RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Mycobacterium tuberculosis
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 Mycobacterium smegmatis, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. It is currently unknown if Ms1 homolog (MTS2823) in M. tuberculosis also binds to RNAP core. We sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor sigma A and total RNA isolated from the lysate (input sample). We expect that putative Ms1 or 6S RNA homologs are enriched in RNA polymerase or sigma A sample compared to the input.