The RSC Complex Localizes to Coding Sequences to Regulate Pol II and Histone Occupancy

Abstract

Summary ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome-wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions.

Coordinated Action of Nap1 and RSC in Disassembly of Tandem Nucleosomes

“…The colocalization of RSC and Nap1 at promoters and coding regions in yeast, as shown by chromatin immunoprecipitation-sequencing, is consistent with our biochemical evidence that they cooperatively modulate nucleosome dynamics (26,(41)(42)(43)(44)(45). Nap1 and RSC associate with actively transcribed genes and promote efficient RNA polymerase II elongation through a nucleosomal template (14,46).…”

“…RSC is recruited to coding regions through its direct interactions with acetylated histones, either through its multiple bromodomains or by binding directly to RNA polymerase II. RSC recruitment to coding regions is required, in many cases, for active transcription (42). The activities we observed for RSC and Nap1 in our studies indicate how these proteins facilitate early stages of transcription elongation but do not address the question of how these factors might be involved in reassembling chromatin on the template following the passage of the transcription complex (42,47).…”

“…RSC recruitment to coding regions is required, in many cases, for active transcription (42). The activities we observed for RSC and Nap1 in our studies indicate how these proteins facilitate early stages of transcription elongation but do not address the question of how these factors might be involved in reassembling chromatin on the template following the passage of the transcription complex (42,47). It is not known which factors promote Nap1 association with promoters and coding regions, but one possibility suggested by our studies is that RSC helps tether Nap1 to these sites, thereby increasing its efficiency in disassembling nucleosomes that are encountered by the transcription complex.…”

Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation

“…SWI/SNF also contributes to nucleosome eviction at heat-shock-induced genes (Shivaswamy and Iyer 2008), but functional redundancy between SWI/SNF and Isw1 in histone eviction at heat-shock promoters involved effects on activator Hsf1 binding (Erkina et al 2010). Depleting the essential catalytic subunit of RSC, Sth1, was found to increase nucleosome occupancy at a subset of 100-200 yeast promoters in the region of the +1 nucleosome (Parnell et al 2008) or NDR (Hartley and Madhani 2009), implicating RSC in nucleosome eviction from promoters; however, the opposite conclusion emerged from a reduction in promoter H3 occupancies evoked by Sth1 depletion for the genes enriched for RSC in promoter regions (Spain et al 2014).…”

A role for histone acetylation in regulating transcription elongation

“…For example, the Snf2 subunit of the Swi-Snf complex contains a bromodomain which has an affinity for H3 acetylated chromatin which has been shown to determine its association with active gene promoters and DNA double-strand break sites [28,29]. The RSC ATP-dependent chromatin remodelling complex also contains bromodomains in the Sth1, Rsc1, Rsc2 and Rsc4 subunits, and is localised in an acetylation-dependent manner to gene coding sequences where it regulates histone and Pol II occupancy [16,30]. Interestingly, the tandem bromodomains within the RSC4 subunit have been biochemically shown to preferentially bind H4K14ac [31].…”