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Xu L, Liu Y. Identification, Design, and Application of Noncoding Cis-Regulatory Elements. Biomolecules 2024; 14:945. [PMID: 39199333 PMCID: PMC11352686 DOI: 10.3390/biom14080945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 09/01/2024] Open
Abstract
Cis-regulatory elements (CREs) play a pivotal role in orchestrating interactions with trans-regulatory factors such as transcription factors, RNA-binding proteins, and noncoding RNAs. These interactions are fundamental to the molecular architecture underpinning complex and diverse biological functions in living organisms, facilitating a myriad of sophisticated and dynamic processes. The rapid advancement in the identification and characterization of these regulatory elements has been marked by initiatives such as the Encyclopedia of DNA Elements (ENCODE) project, which represents a significant milestone in the field. Concurrently, the development of CRE detection technologies, exemplified by massively parallel reporter assays, has progressed at an impressive pace, providing powerful tools for CRE discovery. The exponential growth of multimodal functional genomic data has necessitated the application of advanced analytical methods. Deep learning algorithms, particularly large language models, have emerged as invaluable tools for deconstructing the intricate nucleotide sequences governing CRE function. These advancements facilitate precise predictions of CRE activity and enable the de novo design of CREs. A deeper understanding of CRE operational dynamics is crucial for harnessing their versatile regulatory properties. Such insights are instrumental in refining gene therapy techniques, enhancing the efficacy of selective breeding programs, pushing the boundaries of genetic innovation, and opening new possibilities in microbial synthetic biology.
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Affiliation(s)
- Lingna Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China
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Zeng B, Bendl J, Deng C, Lee D, Misir R, Reach SM, Kleopoulos SP, Auluck P, Marenco S, Lewis DA, Haroutunian V, Ahituv N, Fullard JF, Hoffman GE, Roussos P. Genetic regulation of cell type-specific chromatin accessibility shapes brain disease etiology. Science 2024; 384:eadh4265. [PMID: 38781378 DOI: 10.1126/science.adh4265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/20/2023] [Indexed: 05/25/2024]
Abstract
Nucleotide variants in cell type-specific gene regulatory elements in the human brain are risk factors for human disease. We measured chromatin accessibility in 1932 aliquots of sorted neurons and non-neurons from 616 human postmortem brains and identified 34,539 open chromatin regions with chromatin accessibility quantitative trait loci (caQTLs). Only 10.4% of caQTLs are shared between neurons and non-neurons, which supports cell type-specific genetic regulation of the brain regulome. Incorporating allele-specific chromatin accessibility improves statistical fine-mapping and refines molecular mechanisms that underlie disease risk. Using massively parallel reporter assays in induced excitatory neurons, we screened 19,893 brain QTLs and identified the functional impact of 476 regulatory variants. Combined, this comprehensive resource captures variation in the human brain regulome and provides insights into disease etiology.
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Affiliation(s)
- Biao Zeng
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth Misir
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sarah M Reach
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven P Kleopoulos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pavan Auluck
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, MD 20892, USA
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, MD 20892, USA
| | - David A Lewis
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, NY 10468, USA
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