Genome-wide histone modification profiling of inner cell mass and trophoectoderm of blastocyst stage bovine embryos by novel low input RAT-ChIP

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 such as highly pure cell populations or early developmental stages of mammalian preimplantation embryo where only few hundred cells might be available. Numerous attempts have been made to reduce the number of cells needed for successful ChIP-seq experiment, however, the developed methods are often complex, laborious or not sensitive enough. Here we describe a new simple method called Restrictase Assisted Tagmentation Chromatin Immunoprecipitation (RAT-ChIP) that enables to obtain high quality genome-wide histone modification profiles from as few as 100 cells. The method is simple, cost-effective, takes one day to complete and can potentially be automated. We subsequently use the novel method to derive the first genome-wide maps of histone H3K4me3 and H3K27me3 modifications of inner cell mass (ICM) and trophoectoderm (TE) of bovine blastocyst stage embryos. Examination of histone H3K4me3 and H3K27me3 modifications in K562, H1299 cell-lines and in inner cell mass and trophoectoderm of blastocyst stage bovine embryos