CHD7 marks TAD boundaries during neuronal differentiation [RNA-Seq]

The chromodomain helicase DNA binding protein 7 (CHD7) is a nucleosome repositioner implicated in multiple cellular processes, including neuronal differentiation. We identified CHD7 marked sites at TAD boundaries that regulate neuronal differentiation in an otic stem cell line. We showed that CHD7 co-occupied CTCF sites genome-wide. We identified CTCF+ CHD7+ sites near an essential transcription factor, Sox11, required for otic neuronal differentiation. The Sox11 promoter and 3’ untranslated region (UTR) showed CHD7 enrichment. The CHD7-marked sites at the 3’UTR displayed histone marks corresponding to active transcription that resulted in Sox11 antisense transcripts. Blocking the singular CHD7-marked site with CRISPRi decreased neurite lengths, reduced neuronal marker expression (TUBB3), and attenuated Sox11 antisense transcripts. Sox11 antisense transcripts were previously suggested to form double-stranded RNA and degrade the Sox11 transcript. Surprisingly, the level of the Sox11 sense transcripts remained unaffected after CRISPRi. We propose that CHD7 at TAD boundaries modulate the chromatin accessibility of CTCF-marked insulators, altering the 3D chromatin organization and ultimately affecting gene expression. Our results implicate a general mechanism of CHD7 in facilitating neuronal differentiation and provide insight into CHD7 dysfunction in CHARGE syndrome, an intellectual developmental disability disorder.