Constraint of gene expression by chromatin remodelling protein CHD4 facilitates lineage specification

Abstract

Chromatin remodelling proteins are essential for different aspects of metazoan biology, yet functional details of why these proteins are important are lacking. Although it is possible to describe the biochemistry of how they remodel chromatin, their chromatin-binding profiles in cell lines, and gene expression changes upon loss of a given protein, in very few cases can this easily translate into an understanding of how the function of that protein actually influences a developmental process. Here, we investigate how the chromatin remodelling protein CHD4 facilitates the first lineage decision in mammalian embryogenesis. Embryos lacking CHD4 can form a morphologically normal early blastocyst, but are unable to successfully complete the first lineage decision and form functional trophectoderm (TE). In the absence of a functional TE, Chd4 mutant blastocysts do not implant and are hence not viable. By measuring transcript levels in single cells from early embryos, we show that CHD4 influences the frequency at which unspecified cells in preimplantation stage embryos express lineage markers prior to the execution of this first lineage decision. In the absence of CHD4, this frequency is increased in 16-cell embryos, and by the blastocyst stage cells fail to properly adopt a TE gene expression programme. We propose that CHD4 allows cells to undertake lineage commitment in vivo by modulating the frequency with which lineage-specification genes are expressed. This provides novel insight into both how lineage decisions are made in mammalian cells, and how a chromatin remodelling protein functions to facilitate lineage commitment.

Novel key roles for structural maintenance of chromosome flexible domain containing 1 (Smchd1) during preimplantation mouse development

“…The upregulation of such lineage‐related marker genes at the morula stage following Smchd1 knockdown, including some that are upregulated later in development of the TE lineage and placenta, is reminiscent of other studies (e.g., CHD4 ablation) in which multiple lineage‐appropriate marker genes display precocious and/or continued expression leading to indeterminate lineage specification (O’Shaughnessy‐Kirwan et al, ). Deficiency or Smchd1 may thus lead to precocious and/or prolonged expression of certain lineage‐related genes, resulting in the establishment of intermediate cell states with a mixed marker gene expression profile and inadequate specialization, compromising long‐term viability.…”

EcR recruits dMi-2 and increases efficiency of dMi-2-mediated remodelling to constrain transcription of hormone-regulated genes

“…The increase in chromatin accessibility in dMi-2 depleted cells correlates with increased transcription arguing that dMi-2-mediated chromatin alterations help to limit the dynamic range of gene transcription. This is reminiscent of the role of CHD4 in the early mouse embryo where it limits the frequency of expression of lineage-specific genes14. Furthermore, dMi-2 extensively colocalizes with active RNA polymerase II on polytene chromosomes, suggesting that it constrains the transcription of many genes4042.…”

“…They are central subunits of Nucleosome Remodelling and Deacetylation (NuRD) complexes and play important roles in development9101112. NuRD and CHD4 are indispensable for proper blastocyst and embryonic stem cell differentiation1314. Moreover, CHD4 and dMi-2 are important for cell fate determination in several developmental lineages where they cooperate with transcription factors to establish differentiation-specific transcription programmes by generating chromatin environments conducive to gene repression or activation151617.…”

ATP-dependent chromatin remodeling during mammalian development

“…Regulation of ICM and TE gene expression by CHD1 is thought to be mediated by its activation of high-mobility group protein transcription factor HMGPI (Suzuki et al, 2015). CHD4 also has a redundant role during the differentiation of ICM and TE as it facilitates the expression of appropriate genes and restricts expression of inappropriate genes in the ICM and TE (O'Shaughnessy- Kirwan et al, 2015). In ESCs and epiblast cells, CHD1 maintains optimal transcriptional output by engaging with RNA polymerases I and II to regulate both mRNA and rRNA transcription (Guzman-Ayala et al, 2015).…”