Heavy Transcription of Yeast Genes Correlates With Differential Loss of Histone H2B Relative to H4 and Queued RNA Polymerases

Nucleic Acids Res. 2014 Nov 10;42(20):12512-22. doi: 10.1093/nar/gku1013. Epub 2014 Oct 27.

Abstract

Eukaryotic chromatin is composed of nucleosomes, which contain nearly two coils of DNA wrapped around a central histone octamer. The octamer contains an H3-H4 tetramer and two H2A-H2B dimers. Gene activation is associated with chromatin disruption: a wider nucleosome-depleted region (NDR) at the promoter and reduced nucleosome occupancy over the coding region. Here, we examine the nature of disrupted chromatin after induction, using MNase-seq to map nucleosomes and subnucleosomes, and a refined high-resolution ChIP-seq method to map H4, H2B and RNA polymerase II (Pol II) genome-wide. Over coding regions, induced genes show a differential loss of H2B relative to H4, which correlates with Pol II density and the appearance of subnucleosomes. After induction, Pol II is surprisingly low at the promoter, but accumulates on the gene and downstream of the termination site, implying that dissociation is very slow. Thus, induction-dependent chromatin disruption reflects both eviction of H2A-H2B dimers and the presence of queued Pol II elongation complexes. We propose that slow Pol II dissociation after transcription is a major factor in chromatin disruption and that it may be of critical importance in gene regulation.

Publication types

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

MeSH terms

  • Arginase / biosynthesis
  • Arginase / genetics
  • Gene Expression Regulation, Fungal*
  • Histones / metabolism*
  • Nucleosomes / metabolism
  • RNA Polymerase II / metabolism*
  • Saccharomyces cerevisiae Proteins / biosynthesis
  • Saccharomyces cerevisiae Proteins / genetics
  • Transcriptional Activation*

Substances

  • Histones
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • RNA Polymerase II
  • ARG1 protein, S cerevisiae
  • Arginase

Associated data

  • GEO/GSE54524