Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly

PLoS Genet. 2022 Jul 6;18(7):e1010277. doi: 10.1371/journal.pgen.1010277. eCollection 2022 Jul.

Abstract

The nucleosome remodeling complexes (CRs) SWI/SNF, RSC, and Ino80C cooperate in evicting or repositioning nucleosomes to produce nucleosome depleted regions (NDRs) at the promoters of many yeast genes induced by amino acid starvation. We analyzed mutants depleted of the catalytic subunits of these CRs for binding of transcriptional activator Gcn4 and recruitment of TATA-binding protein (TBP) during preinitiation complex (PIC) assembly. RSC and Ino80 were found to enhance Gcn4 binding to both UAS elements in NDRs upstream of promoters and to unconventional binding sites within nucleosome-occupied coding sequences; and SWI/SNF contributes to UAS binding when RSC is depleted. All three CRs are actively recruited by Gcn4 to most UAS elements and appear to enhance Gcn4 binding by reducing nucleosome occupancies at the binding motifs, indicating a positive regulatory loop. SWI/SNF acts unexpectedly in WT cells to prevent excessive Gcn4 binding at many UAS elements, indicating a dual mode of action that is modulated by the presence of RSC. RSC and SWI/SNF collaborate to enhance TBP recruitment at Gcn4 target genes, together with Ino80C, in a manner associated with nucleosome eviction at the TBP binding sites. Cooperation among the CRs in TBP recruitment is also evident at the highly transcribed ribosomal protein genes, while RSC and Ino80C act more broadly than SWI/SNF at the majority of other constitutively expressed genes to stimulate this step in PIC assembly. Our findings indicate a complex interplay among the CRs in evicting promoter nucleosomes to regulate activator binding and stimulate PIC assembly.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Basic-Leucine Zipper Transcription Factors / genetics
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Assembly and Disassembly / genetics
  • Nucleosomes* / genetics
  • Nucleosomes* / metabolism
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins* / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Basic-Leucine Zipper Transcription Factors
  • Chromatin
  • GCN4 protein, S cerevisiae
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors

Grants and funding

This work was supported by the Eunice Kennedy Shriver National Institute of Child Health and Human Development, project HD008899-12, of the Intramural Research Program of the National Institutes of Health (AGH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.