The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5' structure element

In this study we report here on a detailed characterization of the standby site in <i>tisB</i> mRNA. 30S subunits bind to a single-stranded region and a 5'- stem loop structure, as shown by fluorescence anisotropy experiments and footprint mapping by CLIP experiments. <br>The data presented in figshare includes raw and processed RNA reads obtained from our in vitro CLIP experiment. Briefly, purified tisB mRNA was incubated with sub-stoichiometric concentrations of either purified 30S subunits (carrying S1-3xFLAG) or S1-3xFLAG only, followed by UV-crosslinking (250 mJ/cm2). 30S, S1 and cross-linked RNAs were isolated by immuno-precipitation using Anti-FLAG coupled magnetic beads. RNA footprints were generated on the beads with benzonase. Proteins were digested with proteinase K, and, after labeling with radioactive gamma-ATP, labeled RNA footprints (25-50 nt) were gel-purified. Eluted RNAs were converted into cDNA using the CATS RNA-Seq kit v2 (diagenode) and sequenced on an Illumina Miseq device. Reads were then aligned either to the tisB sequence or the 16S rRNA sequence (as control). <br>The files available comprised: - The raw data from the 30S and S1 CLIP experiments (Romilly_30S.fa and Romilly_S1.fa) - Bam/bai files of reads mapped to the tisB mRNA or the 16S rRNA, from the 30S and S1 pulldown assay (30S_tisB.bam/bai, 30S_16S.bam.bai, S1_tisB.bam/bai, S1_16S.bam/bai) - The sequence file containing the tisB sequence and 16S rRNA, respectively (tisB_sequence.fa, 16S_sequence.fa) - A gff files containing the postions of the CDS and the standby site for the tisB sequence (tisB_annotation.gff) - Files with bowtie 2 summary and stats for each of the processing step (Bowtie2 sumary, stats.30S.tabular, stats.S1.tabular, stats.30Svs16SrRNA.tabular, stats.S1vs16SrRNA.tabular)<br> The figure representing the data in the paper was generated using the visualization tool IGV 2.3.68<br> For more information on data processing, please refer to the paper SI, or contact [e-mail] or [e-mail].