Mapping Cis-Regulatory Chromatin Contacts in Neural Cells Links Neuropsychiatric Disorder Risk Variants to Target Genes

Nat Genet. 2019 Aug;51(8):1252-1262. doi: 10.1038/s41588-019-0472-1. Epub 2019 Jul 31.

Abstract

Mutations in gene regulatory elements have been associated with a wide range of complex neuropsychiatric disorders. However, due to their cell-type specificity and difficulties in characterizing their regulatory targets, the ability to identify causal genetic variants has remained limited. To address these constraints, we perform an integrative analysis of chromatin interactions, open chromatin regions and transcriptomes using promoter capture Hi-C, assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing, respectively, in four functionally distinct neural cell types: induced pluripotent stem cell (iPSC)-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus-like neurons and primary astrocytes. We identify hundreds of thousands of long-range cis-interactions between promoters and distal promoter-interacting regions, enabling us to link regulatory elements to their target genes and reveal putative processes that are dysregulated in disease. Finally, we validate several promoter-interacting regions by using clustered regularly interspaced short palindromic repeats (CRISPR) techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP and DRD2 are transcriptionally regulated by physically linked enhancers.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Lineage / genetics*
  • Chromatin / genetics*
  • Chromosome Mapping
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Enhancer Elements, Genetic*
  • Gene Editing
  • Gene Expression Regulation*
  • Genetic Markers*
  • Genome, Human
  • Genome-Wide Association Study
  • Humans
  • Induced Pluripotent Stem Cells / cytology
  • Induced Pluripotent Stem Cells / metabolism
  • Infant
  • Male
  • Mental Disorders / genetics*
  • Neurons / cytology
  • Neurons / metabolism*
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic*

Substances

  • Chromatin
  • Genetic Markers