HEB associates with PRC2 and SMAD2/3 to regulate developmental fates

Abstract

In embryonic stem cells, extracellular signals are required to derepress developmental promoters to drive lineage specification, but the proteins involved in connecting extrinsic cues to relaxation of chromatin remain unknown. We demonstrate that the helix-loop-helix (HLH) protein, HEB, directly associates with the Polycomb repressive complex 2 (PRC2) at a subset of developmental promoters, including at genes involved in mesoderm and endoderm specification and at the Hox and Fox gene families. While we show that depletion of HEB does not affect mouse ESCs, it does cause premature differentiation after exposure to Activin. Further, we find that HEB deposition at developmental promoters is dependent upon PRC2 and independent of Nodal, whereas HEB association with SMAD2/3 elements is dependent of Nodal, but independent of PRC2. We suggest that HEB is a fundamental link between Nodal signalling, the derepression of a specific class of poised promoters during differentiation, and lineage specification in mouse ESCs.

Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo

“…These results confirm that Nodal signalling is required to induce Eomes expression during the transition from pluripotency to lineage commitment. Additionally, when we compared Smad2/3 ChIP-seq datasets in ESC and DE cultures (Yoon et al, 2015), we found evidence for Smad2/3 occupancy at the VPE specifically in DE cultures (Fig. 4B).…”

“…Error bars represent s.e.m. (B) ChIP-seq of Smad2/3 in definitive endoderm (DE) reveals binding to the VPE (Yoon et al, 2015), overlapping a predicted and conserved binding site for Foxh1, identified with JASPAR at >80% confidence (Mathelier et al, 2016). (C) Whole-mount in situ hybridisation of Eomes mRNA in control and Foxh1 -null embryos.…”

“…(B) Enlargement of the region of the Eomes compartment showing highest association with the promoter, from chr9: 118,252,500-118,405,500. Open chromatin was generated using ATAC-seq in ESC and DE ( n =3), with the addition of MACS2 called peaks annotated beneath each ATAC-seq track and Smad2/3 ChIP-seq in ESCs (blue) and DE (green) (Yoon et al, 2015). Regions of chromatin accessibility unique to ESCs (−73 kb) and those associated with Smad2/3 occupancy in DE (−93 kb, −45 kb, −38 kb, PSE_a, VPE and +9 kb) are indicated.…”

Activin/Smad2-induced Histone H3 Lys-27 Trimethylation (H3K27me3) Reduction Is Crucial to Initiate Mesendoderm Differentiation of Human Embryonic Stem Cells

“…The helix-loop-helix protein HEB was reported to be a functional link between Nodal/Smad signaling and the derepression of the PRC2 complex-repressed developmental genes in mouse ESCs (17). The mechanism for direct regulatory networks between activin/Smad2 and PRC2 is still unclear and needs further exploration.…”

“…These observations demonstrate an essential role of PRC2 in early mouse development. Accumulating evidence also suggests that PRC2 plays an important role in ESC differentiation toward mesoderm and endoderm lineages (8,17,18).…”