Global analysis of small RNA and mRNA targets of Hfq

被引:413
作者
Zhang, AX
Wassarman, KM
Rosenow, C
Tjaden, BC
Storz, G [1 ]
Gottesman, S
机构
[1] Natl Inst Child Hlth & Dev, Cell Biol & Metab Branch, Bethesda, MD 20892 USA
[2] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA
[3] Affymetrix, Santa Clara, CA 95051 USA
[4] Univ Washington, Dept Comp Sci, Seattle, WA 98195 USA
[5] NCI, Mol Biol Lab, Bethesda, MD 20892 USA
关键词
D O I
10.1046/j.1365-2958.2003.03734.x
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Hfq, a bacterial member of the Sm family of RNA-binding proteins, is required for the action of many small regulatory RNAs that act by basepairing with target mRNAs. Hfq binds this family of small RNAs efficiently. We have used co-immunoprecipitation with Hfq and direct detection of the bound RNAs on genomic microarrays to identify members of this small RNA family. This approach was extremely sensitive; even Hfq-binding small RNAs expressed at low levels were readily detected. At least 15 of 46 known small RNAs in E. coli interact with Hfq. In addition, high signals in other intergenic regions suggested up to 20 previously unidentified small RNAs bind Hfq; five were confirmed by Northern analysis. Strong signals within genes and operons also were detected, some of which correspond to known Hfq targets. Within the argX-hisR-leuT-proM operon, Hfq appears to compete with RNase E and modulate RNA processing and degradation. Thus Hfq immunoprecipitation followed by microarray analysis is a highly effective method for detecting a major class of small RNAs as well as identifying new Hfq functions.
引用
收藏
页码:1111 / 1124
页数:14
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