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Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor.

Vockenhuber, Michael-Paul ; Sharma, Cynthia M. ; Statt, Michaela G. ; Schmidt, Denis ; Xu, Zhenjiang ; Dietrich, Sascha ; Liesegang, Heiko ; Mathews, David H. ; Suess, Beatrix (2011):
Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor.
In: RNA biology, 8 (3), pp. 468-77. ISSN 1555-8584,
[Article]

Abstract

Streptomyces coelicolor is considered the model organism among Gram positive, GC rich bacteria. Its genome has been sequenced but little is known about the occurrence and distribution of small non-coding RNAs in this biotechnologically relevant organism. Using deep sequencing we analyzed the transcriptome at the end of exponential growth, which corresponds to the onset of secondary metabolism. We mapped 193 transcriptional start sites of mRNA genes and identified putative new and alternative open reading frames. We identified 63 non-coding RNAs including 29 cis encoded antisense RNAs, and confirmed expression for 11, most of them being growth-phase dependent. A comparison between the sequencing results and bioinformatic sRNA predictions using Dynalign and RNAz revealed only a small overlap between the different approaches.

Item Type: Article
Erschienen: 2011
Creators: Vockenhuber, Michael-Paul ; Sharma, Cynthia M. ; Statt, Michaela G. ; Schmidt, Denis ; Xu, Zhenjiang ; Dietrich, Sascha ; Liesegang, Heiko ; Mathews, David H. ; Suess, Beatrix
Title: Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor.
Language: English
Abstract:

Streptomyces coelicolor is considered the model organism among Gram positive, GC rich bacteria. Its genome has been sequenced but little is known about the occurrence and distribution of small non-coding RNAs in this biotechnologically relevant organism. Using deep sequencing we analyzed the transcriptome at the end of exponential growth, which corresponds to the onset of secondary metabolism. We mapped 193 transcriptional start sites of mRNA genes and identified putative new and alternative open reading frames. We identified 63 non-coding RNAs including 29 cis encoded antisense RNAs, and confirmed expression for 11, most of them being growth-phase dependent. A comparison between the sequencing results and bioinformatic sRNA predictions using Dynalign and RNAz revealed only a small overlap between the different approaches.

Journal or Publication Title: RNA biology
Journal volume: 8
Number: 3
Divisions: 10 Department of Biology > Synthetic Genetic Circuits
10 Department of Biology
Date Deposited: 22 Feb 2012 10:18
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