Uncoupling transcription from covalent histone modification

PLoS Genet. 2014 Apr 10;10(4):e1004202. doi: 10.1371/journal.pgen.1004202. eCollection 2014 Apr.

Abstract

It is widely accepted that transcriptional regulation of eukaryotic genes is intimately coupled to covalent modifications of the underlying chromatin template, and in certain cases the functional consequences of these modifications have been characterized. Here we present evidence that gene activation in the silent heterochromatin of the yeast Saccharomyces cerevisiae can occur in the context of little, if any, covalent histone modification. Using a SIR-regulated heat shock-inducible transgene, hsp82-2001, and a natural drug-inducible subtelomeric gene, YFR057w, as models we demonstrate that substantial transcriptional induction (>200-fold) can occur in the context of restricted histone loss and negligible levels of H3K4 trimethylation, H3K36 trimethylation and H3K79 dimethylation, modifications commonly linked to transcription initiation and elongation. Heterochromatic gene activation can also occur with minimal H3 and H4 lysine acetylation and without replacement of H2A with the transcription-linked variant H2A.Z. Importantly, absence of histone modification does not stem from reduced transcriptional output, since hsp82-ΔTATA, a euchromatic promoter mutant lacking a TATA box and with threefold lower induced transcription than heterochromatic hsp82-2001, is strongly hyperacetylated in response to heat shock. Consistent with negligible H3K79 dimethylation, dot1Δ cells lacking H3K79 methylase activity show unimpeded occupancy of RNA polymerase II within activated heterochromatic promoter and coding regions. Our results indicate that large increases in transcription can be observed in the virtual absence of histone modifications often thought necessary for gene activation.

Publication types

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

MeSH terms

  • Acetylation
  • HSP90 Heat-Shock Proteins / genetics
  • Heterochromatin / genetics
  • Histones / genetics*
  • Lysine / genetics
  • Methylation
  • Nucleosomes / genetics
  • Promoter Regions, Genetic / genetics
  • RNA Polymerase II / genetics
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins / genetics
  • Transcription, Genetic / genetics*
  • Transcriptional Activation / genetics*

Substances

  • HSP82 protein, S cerevisiae
  • HSP90 Heat-Shock Proteins
  • Heterochromatin
  • Histones
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • RNA Polymerase II
  • Lysine

Grants and funding

This work was funded by National Science Foundation (NSF.gov) grants MCB-0747227, MCB-1025025, and MCB-1158516. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.