WAVE2 and REST/NRSF Regulate Clustered Gene Expression by Maintaining Heterochromatin Organization

The actin polymerization machinery, comprising the ARP2/3 complex and its activators, the WASP family proteins, has been implicated in regulating a broad spectrum of nuclear processes, such as transcriptional regulation and nuclear organization. Here, using clustered protocadherin (cPcdh) and β-globin genes as model systems, we showed that WAVE2, a member of the WASP family, regulates chromatin organization by maintaining heterochromatin dynamics. Specifically, by CRISPR DNA-fragment editing, in conjunction with integrated analyses of ChIP-seq, MeDIP-seq, ATAC-seq, QHR-4C, and RNA-seq, we showed that deposition of H3K9me3, a key heterochromatin mark, is significantly decreased at the cPcdh locus upon WAVE2 deletion, concurrent with aberrant accumulation of CTCF/cohesin complex at promoter regions and spatial reorganization of chromatin architecture around the nucleolus. In addition, REST/NRSF exerts a similar heterochromatin-dependent effect on the cPcdh locus. Finally, genetic and genomic data showed that WAVE2 regulates β-globin gene expression by maintaining heterochromatin status. Together, our data suggested that WAVE2 and REST/NRSF regulate developmental expression of clustered genes in a heterochromatin-dependent manner.