RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Corynebacterium glutamicum
6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. In mycobacteria, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. Ms1 has been predicted in many actinobacterial species, except of corynebacteria. To identify RNAs that have a similar function as Ms1 or 6S RNA in Corynebacterium glutamicum, we sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor sigma A. We also sequenced total RNA isolated from the lysate (input sample). We expect that Ms1 or 6S RNA homologs are enriched in RNA polymerase or sigma A samples compared to the inputs. The experiment was performed in exponential and stationary phase of growth.