Hfq-associated RNAs in the human pathogen Clostridium difficile

We performed RNA immunoprecipitation deep sequencing (RIP-Seq) analysis on Hfq-associated RNAs in the human pathogen Clostridium difficile. A large set of interacting noncoding RNAs and mRNAs was identified. We found that Hfq associated with antisense RNAs, antitoxin transcripts, and mRNA leaders. Possible interactions between the identified partners (sRNAs and/or mRNA targets) were postulated through computational target predictions. Based on this data, we confirm an Hfq-dependent regulation in late sporulation by validating the association of Hfq, RCd1, and some of its mRNA targets.We performed RNA immunoprecipitation high-throughput sequencing (RIP-Seq) analysis to identify Hfq-associated RNAs in Clostridium difficile. Our work revealed a large set of Hfq-interacting ncRNAs and mRNAs. We found that Hfq associates with different classes of RNAs in C. difficile, including mRNA leaders and coding regions, known regulatory RNAs and potential new ncRNAs. Among previously identified noncoding RNAs, in addition to trans-encoded RNAs, a number of cis-antisense RNAs including antitoxins from all recently identified type I toxin-antitoxin modules, numerous riboswitches and CRISPR RNAs have been enriched in Hfq-associated samples constituting new categories of Hfq ligands. Possible interactions between the identified partners including ncRNA-mRNA and ncRNA-ncRNA pairing were postulated through computational target predictions. Detailed investigation of one of Hfq-associated ncRNAs, RCd1, suggests that this RNA contributes to the control of late stages of sporulation in C. difficile. Altogether, these data provide essential molecular basis for further studies on post-transcriptional regulatory network in this emerging enteropathogen.