ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial to mesenchymal transition in cranial neural crest lineage commitment.
The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. BAF subunit mutations cause Coffin-Siris Syndrome (CSS), a congenital disorder characterized by distinct craniofacial features and intellectual disability. Approximately 50% of CSS patients carry mutations in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS patient-derived ARID1A+/- iPSCs to model CNCC specification, we discovered that ARID1A-haploinsufficency impairs epithelial to mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube. Furthermore, wild-type ARID1A-BAF regulates enhancers associated with EMT genes. ARID1A-BAF binding at these enhancers is impaired in heterozygotes, while binding at promoters is unaffected. At the sequence level, these EMT enhancers contain binding motifs for ZIC2, and ZIC2 binding at these sites is ARID1A-dependent. When excluded from EMT enhancers, ZIC2 relocates to neuronal enhancers, triggering aberrant neuronal gene activation. In mice, deletion of Zic2 impairs NCC delamination, while ZIC2 overexpression in chick embryos at pre-migratory neural crest stages elicits abnormal cell delamination from the neural tube. These findings reveal a novel ARID1A-ZIC2 axis essential for EMT and CNCC delamination. Overall design: RNA-seq of two Coffin Siris Syndrome patient-derived ARID1A-haploinsufficient iPSC lines and two control iPSC lines  (3 replicates per line) RNA-seq of two Coffin Siris Syndrome patient-derived ARID1A-haploinsufficient cell lines and two control cell lines at day 10 of in vitro cranial neural crest cell specification (3 replicates per line) RNA-seq of two Coffin Siris Syndrome patient-derived ARID1A-haploinsufficient cell lines and two control cell lines at day 14 of in vitro cranial neural crest cell specification in early maintenance media (3 replicates per line) RNA-seq of two Coffin Siris Syndrome patient-derived ARID1A-haploinsufficient cell lines and two control cell lines at day 14 of in vitro cranial neural crest cell specification in late maintenance media (at least 2 replicates per line) ChIP-seq of ZIC2 in two Coffin Siris Syndrome patient-derived ARID1A-haploinsufficient cell lines and two control cell lines at day 10 of in vitro cranial neural crest cell specification ChIP-seq of H3K27ac in two Coffin Siris Syndrome patient-derived ARID1A-haploinsufficient cell lines and two control cell lines at day 10 of in vitro cranial neural crest cell specification ChIP-seq of ARID1A in two Coffin Siris Syndrome patient-derived ARID1A-haploinsufficient cell lines and two control cell lines at day 10 of in vitro cranial neural crest cell specification ATAC-seq of two Coffin Siris Syndrome patient-derived ARID1A-haploinsufficient cell lines and two control cell lines at day 10 of in vitro cranial neural crest cell specification (2 replicates per line)