Bilusic Ivana, Popitsch Niko, Rescheneder Philipp, Schroeder Renée, Lybecker Meghan
Department of Biochemistry and Cell Biology; Max F Perutz Laboratories; University of Vienna; Vienna, Austria.
Center for Integrative Bioinformatics Vienna; Max F Perutz Laboratories; Medical University of Vienna; University of Vienna; Vienna, Austria.
RNA Biol. 2014;11(5):641-54. doi: 10.4161/rna.29299. Epub 2014 Jun 12.
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 Hfq-binding RNAs identified are regulated by Hfq.
Hfq是细菌在适应不断变化的环境条件过程中基因表达的全局调节因子。其主要功能是促进调控性小RNA（sRNA）与其靶标mRNA之间的RNA-RNA相互作用。此前，我们证明Hfq在体外能结合许多反义RNA（asRNA），并推测Hfq可能通过asRNA在基因表达调控中发挥作用。为了更详细地研究大肠杆菌中与Hfq结合的转录组，我们在体内对与Hfq结合的RNA进行了免疫共沉淀和深度测序。我们检测到许多新的与Hfq结合的sRNA，并观察到近300种mRNA与Hfq结合。其中，有几种已知是sRNA的靶标。我们鉴定出25种新的RNA，它们从蛋白质编码区域内转录而来，并将其命名为基因内RNA（intraRNA）。此外，67种asRNA与Hfq进行了免疫共沉淀，表明Hfq在体内能结合反义转录本。Northern印迹分析证实了深度测序结果，并表明所鉴定的许多新的与Hfq结合的RNA受Hfq调控。
