Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

Abstract

How the chromatin regulatory landscape in the inner cell mass cells is established from differentially packaged sperm and egg genomes during preimplantation development is unknown. Here, we develop a low-input DNase I sequencing (liDNase-seq) method that allows us to generate maps of DNase I-hypersensitive site (DHS) of mouse preimplantation embryos from 1-cell to morula stage. The DHS landscape is progressively established with a drastic increase at the 8-cell stage. Paternal chromatin accessibility is quickly reprogrammed after fertilization to the level similar to maternal chromatin, while imprinted genes exhibit allelic accessibility bias. We demonstrate that transcription factor Nfya contributes to zygotic genome activation and DHS formation at the 2-cell stage and that Oct4 contributes to the DHSs gained at the 8-cell stage. Our study reveals the dynamic chromatin regulatory landscape during early development and identifies key transcription factors important for DHS establishment in mammalian embryos.

CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer

“…Mechanistically, different experiments in the mammalian system suggested that the CCAAT box and NF-Y serve a "pioneering" role in gene activation, namely, that this TF is able to penetrate "hostile" chromatin territories and set the stage for binding of other TFs required for full gene activation (Fleming et al, 2013;Sherwood et al, 2014;Oldfield et al, 2014). This hypothesis is further supported by recent experiments with mouse zygotes, where NF-Y appears to be the major TF opening chromatin as early as the two-and four-cell stages (Lu et al, 2016).…”

“…However, we provide biochemical evidence that the trimer is a much more efficient DNA binding entity in vitro, and a physiological one in vivo, as the matrices of the HFD mutants resemble those of co. The HFD importance could be linked to their histonelike nature, as they might play the known "pioneer" role of NF-Y in penetration of chromatin territories devoid of positive histone marks (Fleming et al, 2013;Oldfield et al, 2014;Sherwood et al, 2014;Lu et al, 2016).…”

Genetic mosaics and time-lapse imaging identify functions of histone H3.3 residues in mouse oocytes and embryos

“…In recent years, application of high-throughput sequencing technologies in oocytes (Stewart et al, 2015) and early embryos (Dahl et al, 2016;Liu et al, 2016;Lu et al, 2016;Wu et al, 2016) has improved our understanding of the epigenetic landscape and has led to greater insight into molecular mechanisms of chromatin reorganization. The combination of these sequencing technologies and our new techniques will facilitate exploration of regulatory networks to identify key chromatin modulators and determine their importance in the oocyte-to-embryo transition.…”

Technologies of High-Throughput Tissue-Specific Gene Expression Profiling

“…Microarrays are capable of producing large amounts of gene expression data based on hybridization of mRNA output to probes [6] . Meanwhile, approaches based on next-generation sequencing technology (SGS) such as serial analysis of gene expression (SAGE) [7] , RNA-Seq [8] , chromatin immunoprecipitation sequencing (ChIP-Seq) [9,10] , DNase I hypersensitive sites sequencing (DNase-Seq) [11,12] and assay for transposase-accessible chromatin with high throughput sequencing (ATAC-Seq) [13] can profile gene expression in the form of sequence read, which is feasible to quantification and automated analysis. In this way, gene expression patterns and regulatory networks can be characterized systematically.…”