Dataset Information

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

ABSTRACT: 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 408 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Neural Progenitor Cell

SUBMITTER: Romina Belli

LAB HEAD: Marta Biagioli

PROVIDER: PXD025739 | Pride | 2023-03-11

REPOSITORIES: Pride

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			Action	DRS
	Biagioli-Arnoldi_HM20206_H_gelTryp_IP-17_5ul_r1.mzML	Mzml
	Biagioli-Arnoldi_HM20206_H_gelTryp_IP-17_5ul_r1.raw	Raw
	Biagioli-Arnoldi_HM20209_H_gelTryp_IP-18_5ul_r1bis.msf	Msf
	Biagioli-Arnoldi_HM20209_H_gelTryp_IP-18_5ul_r1bis.mzML	Mzml
	Biagioli-Arnoldi_HM20209_H_gelTryp_IP-18_r1bis.raw	Raw

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Publications

CHD8 suppression impacts on histone H3 lysine 36 trimethylation and alters RNA alternative splicing.

Kerschbamer Emanuela E Arnoldi Michele M Tripathi Takshashila T Pellegrini Miguel M Maturi Samuele S Erdin Serkan S Salviato Elisa E Di Leva Francesca F Sebestyén Endre E Dassi Erik E Zarantonello Giulia G Benelli Matteo M Campos Eric E Basson M Albert MA Gusella James F JF Gustincich Stefano S Piazza Silvano S Demichelis Francesca F Talkowski Michael E ME Ferrari Francesco F Biagioli Marta M

Nucleic acids research 20221201 22

Disruptive mutations in the chromodomain helicase DNA-binding protein 8 gene (CHD8) have been recurrently associated with autism spectrum disorders (ASDs). 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. H3K36me ...[more]

PMID: 36537238

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Project description:Whole genome profiling of 4 histone modifications (H3K27me1, H3K27me3,H3K36me1 and H3K36me3) using ChIP-on-chip. It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons ("exon-intron marking"), linking chromatin structure and function to co- transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.