Publication Date:
2014-03-29
Description:
Animal transcriptomes are dynamic, with each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. Here we have identified new genes, transcripts and proteins using poly(A)+ RNA sequencing from Drosophila melanogaster in cultured cell lines, dissected organ systems and under environmental perturbations. We found that a small set of mostly neural-specific genes has the potential to encode thousands of transcripts each through extensive alternative promoter usage and RNA splicing. The magnitudes of splicing changes are larger between tissues than between developmental stages, and most sex-specific splicing is gonad-specific. Gonads express hundreds of previously unknown coding and long non-coding RNAs (lncRNAs), some of which are antisense to protein-coding genes and produce short regulatory RNAs. Furthermore, previously identified pervasive intergenic transcription occurs primarily within newly identified introns. The fly transcriptome is substantially more complex than previously recognized, with this complexity arising from combinatorial usage of promoters, splice sites and polyadenylation sites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152413/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152413/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, James B -- Boley, Nathan -- Eisman, Robert -- May, Gemma E -- Stoiber, Marcus H -- Duff, Michael O -- Booth, Ben W -- Wen, Jiayu -- Park, Soo -- Suzuki, Ana Maria -- Wan, Kenneth H -- Yu, Charles -- Zhang, Dayu -- Carlson, Joseph W -- Cherbas, Lucy -- Eads, Brian D -- Miller, David -- Mockaitis, Keithanne -- Roberts, Johnny -- Davis, Carrie A -- Frise, Erwin -- Hammonds, Ann S -- Olson, Sara -- Shenker, Sol -- Sturgill, David -- Samsonova, Anastasia A -- Weiszmann, Richard -- Robinson, Garret -- Hernandez, Juan -- Andrews, Justen -- Bickel, Peter J -- Carninci, Piero -- Cherbas, Peter -- Gingeras, Thomas R -- Hoskins, Roger A -- Kaufman, Thomas C -- Lai, Eric C -- Oliver, Brian -- Perrimon, Norbert -- Graveley, Brenton R -- Celniker, Susan E -- 1U01HG007031-01/HG/NHGRI NIH HHS/ -- 5U01HG004695-04/HG/NHGRI NIH HHS/ -- K99 HG006698/HG/NHGRI NIH HHS/ -- P30 CA045508/CA/NCI NIH HHS/ -- R01 GM076655/GM/NIGMS NIH HHS/ -- R01 GM083300/GM/NIGMS NIH HHS/ -- R01 GM097231/GM/NIGMS NIH HHS/ -- RC2-HG005639/HG/NHGRI NIH HHS/ -- U01 HG004271/HG/NHGRI NIH HHS/ -- U01 HG007031/HG/NHGRI NIH HHS/ -- U01-HG004261/HG/NHGRI NIH HHS/ -- U54 HG006944/HG/NHGRI NIH HHS/ -- ZIA DK015600-18/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Aug 28;512(7515):393-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24670639" target="_blank"〉PubMed〈/a〉
Keywords:
Alternative Splicing/genetics
;
Animals
;
Drosophila melanogaster/anatomy & histology/cytology/*genetics
;
Female
;
*Gene Expression Profiling
;
Male
;
Molecular Sequence Annotation
;
Nerve Tissue/metabolism
;
Organ Specificity
;
Poly A/genetics
;
Polyadenylation
;
Promoter Regions, Genetic/genetics
;
RNA, Long Noncoding/genetics
;
RNA, Messenger/genetics/metabolism
;
Sex Characteristics
;
Stress, Physiological/genetics
;
Transcriptome/*genetics
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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