CHD8 Suppression Impacts on Histone H3 Lysine 36 Trimethylation and Alters RNA Alternative Splicing

Disruptive mutations in the chromodomain helicase DNA binding protein 8 (CHD8) have been recurrently associated with Autism Spectrum Disorders (ASD). Here we investigated how chromatin reacts to CHD8 suppression by analyzing a panel of histone modifications in induced pluripotent stem cell-derived neural progenitors. CHD8 suppression led to significant reduction (47.82%) in histone H3K36me3 peaks at gene bodies, particularly impacting on transcriptional elongation chromatin states. H3K36me3 reduction specifically affects highly expressed, CHD8-bound genes and correlates with altered alternative splicing patterns of 462 genes implicated in “regulation of RNA splicing”, “mRNA catabolic process”. Interestingly, mass-spectrometry analysis uncovered a novel interaction between CHD8 and the splicing regulator Heterogeneous Nuclear Ribonucleoprotein L (hnRNPL), providing the first mechanistic insights to explain CHD8-suppression splicing phenotype, partially implicating SETD2, H3K36me3 methyltransferase. In summary, our results point toward broad molecular consequences of CHD8 suppression, entailing altered histone deposition/maintenance and RNA processing regulation as important regulatory processes in ASD. ChIP sequencing was conducted to examine 6 different histone modifications in 2 experimental conditions, CHD8 knock-down (obtained by short-hairpin (sh) administration, 3 different Sh were used and tested) and control (2 replicates from cells treated with control Sh, Sh-GFP) human neural progenitor cells. Poly-A RNA sequencing was conducted to examine alternative splicing comparing 2 experimental conditions: siRNA-mediated hnRNPL knock-down (si-C) versus si-Scrambled controls (si-SCR). iPS-derived human neuronal progenitors were used. siRNA treatment was conducted for 72h.