Dynamic transitions in RNA polymerase II density profiles during transcription termination

Abstract

Eukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAP II) through a cycle composed of three main phases: initiation, elongation and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAP II molecules is higher at the 3' end relative to the gene body. Here we show that this view is biased due to averaging density profiles for "metagene" analysis. Indeed, the majority of genes exhibit little if any detectable accumulation of polymerases during transcription termination. Compared to genes with no enrichment, genes that accumulate RNAP II at the 3' end are shorter, contain more frequently the canonical polyA signal, and have higher levels of expression. In 1 to 4% of actively transcribing genes, the RNAP II enriched at the 3' end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAP II accumulation and nucleosome organization suggesting that the presence of nucleosomes after the polyA site induces pausing of polymerases, leading to their accumulation. Yet, we further observe that nucleosome occupancy at the 3' end of genes is dynamic and correlates with RNAP II density. Thus, accumulation of polymerases paused at the termination region may act as a barrier for nucleosome organization, as recently proposed for RNAP II stalled at the promoter. Our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.