期刊
RNA BIOLOGY
卷 11, 期 5, 页码 641-654出版社
TAYLOR & FRANCIS INC
DOI: 10.4161/rna.29299
关键词
Hfq; Hfq co-immunoprecipitation; Hfq aptamers; sRNA; asRNAs; igRNAs; intraRNAs
资金
- Austrian Science Fund FWF [I538, F4301]
- University of Vienna
- Austrian Science Fund (FWF) [I538] Funding Source: Austrian Science Fund (FWF)
- Austrian Science Fund (FWF) [I 538] Funding Source: researchfish
Hfq is a global regulator of gene expression in bacteria undergoing adaptation to changing environmental conditions. Its major function is to promote RNA-RNA interactions between regulatory small RNAs (sRNAs) and their target mRNAs. Previously, we demonstrated that Hfq binds many antisense RNAs (asRNAs) in vitro and hypothesized that Hfq may play a role in regulating gene expression via asRNAs. To investigate the E. coli Hfq-binding transcriptome in more detail, we co-immunoprecipitated and deep-sequenced RNAs bound to Hfq in vivo. We detected many new Hfq-binding sRNAs and observed that almost 300 mRNAs bind to Hfq. Among these, several are known to be sRNA targets. We identified 25 novel RNAs, which are transcribed from within protein coding regions and named them intragenic RNAs (intraRNAs). Furthermore, 67 asRNAs were co-immunoprecipitated with Hfq, demonstrating that Hfq binds antisense transcripts in vivo. Northern blot analyses confirmed the deep sequencing results and demonstrated that many of the novel Hfqbinding RNAs identified are regulated by Hfq.
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