Pervasive Targeting of Nascent Transcripts by Hfq

• Published in: Cell reports (Cambridge) 2018-05, Vol.23 (5), p.1543-1552
• Main Authors: Kambara, Tracy K., Ramsey, Kathryn M., Dove, Simon L.
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - genetics; Bacterial Proteins - metabolism; ChIP; Crc; gene regulation; Hfq; Host Factor 1 Protein - genetics; Host Factor 1 Protein - metabolism; Pseudomonas aeruginosa; Pseudomonas aeruginosa - genetics; Pseudomonas aeruginosa - metabolism; Repressor Proteins - genetics; Repressor Proteins - metabolism; RNA, Bacterial - biosynthesis; RNA, Bacterial - genetics; sRNA; Transcription, Genetic - physiology
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2018.03.134

Hfq is an RNA chaperone and an important post-transcriptional regulator in bacteria. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq), we show that Hfq associates with hundreds of different regions of the Pseudomonas aeruginosa chromosome. These associations are abolished when transcription is inhibited, indicating that they reflect Hfq binding to transcripts during their synthesis. Analogous ChIP-seq analyses with the post-transcriptional regulator Crc reveal that it associates with many of the same nascent transcripts as Hfq, an activity we show is Hfq dependent. Our findings indicate that Hfq binds many transcripts co-transcriptionally in P. aeruginosa, often in concert with Crc, and uncover direct regulatory targets of these proteins. They also highlight a general approach for studying the interactions of RNA-binding proteins with nascent transcripts in bacteria. The binding of post-transcriptional regulators to nascent mRNAs may represent a prevalent means of controlling translation in bacteria where transcription and translation are coupled. [Display omitted] •ChIPPAR-seq identifies nascent transcripts that associate with RNA-binding proteins•RNA chaperone Hfq associates with hundreds of nascent transcripts in P. aeruginosa•Accessory factor Crc associates with many of the same nascent transcripts as Hfq•The post-transcriptional regulators Hfq and Crc frequently act co-transcriptionally Using a modified ChIP-seq procedure, Kambara et al. find that the post-transcriptional regulator Hfq associates with hundreds of nascent transcripts in Pseudomonas aeruginosa. These findings suggest that Hfq exerts its regulatory effects on many target transcripts as soon as they emerge from RNA polymerase.