RNA-DNA interactome of a prokaryotic cell uncovered by proximity ligation

We used one of the RNA-DNA proximity ligation approaches, RedC, for the analysis of an RNA-DNA interactome of microbial cells. We assess the distribution of main RNA types — mRNA, tRNA and rRNA — along the genomes of E.coli, B.subtilis, and thermophilic archaea T. adornatum. The RedC experimental protocol for mapping RNA-DNA interactions is based on formaldehyde fixation of RNA-protein-DNA complexes in vivo followed by ligation of RNA and DNA fragments present in one nucleoprotein complex via a biotinylated bridge adapter with a subsequent identification of ligated fragments using a paired end sequencing