CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression

Hui Yao,Wenjia Lou,Peter Scacheri,Alina Saiakhova,Douglas F Hannum,Jennifer M Skidmore,Donna M Martin,Stephanie L Bielas,Sophie F Hill,Ricardo D.’Oliveira Albanus,Gilson Sanchez,Yiwen Zhai,Stephen C J Parker,Mats Ljungman

doi:10.1038/s41598-020-74537-4

Abstract

CHARGE syndrome, a rare multiple congenital anomaly condition, is caused by haploinsufficiency of the chromatin remodeling protein gene CHD7 (Chromodomain helicase DNA binding protein 7). Brain abnormalities and intellectual disability are commonly observed in individuals with CHARGE, and neuronal differentiation is reduced in CHARGE patient-derived iPSCs and conditional knockout mouse brains. However, the mechanisms of CHD7 function in nervous system development are not well understood. In this study, we asked whether CHD7 promotes gene transcription in neural progenitor cells via changes in chromatin accessibility. We used Chd7 null embryonic stem cells (ESCs) derived from Chd7 mutant mouse blastocysts as a tool to investigate roles of CHD7 in neuronal and glial differentiation. Loss of Chd7 significantly reduced neuronal and glial differentiation. Sholl analysis showed that loss of Chd7 impaired neuronal complexity and neurite length in differentiated neurons. Genome-wide studies demonstrated that loss of Chd7 leads to modified chromatin accessibility (ATAC-seq) and differential nascent expression (Bru-Seq) of neural-specific genes. These results suggest that CHD7 acts preferentially to alter chromatin accessibility of key genes during the transition of NPCs to neurons to promote differentiation. Our results form a basis for understanding the cell stage-specific roles for CHD7-mediated chromatin remodeling during cell lineage acquisition.

Highlights

CHARGE syndrome, a rare multiple congenital anomaly condition, is caused by haploinsufficiency of the chromatin remodeling protein gene Chromodomain Helicase DNA binding protein 7 (CHD7) (Chromodomain helicase DNA binding protein 7)
Chd[7] is highly expressed in developing neurons in vivo[14]; we hypothesized that CHD7 may play an active role in the differentiation of embryonic stem cells (ESCs) to neural progenitor cells (NPCs) and subsequently to neurons and glia (Fig. 1a)
Neither Chd7+/+ or Chd7Gt/Gt ESCs showed defects in proliferation at passages up to P21 when measured over 6 days in standard ESC culture medium (Fig. 1d)

Summary

Introduction

CHARGE syndrome, a rare multiple congenital anomaly condition, is caused by haploinsufficiency of the chromatin remodeling protein gene CHD7 (Chromodomain helicase DNA binding protein 7). Genome-wide studies demonstrated that loss of Chd[7] leads to modified chromatin accessibility (ATACseq) and differential nascent expression (Bru-Seq) of neural-specific genes. In adult Chd[7] conditional knockout mice, SVZ neural stem/progenitor cells exhibit impaired n eurogenesis[11], and loss of Chd[7] leads to reduced neurogenesis and abnormal dendritic development of newly born neurons in the adult mouse SVZ and S GZ10. Midbrain and spinal cord, neuroepithelial thickness is reduced in E10.5 heterozygous gene trap (Chd7Gt/+) embryos[13] Together, these observations implicate CHD7 in a wide variety of central nervous system and neuron-specific processes. These observations demonstrate that CHD7 promotes neurogenesis and gliogenesis in early embryonic central and peripheral nervous system development

Methods

Results

Conclusion