Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP

PLoS One. 2019 Nov 25;14(11):e0225801. doi: 10.1371/journal.pone.0225801. eCollection 2019.

Abstract

Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin-related biological processes. The method, however, requires thousands of cells and has therefore limited applications in situations where cell numbers are limited. Here we describe a novel method called Restriction Assisted Tagmentation Chromatin Immunoprecipitation (RAT-ChIP) that enables global histone modification profiling from as few as 100 cells. The method is simple, cost-effective and takes a single day to complete. We demonstrate the sensitivity of the method by deriving the first genome-wide maps of histone H3K4me3 and H3K27me3 modifications of inner cell mass and trophectoderm of bovine blastocyst stage embryos.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Blastocyst / cytology
  • Blastocyst / metabolism
  • Blastocyst Inner Cell Mass / metabolism*
  • Cattle
  • Cell Line
  • Chromatin / chemistry
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation*
  • Fertilization in Vitro
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Histones / genetics
  • Histones / metabolism*
  • Humans
  • Oocytes / cytology
  • Protein Processing, Post-Translational
  • Sequence Analysis, DNA
  • Trophoblasts / metabolism*

Substances

  • Chromatin
  • Histones

Grants and funding

This research was supported by Estonian Research Council (personal research grant PUT1177) to TO; by Estonian Ministry of Education and Research (grant IUT34-16), Enterprise Estonia (grant EU48695) and EU-FP7 Marie Curie Industry-Academia Partnerships and Pathways (IAPP, grant SARM, EU324509) to AS; by Horizon 2020 innovation programme (WIDENLIFE, 692065) to AS and AK; by Horizon 2020 Twinning project 692299 SEARMET, Estonian Ministry of Education and Research (grant IUT 8-1) to ÜJ and by the EU ERDF through the Estonian Centre of Excellence in Genomics and Translational Medicine (project No. 2014-2020.4.01.15-0012) and by the Estonian Ministry of Education and Research (institutional grant IUT34-11) and by the European Union through the European Regional Development Fund (project No. 2014-2020.4.01.16-0125) to RA. Authors wish to thank the Sequencing core of Estonian Biocentre, Estonian Genome Center Core Facility and the High Performance Computing Center of University of Tartu. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.