دورية أكاديمية
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts.
العنوان: | RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. |
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المؤلفون: | Sorber K; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA., Dimon MT, DeRisi JL |
المصدر: | Nucleic acids research [Nucleic Acids Res] 2011 May; Vol. 39 (9), pp. 3820-35. Date of Electronic Publication: 2011 Jan 17. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
اللغة: | English |
بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE |
أسماء مطبوعة: | Publication: 1992- : Oxford : Oxford University Press Original Publication: London, Information Retrieval ltd. |
مواضيع طبية MeSH: | Alternative Splicing* , RNA Splice Sites*, Plasmodium falciparum/*genetics , RNA, Antisense/*metabolism, Algorithms ; Genome, Protozoan ; Introns ; Plasmodium falciparum/metabolism ; Protozoan Proteins/chemistry ; RNA-Binding Proteins/chemistry ; Sequence Analysis, RNA |
مستخلص: | Over 50% of genes in Plasmodium falciparum, the deadliest human malaria parasite, contain predicted introns, yet experimental characterization of splicing in this organism remains incomplete. We present here a transcriptome-wide characterization of intraerythrocytic splicing events, as captured by RNA-Seq data from four timepoints of a single highly synchronous culture. Gene model-independent analysis of these data in conjunction with publically available RNA-Seq data with HMMSplicer, an in-house developed splice site detection algorithm, revealed a total of 977 new 5' GU-AG 3' and 5 new 5' GC-AG 3' junctions absent from gene models and ESTs (11% increase to the current annotation). In addition, 310 alternative splicing events were detected in 254 (4.5%) genes, most of which truncate open reading frames. Splicing events antisense to gene models were also detected, revealing complex transcriptional arrangements within the parasite's transcriptome. Interestingly, antisense introns overlap sense introns more than would be expected by chance, perhaps indicating a functional relationship between overlapping transcripts or an inherent organizational property of the transcriptome. Independent experimental validation confirmed over 30 new antisense and alternative junctions. Thus, this largest assemblage of new and alternative splicing events to date in Plasmodium falciparum provides a more precise, dynamic view of the parasite's transcriptome. (© The Author(s) 2011. Published by Oxford University Press.) |
References: | Mol Cell Biol. 2008 Oct;28(19):6033-43. (PMID: 18644864) Science. 2005 Sep 2;309(5740):1564-6. (PMID: 16141073) RNA. 2004 Jun;10(6):929-41. (PMID: 15146077) Nucleic Acids Res. 2008 May;36(9):3001-10. (PMID: 18390578) Mol Biochem Parasitol. 2005 Sep;143(1):100-10. (PMID: 16026866) Genome Res. 2004 Jun;14(6):1188-90. (PMID: 15173120) Int J Parasitol. 2008 Dec;38(14):1625-37. (PMID: 18590734) Genome Res. 2002 Oct;12(10):1599-610. (PMID: 12368253) J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712) RNA. 2001 Nov;7(11):1543-53. (PMID: 11720284) Parasitol Int. 2009 Jun;58(2):196-9. (PMID: 19268714) Genome Biol. 2009;10(3):R25. (PMID: 19261174) Nucleic Acids Res. 2007;35(1):125-31. (PMID: 17158149) Biochem J. 2009 Jan 1;417(1):15-27. (PMID: 19061484) Nucleic Acids Res. 2005 Oct 04;33(17):5533-43. (PMID: 16204454) J Biol Chem. 1991 Apr 15;266(11):7148-54. (PMID: 1707880) Arch Biochem Biophys. 