دورية أكاديمية
أعرض في EDS

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts.

التفاصيل البيبلوغرافية
العنوان: RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts.
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.)
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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
الوصف
تدمد:1362-4962
DOI:10.1093/nar/gkq1223