Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1

Elife. 2016 Dec 6;5:e18919. doi: 10.7554/eLife.18919.

Abstract

Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel. Screening of a barcoded yeast knock-out collection for regulators of histone H3K79 methylation by Dot1 identified all known regulators as well as novel players and processes. These include histone deposition, homologous recombination, and adenosine kinase, which influences the methionine cycle. Gcn5, the acetyltransferase within the SAGA complex, was found to regulate histone methylation and H2B ubiquitination. The concept of Epi-ID is widely applicable and can be readily applied to other chromatin features.

Keywords: DNA repair; Dot1; H3K79 methylation; S. cerevisiae; SAGA; adenosine kinase; chromosomes; genes; histone modifications.

MeSH terms

  • Chromatin / chemistry*
  • Chromatin Immunoprecipitation
  • DNA, Fungal / chemistry
  • DNA, Fungal / genetics
  • DNA, Fungal / metabolism*
  • Gene Expression Regulation, Fungal*
  • Genetic Testing
  • Genetics, Microbial / methods
  • Histone-Lysine N-Methyltransferase / metabolism*
  • Histones / metabolism*
  • Methylation
  • Molecular Biology / methods
  • Nuclear Proteins / metabolism*
  • Protein Processing, Post-Translational*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Sequence Analysis, DNA

Substances

  • Chromatin
  • DNA, Fungal
  • Histones
  • Nuclear Proteins
  • Saccharomyces cerevisiae Proteins
  • Dot1 protein, S cerevisiae
  • Histone-Lysine N-Methyltransferase

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.