Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals

George E Gentsch,Nick D L Owens,Thomas Spruce,James C Smith

doi:10.1038/s41467-019-12263-w

Abstract

Embryonic development yields many different cell types in response to just a few families of inductive signals. The property of signal-receiving cells that determines how they respond to inductive signals is known as competence, and it differs in different cell types. Here, we explore the ways in which maternal factors modify chromatin to specify initial competence in the frog Xenopus tropicalis. We identify early-engaged regulatory DNA sequences, and infer from them critical activators of the zygotic genome. Of these, we show that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 determines competence for germ layer formation by extensively remodelling compacted chromatin before the onset of inductive signalling. This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.

Highlights

Embryonic development yields many different cell types in response to just a few families of inductive signals
In an effort to understand how early chromatin dynamics influence the recruitment of signal mediators to the genome (Fig. 1b), we first identified ∼27,000 pCRMs from the 32-cell to the late gastrula stage by mapping focal RNA polymerase II (RNAPII) depositions on a genome-wide scale by means of Chromatin immunoprecipitation (ChIP)-Seq (Fig. 1c and Supplementary Data 1 and 2)
The number of RNAPII-engaged (RNAPII+) pCRMs increased from ∼650 at the 32-cell stage to >10,000 at the 1024-cell and later developmental stages (Supplementary Fig. 1a)

Summary

Introduction

Embryonic development yields many different cell types in response to just a few families of inductive signals. We show that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox[3] determines competence for germ layer formation by extensively remodelling compacted chromatin before the onset of inductive signalling This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. A more plausible and more frequent way in which tissuespecific competence might arise is through the recruitment of these signal mediators to different gene regulatory sites, which in turn would drive the specification of different cell types. Cell lineage determinants such as sequence-specific transcription factors (TFs) may play a role in determining competence. Our understanding of how chromatin interprets inductive signals is especially important because the generation of therapeutically relevant cells like insulinproducing pancreatic β-cells frequently relies on the deployment of signal modulators at different stages of cell differentiation in vitro[6]

Methods

Results

Conclusion