RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription

Abstract

The directionality of gene promoters—the ratio of protein-coding over divergent noncoding transcription—is highly variable. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription relative to protein-coding transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus to a decrease in promoter directionality. We find that RSC has a modest effect on nucleosome positioning upstream in promoters at the sites of divergent transcription. These promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 DNA-binding protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription relative to coding direction transcription. We propose that any DNA-binding factor, when stably associated with cryptic transcription start sites, forms a barrier which represses divergent transcription, thereby promoting promoter directionality.

Size fractionated NET‐Seq reveals a conserved architecture of transcription units around yeast genes

“…Reb1 is a transcription factor that is proposed to act as a roadblock to terminate the transcription of RNAPII (Candelli et al, 2018; Colin et al, 2014) to create a nucleosome‐depleted region by recruiting chromatin remodellers to promoters (Hartley & Madhani, 2009; Krietenstein et al, 2016; Rossi et al, 2021) and to limit divergent noncoding transcription (Challal et al, 2018; Wu et al, 2022). To investigate how Reb1 functions in the context of divergent noncoding:coding transcription units, a previously created hybrid divergent transcription unit, made by inserting the p TEF ‐ KanMX ‐t TEF cassette into the HMS2 locus so that the two protein‐coding genes flank pairs of Reb1 and Rap1 binding sites in the TEF promoter, was subject to mutational analysis (Figure 7 and Figure ) (Nguyen et al, 2014).…”