Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing.

Genome Biology
Anna WetterbomLucia Cavelier

Abstract

We profile the chimpanzee transcriptome by using deep sequencing of cDNA from brain and liver, aiming to quantify expression of known genes and to identify novel transcribed regions. Using stringent criteria for transcription, we identify 12,843 expressed genes, with a majority being found in both tissues. We further identify 9,826 novel transcribed regions that are not overlapping with annotated exons, mRNAs or ESTs. Over 80% of the novel transcribed regions map within or in the vicinity of known genes, and by combining sequencing data with de novo splice predictions we predict several of the novel transcribed regions to be new exons or 3' UTRs. For approximately 350 novel transcribed regions, the corresponding DNA sequence is absent in the human reference genome. The presence of novel transcribed regions in five genes and in one intergenic region is further validated with RT-PCR. Finally, we describe and experimentally validate a putative novel multi-exon gene that belongs to the ATP-cassette transporter gene family. This gene does not appear to be functional in human since one exon is absent from the human genome. In addition to novel exons and UTRs, novel transcribed regions may also stem from different types of noncoding t...Continue Reading

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Citations

Jan 31, 2012·Bioinformatics·Daniel C JonesMichael G Katze
May 26, 2011·BMC Developmental Biology·Liselotte VesterlundJuha Kere
Sep 16, 2011·Genome Biology·Eric J Vallender
Jan 5, 2011·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Genevieve Konopka
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Sep 24, 2014·Journal of Bioinformatics and Computational Biology·Harshal InamdarRajendra Joshi
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Mar 6, 2016·Science China. Life Sciences·Yuhui ZhaoSongnian Hu
Feb 17, 2017·BMC Genomics·Aroa Suárez-VegaJuan José Arranz

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Datasets Mentioned

BETA
ERA000160

Methods Mentioned

BETA
RNA-Seq
cDNA
PCR

Software Mentioned

liftOver
SplitSeek Genome Browser
DAVID
SplitSeek
UCSC Genome Browser
liftOver Genome Browser
Biosystems
Applied
RepeatMasker Genome Browser
SOLiD

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