2008 Oct 15;478(2):143-53. (PMID: 18722339) RNA. 2010 Mar;16(3):516-28. (PMID: 20089683) Genome Biol. 2007;8(7):R134. (PMID: 17612404) Cell. 1986 Apr 11;45(1):81-93. (PMID: 3513966) Nucleic Acids Res. 2006 Jul 18;34(12):3465-75. (PMID: 16849434) Science. 2003 Sep 12;301(5639):1503-8. (PMID: 12893887) Nature. 2008 Apr 17;452(7189):846-50. (PMID: 18322460) Nucleic Acids Res. 2001 Jan 1;29(1):37-40. (PMID: 11125043) Cell. 1996 Mar 8;84(5):801-11. (PMID: 8625417) Mol Microbiol. 2010 Apr;76(1):12-24. (PMID: 20141604) Cell. 1991 Sep 20;66(6):1257-68. (PMID: 1840507) Nucleic Acids Res. 2000 Nov 1;28(21):4364-75. (PMID: 11058137) PCR Methods Appl. 1991 Aug;1(1):17-24. (PMID: 1842916) Mol Biochem Parasitol. 2005 Dec;144(2):149-58. (PMID: 16183147) Nat Rev Mol Cell Biol. 2009 Sep;10(9):637-43. (PMID: 19638999) Nature. 2008 Jun 26;453(7199):1239-43. (PMID: 18488015) Curr Opin Cell Biol. 1993 Dec;5(6):1006-14. (PMID: 8129938) Nucleic Acids Res. 2010 Jan;38(2):608-17. (PMID: 19864253) Nat Struct Mol Biol. 2010 Mar;17(3):306-12. (PMID: 20139984) Retrovirology. 2006 Feb 03;3:10. (PMID: 16457729) Curr Opin Cell Biol. 2005 Jun;17(3):316-25. (PMID: 15901503) Bioessays. 1993 Sep;15(9):595-603. (PMID: 8240312) Nature. 2002 Oct 3;419(6906):498-511. (PMID: 12368864) RNA. 2005 Apr;11(4):365-70. (PMID: 15703443) Nat Biotechnol. 2006 Apr;24(4):423-5. (PMID: 16601727) Genome Res. 2003 Mar;13(3):443-54. (PMID: 12618375) Genome Biol. 2005;6(6):R51. (PMID: 15960803) Nucleic Acids Res. 2003 Feb 1;31(3):974-80. (PMID: 12560493) Bioinformatics. 2009 May 1;25(9):1105-11. (PMID: 19289445) Nucleic Acids Res. 2001 Jan 1;29(1):66-9. (PMID: 11125051) PLoS One. 2008 May 28;3(5):e2287. (PMID: 18509478) PLoS One. 2008;3(10):e3495. (PMID: 18941527) Genome Res. 2002 Apr;12(4):656-64. (PMID: 11932250) Nucleic Acids Res. 2007 Jan;35(Database issue):D431-8. (PMID: 17151081) RNA. 2004 Feb;10(2):210-20. (PMID: 14730020) Bioinformatics. 2008 Mar 1;24(5):597-605. (PMID: 18187439) PLoS One. 2010 Nov 08;5(11):e13875. (PMID: 21079731) Nucleic Acids Res. 2000 Aug 15;28(16):3003-10. (PMID: 10931913) RNA. 2007 Nov;13(11):1923-39. (PMID: 17901154) J Biol Chem. 2003 Jun 13;278(24):22014-22. (PMID: 12668669) Biochem J. 2000 Apr 1;347 Pt 1:255-63. (PMID: 10727426) BMC Genomics. 2007 Jul 27;8:255. (PMID: 17662120) PLoS Biol. 2003 Oct;1(1):E5. (PMID: 12929205) BMC Genomics. 2009 May 19;10:235. (PMID: 19454033) Bioinformatics. 2008 Feb 1;24(3):319-24. (PMID: 18042555) Hum Mol Genet. 2002 Feb 15;11(4):451-64. (PMID: 11854178) Genomics. 2006 Jul;88(1):127-31. (PMID: 16457984) Cell. 1996 Nov 1;87(3):405-13. (PMID: 8898194) Nature. 2010 May 6;465(7294):53-9. (PMID: 20445623) Mol Biochem Parasitol. 2004 Jul;136(1):35-42. (PMID: 15138065) |
معلومات مُعتمدة: | United States Howard Hughes Medical Institute |
المشرفين على المادة: | 0 (Protozoan Proteins) 0 (RNA Splice Sites) 0 (RNA, Antisense) 0 (RNA-Binding Proteins) |
تواريخ الأحداث: | Date Created: 20110120 Date Completed: 20110801 Latest Revision: 20211020 |
رمز التحديث: | 20221213 |
مُعرف محوري في PubMed: | PMC3089446 |
DOI: | 10.1093/nar/gkq1223 |
PMID: | 21245033 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1362-4962 |
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DOI: | 10.1093/nar/gkq1223 |