The epigenomic landscape of transposable elements across normal human development and anatomy
Year: 2019
Type: article
Abstract: Transposable elements (TEs) have deposited functional regulatory elements throughout the human genome. Although most are silenced, certain TEs have been co-opted by the host. However, a comprehensive, multidimensional picture of the contribution of TEs to normal human gene regulation is still lacking. Here, we quantify the epigenomic status of TEs across human anatomy and development using data from the Roadmap Epigenomics Project. We find that TEs encompass a quarter of the human regulatory epigenome, and 47% of elements can be in an active regulatory state. We demonstrate that SINEs are enriched relative to other classes for active and transcribed marks, that TEs encompass a higher proportion of enhancer states in the hematopoietic lineage, and that DNA methylation of Alu elements decreases with age, corresponding with a loss of CpG islands. Finally, we identify TEs that may perform an evolutionarily conserved regulatory function, providing a systematic profile of TE activity in normal human tissue.
Source: Nature Communications
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,200
Funders: U.S. Department of Health and Human Services, American Cancer Society, European Bioinformatics Institute, National Institutes of Health, National Institute on Drug Abuse, National Human Genome Research Institute, National Cancer Institute, National Institute of Environmental Health Sciences, H2020 Marie Skłodowska-Curie Actions
Awards: G1384347966, G1568783086, G200058312, DECODING THE IMPACT OF TRANSPOSABLE ELEMENTS ON GENE REGULATION, G2139137487, G26147564, G3378495485, CHARTING THE EPIGENOMIC LANDSCAPE OF HUMAN TRANSPOSABLE ELEMENTS, G359264626, THE WASHU TARGET ENVIRONMENTAL EPIGENOMICS DATA COORDINATION CENTER, Connecting transposable elements and regulatory innovation using ENCODE data, RESEARCH EDUCATION PROGRAM ON COMPUTATIONAL AND STATISTICAL TOOL DEVELOPMENT FOR ADDICTION GENETICS, G4128838416, G475783744, G4781995733, ADVANCED EPI/GENOME BROWSER WITH ENHANCED VISUALIZATION AND ANALYSIS TOOLS, G5740585382, G5772697227, The WashU 4DN Network Data Coordination and Integration Center, EMBL Interdisciplinary, International and Intersectorial Postdocs, G8649331918, G9000008527, G9000018247, G9000077927, G9000226449, The Human Pangenome Reference Consortium Coordination Center
OpenAlex ID: W2995160098