title: Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation.
abstract: 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.
authors.affiliation: Department of Biochemistry and Cell Biology; Max F Perutz Laboratories; University of Vienna; Vienna, Austria.
authors.forename: Ivana
authors.initials: I
authors.lastname: Bilusic
authors.affiliation: Center for Integrative Bioinformatics Vienna; Max F Perutz Laboratories; Medical University of Vienna; University of Vienna; Vienna, Austria.
authors.forename: Niko
authors.initials: N
authors.lastname: Popitsch
authors.affiliation: Center for Integrative Bioinformatics Vienna; Max F Perutz Laboratories; Medical University of Vienna; University of Vienna; Vienna, Austria.
authors.forename: Philipp
authors.initials: P
authors.lastname: Rescheneder
authors.affiliation: Department of Biochemistry and Cell Biology; Max F Perutz Laboratories; University of Vienna; Vienna, Austria.
authors.forename: Renée
authors.initials: R
authors.lastname: Schroeder
authors.affiliation: Department of Biochemistry and Cell Biology; Max F Perutz Laboratories; University of Vienna; Vienna, Austria.
authors.forename: Meghan
authors.initials: M
authors.lastname: Lybecker
mesh_terms: D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D035001:Host Factor 1 Protein / Q000378:metabolism*; D016366:Open Reading Frames; D011485:Protein Binding; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D035001:Host Factor 1 Protein; D016372:RNA, Antisense; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D012343:RNA, Transfer
keywords: Hfq; Hfq aptamers; Hfq co-immunoprecipitation; asRNAs; igRNAs; intraRNAs; sRNA