Fraction-wise RNA-seq of the Salmonella Typhimurium SL1344 cell lysate resolved on a 10-40% glycerol gradient

While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant protein with a wide range of targets, including a new class of ProQ-associated small RNAs, and predicted functions in many cellular pathways. ProQ preferentially associates with highly structured RNAs, filling the so-far vacant niche of a global double-stranded RNA-binding protein and expanding the range of the post-transcriptional regulation in bacteria." This dataset is a representative experiment carried out to characterize sedimentation properties of bacterial transcripts genome-wide. Downstream analysis of their sedimentation profiles enables their biochemical classification and is a prerequisite for identification of global RNA-binding proteins. Overall design: The set includes 20 samples corresponding to gradient fractions numbered from the top to the bottom of the gradient. Each fraction is spiked-in with an artificial RNA to enable normalization.