دورية أكاديمية
أعرض في EDS

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

التفاصيل البيبلوغرافية
العنوان: Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.
المؤلفون: Torarinsson E; Section for Genetics and Bioinformatics, IBVH, Faculty of Life Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark., Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J
المصدر: Genome research [Genome Res] 2008 Feb; Vol. 18 (2), pp. 242-51. Date of Electronic Publication: 2007 Dec 20.
نوع المنشور: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9518021 Publication Model: Print-Electronic Cited Medium: Print ISSN: 1088-9051 (Print) Linking ISSN: 10889051 NLM ISO Abbreviation: Genome Res Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press, c1995-
مواضيع طبية MeSH: Nucleic Acid Conformation*, Computational Biology/*methods , Genomics/*methods , RNA, Untranslated/*genetics , Sequence Analysis/*methods, Base Sequence ; Computational Biology/trends ; Databases, Genetic ; Genomics/trends ; Humans
مستخلص: Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment methods to misalign, or even refuse to align, homologous ncRNAs, consequently obscuring that structural signal. We have used CMfinder, a structure-oriented local alignment tool, to search the ENCODE regions of vertebrate multiple alignments. In agreement with other studies, we find a large number of potential RNA structures in the ENCODE regions. We report 6587 candidate regions with an estimated false-positive rate of 50%. More intriguingly, many of these candidates may be better represented by alignments taking the RNA secondary structure into account than those based on primary sequence alone, often quite dramatically. For example, approximately one-quarter of our predicted motifs show revisions in >50% of their aligned positions. Furthermore, our results are strongly complementary to those discovered by sequence-alignment-based approaches--84% of our candidates are not covered by Washietl et al., increasing the number of ncRNA candidates in the ENCODE region by 32%. In a group of 11 ncRNA candidates that were tested by RT-PCR, 10 were confirmed to be present as RNA transcripts in human tissue, and most show evidence of significant differential expression across tissues. Our results broadly suggest caution in any analysis relying on multiple sequence alignments in less well-conserved regions, clearly support growing appreciation for the biological significance of ncRNAs, and strongly support the argument for considering RNA structure directly in any searches for these elements.
References: BMC Bioinformatics. 2006 Sep 04;7:400. (PMID: 16952317)
Trends Genet. 2006 Apr;22(4):187-93. (PMID: 16499991)
Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4667-72. (PMID: 9539796)
Genome Res. 2007 Jun;17(6):760-74. (PMID: 17567995)
Biochem Biophys Res Commun. 2007 Jun 15;357(4):991-6. (PMID: 17451645)
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4. (PMID: 16381832)
J Biol Chem. 1994 Mar 25;269(12):9352-60. (PMID: 8132674)
BMC Bioinformatics. 2005 Mar 24;6:73. (PMID: 15790387)
J Mol Biol. 2004 Sep 3;342(1):19-30. (PMID: 15313604)
J Neurosci. 1995 Apr;15(4):3075-83. (PMID: 7722646)
Bioinformatics. 2007 Apr 15;23(8):926-32. (PMID: 17324941)
BMC Bioinformatics. 2007 Oct 26;8:417. (PMID: 17963514)
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W135-41. (PMID: 15215366)
Nucleic Acids Res. 2005 Apr 28;33(8):2433-9. (PMID: 15860779)
Genome Res. 2007 Jun;17(6):852-64. (PMID: 17568003)
Nature. 2007 Jun 14;447(7146):799-816. (PMID: 17571346)
Genome Biol. 2006;7 Suppl 1:S4.1-9. (PMID: 16925838)
PLoS Comput Biol. 2006 Jan;2(1):e5. (PMID: 16410828)
Science. 2007 Jun 8;316(5830):1484-8. (PMID: 17510325)
Neuroscience. 2001;108(2):207-15. (PMID: 11734355)
Bioinformatics. 2006 Jul 15;22(14):e197-202. (PMID: 16873472)
Genome Res. 2006 Jul;16(7):885-9. (PMID: 16751343)
Nat Biotechnol. 2005 Nov;23(11):1383-90. (PMID: 16273071)
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11. (PMID: 14681370)
J Biol Chem. 2001 Jul 13;276(28):26374-83. (PMID: 11346658)
BMC Bioinformatics. 2007 Apr 19;8:130. (PMID: 17445273)
J Cell Sci. 2007 Aug 1;120(Pt 15):2498-506. (PMID: 17623775)
Genome Res. 2005 Aug;15(8):1034-50. (PMID: 16024819)
Genome Res. 2004 Apr;14(4):708-15. (PMID: 15060014)
FEBS Lett. 2005 Jul 4;579(17):3849-54. (PMID: 15978578)
BMC Genomics. 2007 Sep 10;8:316. (PMID: 17845718)
Science. 2004 Dec 24;306(5705):2242-6. (PMID: 15539566)
Nucleic Acids Res. 2003 Jan 1;31(1):439-41. (PMID: 12520045)
Genome Res. 2006 Jan;16(1):11-9. (PMID: 16344565)
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15. (PMID: 12824337)
Bioinformatics. 2006 Feb 15;22(4):445-52. (PMID: 16357030)
PLoS Comput Biol. 2007 Jul;3(7):e126. (PMID: 17616982)
Genome Res. 2002 Jun;12(6):996-1006. (PMID: 12045153)
PLoS Comput Biol. 2006 Apr;2(4):e33. (PMID: 16628248)
PLoS Comput Biol. 2007 Apr 13;3(4):e65. (PMID: 17432929)
Gene. 2005 Sep 12;357(2):83-94. (PMID: 16111837)
Science. 2005 May 20;308(5725):1149-54. (PMID: 15790807)
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. (PMID: 15665081)
Nucleic Acids Res. 2007;35(14):4809-19. (PMID: 17621584)
Bioinformatics. 2006 Jan 1;22(1):35-9. (PMID: 16267089)
Nature. 2006 Sep 14;443(7108):167-72. (PMID: 16915236)
PLoS Comput Biol. 2007 Oct;3(10):1896-908. (PMID: 17937495)
المشرفين على المادة: 0 (RNA, Untranslated)
تواريخ الأحداث: Date Created: 20071222 Date Completed: 20080423 Latest Revision: 20220316
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC2203622
DOI: 10.1101/gr.6887408
PMID: 18096747
قاعدة البيانات: MEDLINE
الوصف
تدمد:1088-9051
DOI:10.1101/gr.6887408