Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes.

Autor: Song M; Institute for Human Genetics, University of California, San Francisco, CA, USA.; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, USA., Yang X; Institute for Human Genetics, University of California, San Francisco, CA, USA., Ren X; Institute for Human Genetics, University of California, San Francisco, CA, USA., Maliskova L; Institute for Human Genetics, University of California, San Francisco, CA, USA., Li B; Institute for Human Genetics, University of California, San Francisco, CA, USA., Jones IR; Institute for Human Genetics, University of California, San Francisco, CA, USA., Wang C; Gladstone Institute of Neurological Disease, University of California, San Francisco, CA, USA., Jacob F; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Wu K; Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA., Traglia M; Department of Psychiatry, University of California, San Francisco, CA, USA., Tam TW; Institute for Human Genetics, University of California, San Francisco, CA, USA., Jamieson K; Institute for Human Genetics, University of California, San Francisco, CA, USA., Lu SY; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.; State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China.; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China., Ming GL; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA., Li Y; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.; Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.; Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA., Yao J; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.; State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China.; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China., Weiss LA; Institute for Human Genetics, University of California, San Francisco, CA, USA.; Department of Psychiatry, University of California, San Francisco, CA, USA., Dixon JR; Salk Institute for Biological Studies, La Jolla, CA, USA., Judge LM; Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA.; Department of Pediatrics, University of California, San Francisco, CA, USA., Conklin BR; Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA.; Department of Medicine, University of California, San Francisco, CA, USA.; Department of Ophthalmology, University of California, San Francisco, CA, USA., Song H; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA., Gan L; Gladstone Institute of Neurological Disease, University of California, San Francisco, CA, USA.; Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA.; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.; Department of Neurology, University of California, San Francisco, CA, USA., Shen Y; Institute for Human Genetics, University of California, San Francisco, CA, USA. yin.shen@ucsf.edu.; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, CA, USA. yin.shen@ucsf.edu.; Department of Neurology, University of California, San Francisco, CA, USA. yin.shen@ucsf.edu.
Jazyk: angličtina
Zdroj: Nature genetics [Nat Genet] 2019 Aug; Vol. 51 (8), pp. 1252-1262. Date of Electronic Publication: 2019 Jul 31.
DOI: 10.1038/s41588-019-0472-1
Abstrakt: 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.
Databáze: MEDLINE
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