Association of RNAs with Bacillus subtilis Hfq
Figure 4
Hfq enrichment of signal-responsive, cis-acting regulatory RNAs.
(A) An individual representative example is shown for Hfq-mediated enrichment of the leader region of a purine-sensing riboswitch [68]. The ligand-binding aptamer region is denoted by a shaded box to indicate the overlap between this sensory domain and the RNA sequences found to associate with Hfq. Previously measured transcription start site (TSS) mapping data (shown in black; [33]) is also shown in the figure as a means of denoting the 5′ end of the leader region. (B) An example is shown for Hfq-mediated enrichment of the leader region of a magnesium-sensing riboswitch [69]. The magnesium-sensing domain [70] is denoted by a shaded box. (C) Representative data are shown for Hfq-mediated enrichment of the leader region of a protein-responsive cis-acting regulatory RNA. Specifically, the bglP operon has been previously postulated to be subjected to multiple layers of regulatory control, including by transcription initiation factors, a protein-responsive leader region, and a small, putative antisense RNA that appears to base pair with the ribosome binding site. Although the latter antisense RNA was modestly enriched by coIP with Hfq, the protein-binding aptamer region was highly enriched by Hfq in this study (shown in purple). (D) Other leader regions that associated with Hfq are listed herein. More details on these RNAs are included in Table S3. Throughout the figure, the y-axis shows the volume of cDNA reads as a function of genomic position (x-axis) as determined by Illumina-based sequencing of Hfq-associated RNA molecules. Data shown in gray correspond to the negative control reaction (coimmunoprecipitation of Hfq that lacked an epitope tag). Data shown in black correspond to a prior transcription start site (TSS) mapping study and are included in this figure as a means of denoting the 5′ ends [33].