A high-resolution protein architecture of the budding yeast genome

Nature. 2021 Apr;592(7853):309-314. doi: 10.1038/s41586-021-03314-8. Epub 2021 Mar 10.


The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is not well defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP-exo/seq)1,2 to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex. Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI-SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs engaged with their cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Coenzymes / metabolism
  • Fungal Proteins / genetics*
  • Fungal Proteins / metabolism*
  • Genome, Fungal / genetics*
  • Multiprotein Complexes / genetics*
  • Multiprotein Complexes / metabolism
  • Promoter Regions, Genetic
  • RNA Polymerase I / metabolism
  • RNA Polymerase II / metabolism
  • RNA Polymerase III / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism*
  • TATA-Box Binding Protein / genetics
  • TATA-Box Binding Protein / metabolism
  • Transcription Factor TFIIB / genetics
  • Transcription Factor TFIIB / metabolism
  • Transcription Factor TFIID
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism


  • Coenzymes
  • Fungal Proteins
  • Multiprotein Complexes
  • TATA-Box Binding Protein
  • Transcription Factor TFIIB
  • Transcription Factor TFIID
  • Transcription Factors
  • RNA Polymerase II
  • RNA Polymerase I
  • RNA Polymerase III