Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler

Abstract

Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS). This "fragile" nucleosome (FN) promoter architecture relies on the combined action of the essential RSC (Remodels Structure of Chromatin) nucleosome remodeler and pioneer transcription factors (PTFs). FNs are associated with genes whose expression is high, coupled to cell growth, and characterized by low cell-to-cell variability (noise), suggesting that they may promote these features. Recent studies in metazoans suggest that the presence of dynamic nucleosomes upstream of the TSS at highly expressed genes may be conserved throughout evolution.

The RSC complex remodels nucleosomes in transcribed coding sequences and promotes transcription inSaccharomyces cerevisiae

“…We therefore favor the idea that RSC occupancy at Pro-targets might remove nucleosomes from NDRs of Pro-targets. Consistent with this idea, both the +1_Nuc and -1_Nuc are shown to be enriched for RSC genome-wide (Brahma and Henikoff, 2019;Krietenstein et al, 2016;Kubik et al, 2017).…”

“…RSC plays important roles in maintaining NDRs near promoter regions (Krietenstein et al, 2016;Kubik et al, 2015;Kubik et al, 2017;Musladin et al, 2014), and has been implicated in promoting transcription (Carey et al, 2006;Ganguli et al, 2014;Ocampo et al, 2019;Rawal et al, 2018;Spain et al, 2014;Spain and Govind, 2011). The ability to slide nucleosome to widen NDRs appears to enhance PIC assembly and the TSS selection (Klein-Brill et al, 2019;Kubik et al, 2019).…”

“…As such, Pol II occupancies, genome-wide, strongly correlated with RSC occupancies in CDSs (r =0.86; R 2 = 0.71) and only weakly in promoters (r =0.26; R 2 = 0.01) ( Figure 2E). Many recent studies have shown that RSC is important for maintaining NDRs genome-wide (Brahma and Henikoff, 2019;Ganguli et al, 2014;Hartley and Madhani, 2009b;Kubik et al, 2015;Kubik et al, 2017;Kubik et al, 2018). However, low correlation between RSC occupancies in promoters would suggest that keeping NDRs free of nucleosomes might be a general function of RSC and not necessarily linked to high-level of transcription.…”

Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function

“…During transcription for example, different types of transcription factors (TFs) are continuously interacting with chromatin in a variety of ways. Each brings different functions into play: opening or closing chromatin, creating loops, modifying or evicting nucleosomes, recruiting cofactors and, in the case of activation, ultimately causing formation of a pre-initiation complex that includes RNA polymerase (Hahn & Young, 2011;de Laat & Dekker, 2012;Spitz & Furlong, 2012;Struhl & Segal, 2013;Friedman & Rando, 2015;Kubik et al, 2017;Lai & Pugh, 2017;Woo et al, 2017;Cramer, 2019;Brahma & Henikoff, 2020). TFs are therefore constantly moving off and onto different loci, probing for appropriate interactions, also under conditions of steady-state transcriptional output (Hammar et al, 2014).…”

“…Monitoring the time-dependent decay of protein-DNA binding across all genomic locations results in determination of off-rates, also in the form of locus-specific residence times. The method DIVORSEQ (Determining In Vivo Off-Rates by SEQuencing), is applied here to Abf1, a Saccharomyces cerevisiae general regulatory factor akin to chromatin pioneering TFs in mammals (Zaret & Carroll, 2011;Kubik et al, 2017). Alongside roles in shaping chromatin architecture (Venditti et al, 1994;Lascaris et al, 2000;Yarragudi et al, 2004;Hartley & Madhani, 2009), several different functions have been attributed to Abf1, including involvement in transcription regulation (Gailus-Durner et al, 1996), telomere binding (Enomoto et al, 1994;Pryde & Louis, 1999), DNA replication (Marahrens & Stillman, 1992), DNA repair (Reed et al, 1999) and RNA polymerase II roadblock termination (Roy et al, 2016;Candelli et al, 2018).…”