Terminator-dependent facilitated recycling of RNA polymerase III couples transcriptional activation and chromatin remodeling in vivo

Abstract

Termination is a crucial step in generating the functional transcriptome of a cell. The short genes transcribed by RNA polymerase (pol) III are mostly found in the highly transcribed genomic loci. The mechanism responsible for their high transcription rate in vivo is not yet established. Transcription terminator-dependent facilitated recycling of pol III on naked DNA templates is reported to increase transcriptional output in vitro. We found that apart from defining the 3’-end of transcript, the transcription terminator is essential for achieving high-level chromatin transcription by pol III in vitro and in vivo. Using terminator-deficientSNR6gene templates or a recycling deficient pol III mutant, we show that the TFIIIC-dependent transcriptional activation of chromatin is a process with three closely linked components, viz. anti-repression to naked DNA levels with TFIIIC binding, TFIIIC-dependent chromatin remodeling for better accessibility of the sequence elements and terminator-directed full transcriptional activation. Measurement of pol III occupancy on different gene regions demonstrated a direct link between the high transcription rate and the terminator dependent recycling of pol III in vivo. This novel regulatory mechanism may be generally applicable to the highly transcribed genes in any cell and even for cancer management wherein pol III transcription is found highly elevated.

ProA and ProB repeat sequences shape genome organization, and enhancers open domains

“…For Pol.III, unlike Pol.II, the presence of a nucleosome not only does not prevent transcription initiation, but in fact promotes it: (i) TFIIIC, which scaffolds Pol.III pre-initiation complex assembly, can bind nucleosome-embedded DNA; (ii) Transcription by Pol. III can operate without eviction of the nucleosome; (iii) In vitro reconstitution experiments show that transcription activation by TFIIIC is much more efficient if a nucleosome is present (262). Note that some highly transcribed Pol.III-dependent genes, such as tRNA genes in the yeast S.cerevisiae (229), do however exhibit nucleosome eviction, but remarkably, nucleosomes on either side of those genes are H2AZ-depleted and strongly positioned; this is required for efficient transcription (263), emphasizing that nucleosome positioning is important for Pol.III-mediated transcription.…”