The encounter of RNA polymerase with stable nucleosomes facilitates transitions in elongation coupled processes.. The encounter of RNA polymerase with stable nucleosomes facilitates transitions in elongation coupled processes.

The process of transcription elongation involves the translocation of an RNA polymerase coupled to sequential elongation of the nascent RNA transcript. Different factors associate with polymerases at the 5’ and 3’ ends of genes and act to ensure elongation occurs in a regulated fashion coupled to the reassembly of organised chromatin. Here we find that transition points for association with a subset of 5’ and 3’ elongation factors often coincides with the location of the most stable nucleosome within a coding region. The stability of these nucleosomes correlates with the presence of DNA sequences favourable for nucleosome formation. Factors influenced by the locations of these nucleosomes include the termination factor PcfII, methylation of histone H3 at residues K36 and K79. In addition a transition in the way that chromatin remodelling enzymes act to organise chromatin occurs at these nucleosomes. Mutations to histone H4 that reduce the nucleosomal barrier to transcription shifts the transition points for many of these factors downstream. These observations indicate a role for chromatin structure in regulating elongation coupled processes.