A tissue-specific landscape of sense/antisense transcription in the mouse intestine

BMC Genomics

Research Article

Markus B Schilhabel¹  Matthias Barann¹  Robert Häsler¹  Ulrich C Klostermeier¹  Olga Gavrilova¹  Andre Franke¹  Benjamin Kreck¹  Philip Rosenstiel¹  Michael Wittig¹  Christian Sina²  Stefan Schreiber² 

[1] Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany;Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany;Department of General Internal Medicine, Christian-Albrechts-University, Kiel, Germany;

关键词: Annotate Gene;    Transcript Isoforms;    Template Switch;    RefSeq Transcript;    Small Intestine Tissue;   

DOI  :  10.1186/1471-2164-12-305

 received in 2010-10-28, accepted in 2011-06-10,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe intestinal mucosa is characterized by complex metabolic and immunological processes driven highly dynamic gene expression programs. With the advent of next generation sequencing and its utilization for the analysis of the RNA sequence space, the level of detail on the global architecture of the transcriptome reached a new order of magnitude compared to microarrays.ResultsWe report the ultra-deep characterization of the polyadenylated transcriptome in two closely related, yet distinct regions of the mouse intestinal tract (small intestine and colon). We assessed tissue-specific transcriptomal architecture and the presence of novel transcriptionally active regions (nTARs). In the first step, signatures of 20,541 NCBI RefSeq transcripts could be identified in the intestine (74.1% of annotated genes), thereof 16,742 are common in both tissues. Although the majority of reads could be linked to annotated genes, 27,543 nTARs not consistent with current gene annotations in RefSeq or ENSEMBL were identified. By use of a second independent strand-specific RNA-Seq protocol, 20,966 of these nTARs were confirmed, most of them in vicinity of known genes. We further categorized our findings by their relative adjacency to described exonic elements and investigated regional differences of novel transcribed elements in small intestine and colon.ConclusionsThe current study demonstrates the complexity of an archetypal mammalian intestinal mRNA transcriptome in high resolution and identifies novel transcriptionally active regions at strand-specific, single base resolution. Our analysis for the first time shows a strand-specific comparative picture of nTARs in two tissues and represents a resource for further investigating the transcriptional processes that contribute to tissue identity.

【 授权许可】

Unknown   
© Klostermeier et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.