CHD3 regulates BMP signalling response during cranial neural crest cell specification

CHD3 is a component of the NuRD chromatin remodeller. Mutations in CHD3 cause Snijders Blok-Campeau Syndrome, a neurodevelopmental disorder marked by intellectual disability and craniofacial abnormalities. To unveil the role of CHD3 in craniofacial development, we differentiated CHD3-null induced pluripotent stem cells (iPSCs) into cranial neural crest cells (CNCC). We found that CHD3 expression is low in iPSCs and neuroectoderm, but it is upregulated during CNCC specification, where CHD3-containing NuRD opens the chromatin at BMP-responsive enhancers, to allow binding of DLX5 and other factors. CHD3 loss leads to repression of BMP target genes and imbalance between BMP and Wnt signalling, which ultimately results in aberrant mesodermal fate. Consequently, cranial neural crest specification fails, replaced by mesodermal identity, which can be partially rescued by titrating Wnt levels. Our findings highlight a novel role for CHD3 as pivotal regulator of BMP signalling, essential for proper neural crest specification and craniofacial development. Overall design: RNA-seq of CHD3-WT, CHD3-HET-KO and CHD3-KO iPSC lines (3 replicates per line) RNA-seq of CHD3-WT and CHD3-KO cell lines at day 18 of in vitro cranial neural crest cell specification in late maintenance media (at least 2 replicates per line) RNA-seq of CHD3-WT and CHD3-HET-KO cell lines at day 18 of in vitro cranial neural crest cell specification in early maintenance media (3 replicates per line) RNA-seq of CHD3-WT and CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification in early maintenance media (at least 2 replicates per line) ChIP-seq of CHD3 in two CHD3-WT cell lines at day 14 of in vitro cranial neural crest cell specification ChIP-seq of CHD3 in CHD3-WT cell line at day 18 of in vitro cranial neural crest cell specification ChIP-seq of DLX5 in one CHD3-WT cell line and two CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 18 of in vitro cranial neural crest cell specification (2 replicates per line) ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification (2 replicates per line) ATAC-seq of CHD3-WT and CHD3-KO iPSC lines (2 replicates per line) ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 4 of in vitro cranial neural crest cell specification (2 replicates per line) ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 10 of in vitro cranial neural crest cell specification (2 replicates per line) ChIP-seq of MBD3 in two CHD3-WT cell lines at day 14 of in vitro cranial neural crest cell specification