Literature DB >> 16574072

Identifying Hfq-binding small RNA targets in Escherichia coli.

Yong Zhang1, Shiwei Sun, Tao Wu, Jie Wang, Changning Liu, Lan Chen, Xiaopeng Zhu, Yi Zhao, Zhihua Zhang, Baochen Shi, Hongchao Lu, Runsheng Chen.   

Abstract

The Hfq-binding small RNAs (sRNAs) have recently drawn much attention as regulators of translation in Escherichia coli. We attempt to identify the targets of this class of sRNAs in genome scale and gain further insight into the complexity of translational regulation induced by Hfq-binding sRNAs. Using a new alignment algorithm, most known negatively regulated targets of Hfq-binding sRNAs were identified. The results also show several interesting aspects of the regulatory function of Hfq-binding sRNAs.

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Year:  2006        PMID: 16574072     DOI: 10.1016/j.bbrc.2006.02.196

Source DB:  PubMed          Journal:  Biochem Biophys Res Commun        ISSN: 0006-291X            Impact factor:   3.575


  10 in total

1.  sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments.

Authors:  Yuan Cao; Jiayao Wu; Qian Liu; Yalin Zhao; Xiaomin Ying; Lei Cha; Ligui Wang; Wuju Li
Journal:  RNA       Date:  2010-09-15       Impact factor: 4.942

2.  Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions.

Authors:  Asaf Peer; Hanah Margalit
Journal:  J Bacteriol       Date:  2011-01-28       Impact factor: 3.490

3.  Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides.

Authors:  Fabian Hia; Yok Hian Chionh; Yan Ling Joy Pang; Michael S DeMott; Megan E McBee; Peter C Dedon
Journal:  Nucleic Acids Res       Date:  2014-12-24       Impact factor: 16.971

4.  Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli.

Authors:  Eric Guisbert; Virgil A Rhodius; Nidhi Ahuja; Emily Witkin; Carol A Gross
Journal:  J Bacteriol       Date:  2006-12-08       Impact factor: 3.490

5.  Positive regulation of fur gene expression via direct interaction of fur in a pathogenic bacterium, Vibrio vulnificus.

Authors:  Hyun-Jung Lee; So Hyun Bang; Kyu-Ho Lee; Soon-Jung Park
Journal:  J Bacteriol       Date:  2007-01-19       Impact factor: 3.490

6.  sRNATarget: a web server for prediction of bacterial sRNA targets.

Authors:  Yuan Cao; Yalin Zhao; Lei Cha; Xiaomin Ying; Ligui Wang; Ningsheng Shao; Wuju Li
Journal:  Bioinformation       Date:  2009-04-29

7.  sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization.

Authors:  Xiaomin Ying; Yuan Cao; Jiayao Wu; Qian Liu; Lei Cha; Wuju Li
Journal:  PLoS One       Date:  2011-07-22       Impact factor: 3.240

8.  Impact of Hfq on global gene expression and virulence in Klebsiella pneumoniae.

Authors:  Ming-Ko Chiang; Min-Chi Lu; Li-Cheng Liu; Ching-Ting Lin; Yi-Chyi Lai
Journal:  PLoS One       Date:  2011-07-14       Impact factor: 3.240

Review 9.  Small RNA-mediated regulation of host-pathogen interactions.

Authors:  Jennifer F Harris; Sofiya Micheva-Viteva; Nan Li; Elizabeth Hong-Geller
Journal:  Virulence       Date:  2013-08-19       Impact factor: 5.882

Review 10.  Predicting sRNAs and their targets in bacteria.

Authors:  Wuju Li; Xiaomin Ying; Qixuan Lu; Linxi Chen
Journal:  Genomics Proteomics Bioinformatics       Date:  2012-10-23       Impact factor: 7.691

  10 in total

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