Functional disease architectures reveal unique biological role of transposable elements

Farhad Hormozdiari (), Bryce Geijn, Joseph Nasser, Omer Weissbrod, Steven Gazal, Chelsea J. -T. Ju, Luke O’ Connor, Margaux L. A. Hujoel, Jesse Engreitz, Fereydoun Hormozdiari and Alkes L. Price ()
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Farhad Hormozdiari: Harvard T.H. Chan School of Public Health
Bryce Geijn: Harvard T.H. Chan School of Public Health
Joseph Nasser: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard
Omer Weissbrod: Harvard T.H. Chan School of Public Health
Steven Gazal: Harvard T.H. Chan School of Public Health
Chelsea J. -T. Ju: University of California
Luke O’ Connor: Harvard T.H. Chan School of Public Health
Margaux L. A. Hujoel: Harvard T.H. Chan School of Public Health
Jesse Engreitz: Program in Medical and Population Genetics, Broad Institute of MIT and Harvard
Fereydoun Hormozdiari: University of California
Alkes L. Price: Harvard T.H. Chan School of Public Health

Nature Communications, 2019, vol. 10, issue 1, 1-8

Abstract: Abstract Transposable elements (TE) comprise roughly half of the human genome. Though initially derided as junk DNA, they have been widely hypothesized to contribute to the evolution of gene regulation. However, the contribution of TE to the genetic architecture of diseases remains unknown. Here, we analyze data from 41 independent diseases and complex traits to draw three conclusions. First, TE are uniquely informative for disease heritability. Despite overall depletion for heritability (54% of SNPs, 39 ± 2% of heritability), TE explain substantially more heritability than expected based on their depletion for known functional annotations. This implies that TE acquire function in ways that differ from known functional annotations. Second, older TE contribute more to disease heritability, consistent with acquiring biological function. Third, Short Interspersed Nuclear Elements (SINE) are far more enriched for blood traits than for other traits. Our results can help elucidate the biological roles that TE play in the genetic architecture of diseases.

Date: 2019
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DOI: 10.1038/s41467-019-11957-5

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