ArticleProgress in neurobiology2021
3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders.
Article in Progress in neurobiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Cross-trait clustering of sub-threshold sleep genetic signals identifies EGR2 as a conserved regulator of sleep.bioRxiv : the preprint server for biology · 2026Article
- Integrative genomics and single-cell CRISPRi screening dissect Alzheimer GWAS non-coding variants regulating TSPAN14.American journal of human genetics · 2026Article
- Variant-to-gene mapping identifiesbioRxiv : the preprint server for biology · 2026Article
- GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density.Genome biology · 2025Article
- Shared and unique 3D genomic features of substance use disorders across multiple cell types.medRxiv : the preprint server for health sciences · 2025Article
- Integrated genomic analysis and CRISPRi implicatesNPJ dementia · 2025Article
- GWAS-Informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density.bioRxiv : the preprint server for biology · 2024Article
- Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C.Diabetologia · 2024Article
- Article
- Variant-to-function mapping of late-onset Alzheimer's disease GWAS signals in human microglial cell models implicatesbioRxiv : the preprint server for biology · 2024Article
- Article
- Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2.Cell genomics · 2024Article
- Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.Biology open · 2023Article
- Sex Significantly Impacts the Function of Major Depression-Linked Variants In Vivo.Biological psychiatry · 2023Article
- Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR ofbioRxiv : the preprint server for biology · 2023Article
- Technologies, strategies, and cautions when deconvoluting genome-wide association signals: FTO in focus.Obesity reviews : an official journal of the International Association for the Study of Obesity · 2023Review
- Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK.Biophysical reviews · 2023Review
- Abnormal Chromatin Folding in the Molecular Pathogenesis of Epilepsy and Autism Spectrum Disorder: a Meta-synthesis with Systematic Searching.Molecular neurobiology · 2023Review
- Variant-to-gene mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as a regulator of sleep.Science advances · 2023Article
- 3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk.Cell metabolism · 2022Article
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12 authors.
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Abstract
Neurodevelopmental disorders are thought to arise from interrupted development of the brain at an early age. Genome-wide association studies (GWAS) have identified hundreds of loci associated with susceptibility to neurodevelopmental disorders; however, which noncoding variants regulate which genes at these loci is often unclear. To implicate neuronal GWAS effector genes, we performed an integrated analysis of transcriptomics, epigenomics and chromatin conformation changes during the development from Induced pluripotent stem cell-derived neuronal progenitor cells (NPCs) into neurons using a combination of high-resolution promoter-focused Capture-C, ATAC-seq and RNA-seq. We observed that gene expression changes during the NPC-to-neuron transition were highly dependent on both promoter accessibility changes and long-range interactions which connect distal cis-regulatory elements (enhancer or silencers) to developmental-stage-specific genes. These genome-scale promoter-cis-regulatory-element atlases implicated 454 neurodevelopmental disorder-associated, putative causal variants mapping to 600 distal targets. These putative effector genes were significantly enriched for pathways involved in the regulation of neuronal development and chromatin organization, with 27 % expressed in a stage-specific manner. The intersection of open chromatin and chromatin conformation revealed development-stage-specific gene regulatory architectures during neuronal differentiation, providing a rich resource to aid characterization of the genetic and developmental basis of neurodevelopmental disorders.
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