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Regulatory genomic profiling in pure iPSC-derived human cortical neurons

ABSTRACT: For decades, technical and cost hurdles have prevented the systematic investigation of non-coding sequences in complex human diseases, and thus our knowledge about autism spectrum disorders (ASD) has been primarily obtained from analysis of protein-coding sequences. We have combined the analysis of whole genome sequencing with global studies of regulatory sequences of human cortical neurons to reveal the regulatory architecture of ASD. Analysis of de novo mutations from whole genome sequencing of 261 autism families revealed the physical proximity of ASD de novo mutations specifically to the cortical expression quantitative loci (eQTLs) of synaptic genes. We performed ATAC-Seq, ChIP-Seq, RNA-Seq and Hi-C experiments on human cortical neurons, which for the first time provided a paranormal view of the regulatory landscape in these cells. We found that ASD de novo mutations preferentially affect regulatory elements, and the associated genes are shared targets of two ASD syndromic factors, CHD8 and PTEN. Analyzing 15 chromatin states across 127 human tissue/cell types revealed a significant enrichment of ASD de novo mutations in active transcription start sites and the perturbed genes implicated in neuron functions; this distribution enabled us to develop a machine-learning algorithm to assess potential ASD risk for a given individual. Taken together, our study for the first time revealed the regulatory landscape in human neurons, demonstrated the importance of the non-coding genome in ASD and provides a general framework for analyzing regulatory mutations for other complex human diseases.

ORGANISM(S): Homo sapiens

PROVIDER: GSE79965 | GEO | 2022/11/20

REPOSITORIES: GEO

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The chromatin modifier CHD8 targets autism risk genes during human neurodevelopmentM-BM-

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2015-01-21 | E-GEOD-57369 | biostudies-arrayexpress

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2013-08-30 | E-GEOD-43899 | biostudies-arrayexpress

Co-ordinate inhibition of autism candidate genes by topoisomerase inhibitors [Seq]

2013-08-30 | E-GEOD-43526 | biostudies-arrayexpress

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