. 2002 Apr;30(4):363-4. (PMID: 11896390) ; Nat Protoc. 2006;1(2):624-32. (PMID: 17406289) ; Cell. 2002 Apr 19;109(2):137-40. (PMID: 12007398) ; Nucleic Acids Res. 2004 Dec 07;32(21):6284-91. (PMID: 15585662) ; Annu Rev Genomics Hum Genet. 2004;5:15-56. (PMID: 15485342) ; Biotechnology (N Y). 1990 Aug;8(8):759-60. (PMID: 1366903) ; RNA. 2006 Feb;12(2):192-7. (PMID: 16373484) ; PLoS Comput Biol. 2006 May;2(5):e53. (PMID: 16733548) ; Science. 2001 Aug 10;293(5532):1083-5. (PMID: 11498577) ; Nat Rev Genet. 2003 Apr;4(4):251-62. (PMID: 12671656) ; Genes Dev. 1994 Nov 15;8(22):2729-42. (PMID: 7958929) ; Nat Rev Genet. 2005 Mar;6(3):179-93. (PMID: 15738962) ; Nature. 2007 Nov 8;450(7167):203-18. (PMID: 17994087) ; Science. 2003 May 30;300(5624):1439-43. (PMID: 12775843) ; Mol Cell Biol. 2002 Jun;22(11):3565-76. (PMID: 11997494) ; Genome Res. 2001 Jul;11(7):1143-4. (PMID: 11435394) ; Dev Cell. 2006 Jun;10(6):797-807. (PMID: 16740481) ; Science. 2003 Jul 4;301(5629):71-6. (PMID: 12775844) ; Genome Biol. 2002;3(12):RESEARCH0086. (PMID: 12537575) ; Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1566-71. (PMID: 15668397) ; Cell. 2007 Jul 13;130(1):89-100. (PMID: 17599402) ; Genome Res. 2007 Dec;17(12):1850-64. (PMID: 17989254) ; PLoS Biol. 2005 Jan;3(1):e10. (PMID: 15660152) ; Nucleic Acids Res. 2007;35(9):3016-31. (PMID: 17439971) ; Genome Res. 2003 Jan;13(1):64-72. (PMID: 12529307) ; Nat Genet. 2007 Jun;39(6):730-2. (PMID: 17529977) ; Genome Res. 2005 Jan;15(1):1-18. (PMID: 15632085) ; Annu Rev Biochem. 2003;72:449-79. (PMID: 12651739) ; Genome Res. 2005 Dec;15(12):1661-7. (PMID: 16339363) ; PLoS Comput Biol. 2006 Apr;2(4):e33. (PMID: 16628248) ; Nat Rev Genet. 2005 Jan;6(1):9-23. (PMID: 15630418) ; Genome Res. 2005 Jul;15(7):901-13. (PMID: 15965027) ; Genome Res. 2002 Jun;12(6):996-1006. (PMID: 12045153) ; Genome Res. 2007 Dec;17(12):1823-36. (PMID: 17989253) ; Genes Dev. 1995 Nov 1;9(21):2609-22. (PMID: 7590239) ; Cell. 2005 Jan 14;120(1):15-20. (PMID: 15652477) ; Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4487-92. (PMID: 16537387) ; Annu Rev Genet. 1996;30:507-28. (PMID: 8982463) ; Mol Biol Evol. 1995 Nov;12(6):1002-11. (PMID: 8524036) ; Cell. 2003 Dec 26;115(7):787-98. (PMID: 14697198) ; Science. 2002 Aug 9;297(5583):1007-13. (PMID: 12114529) ; Genome Biol. 2003;5(1):R3. (PMID: 14709175) ; Science. 2003 Mar 7;299(5612):1540. (PMID: 12624257) ; Genome Res. 2007 Dec;17(12):1865-79. (PMID: 17989255) ; Science. 2000 Mar 24;287(5461):2185-95. (PMID: 10731132) ; Trends Microbiol. 2007 Feb;15(2):78-86. (PMID: 17187982) ; Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. (PMID: 15665081) ; Genome Res. 2003 Jun;13(6A):1190-202. (PMID: 12743024) ; PLoS One. 2007 Nov 07;2(11):e1115. (PMID: 17973026) ; Genome Res. 2003 Dec;13(12):2507-18. (PMID: 14656959) ; PLoS Comput Biol. 2005 Dec;1(7):e69. (PMID: 16355253) ; Science. 2003 Aug 8;301(5634):832-6. (PMID: 12907802) ; Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80. (PMID: 14681412) ; Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):757-62. (PMID: 11805330) ; Genetics. 2007 Nov;177(3):1429-37. (PMID: 18039876) ; Gene. 2003 Jul 17;312:17-25. (PMID: 12909337) ; Cell. 2005 Jan 14;120(1):21-4. (PMID: 15652478) ; Cell. 2005 Dec 16;123(6):1133-46. (PMID: 16337999) ; Trends Ecol Evol. 2000 Dec 1;15(12):496-503. (PMID: 11114436) ; Cell. 2004 Jan 23;116(2):281-97. (PMID: 14744438) ; Nature. 2005 Mar 17;434(7031):338-45. (PMID: 15735639) ; J Virol. 1990 Mar;64(3):1021-7. (PMID: 2304136) ; Nucleic Acids Res. 2007 Jan;35(Database issue):D486-91. (PMID: 17099233) ; Development. 1991 Feb;111(2):601-9. (PMID: 1893877) ; Mol Cell Biol. 1998 Mar;18(3):1553-61. (PMID: 9488472) ; PLoS Biol. 2003 Dec;1(3):E60. (PMID: 14691535) ; Cancer Res. 2006 Dec 15;66(24):11590-3. (PMID: 17178851) ; Science. 2005 Dec 16;310(5755):1817-21. (PMID: 16308420) ; Science. 2003 Feb 28;299(5611):1391-4. (PMID: 12610304) ; Genome Res. 2002 Jan;12(1):198-202. (PMID: 11779845) ; Dev Cell. 2005 Oct;9(4):449-62. (PMID: 16198288) ; EMBO J. 1997 Apr 15;16(8):2023-31. (PMID: 9155028) ; Genome Res. 2000 Apr;10(4):483-501. (PMID: 10779488) ; PLoS Biol. 2005 Apr;3(4):e93. (PMID: 15757364) ; Nat Genet. 2006 Oct;38(10):1151-8. (PMID: 16951679) Grant Information: R01 GM067031-04 United States GM NIGMS NIH HHS; R01 HG004037 United States HG NHGRI NIH HHS; R01 HG002779-06 United States HG NHGRI NIH HHS; R01 HG004037-01A1 United States HG NHGRI NIH HHS; R01 GM067031 United States GM NIGMS NIH HHS; R01 HG002779-05 United States HG NHGRI NIH HHS; R01 GM083300 United States GM NIGMS NIH HHS Substance Nomenclature: 0 (Drosophila Proteins) ; 0 (MicroRNAs) ; 0 (Untranslated Regions) Entry Date(s): Date Created: 20071113 Date Completed: 20080103 Latest Revision: 20211020 Update Code: 20240513 PubMed Central ID: PMC2474711

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Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.