Human genetic variation recognizes functional elements in noncoding sequence
- David Lomelin1,6,
- Eric Jorgenson2,3 and
- Neil Risch1,4,5
- 1Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, USA;
- 2Department of Neurology, University of California, San Francisco, San Francisco, California 94143, USA;
- 3Ernest Gallo Clinic and Research Center, University of California, San Francisco, Emeryville, California 94608, USA;
- 4Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94143, USA;
- 5Division of Research, Kaiser Permanente Northern California, Oakland, California 94612, USA
Abstract
Noncoding DNA, particularly intronic DNA, harbors important functional elements that affect gene expression and RNA splicing. Yet, it is unclear which specific noncoding sites are essential for gene function and regulation. To identify functional elements in noncoding DNA, we characterized genetic variation within introns using ethnically diverse human polymorphism data from three public databases—PMT, NIEHS, and SeattleSNPs. We demonstrate that positions within introns corresponding to known functional elements involved in pre-mRNA splicing, including the branch site, splice sites, and polypyrimidine tract show reduced levels of genetic variation. Additionally, we observed regions of reduced genetic variation that are candidates for distance-dependent localization sites of functional elements, possibly intronic splicing enhancers (ISEs). Using several bioinformatics approaches, we provide additional evidence that supports our hypotheses that these regions correspond to ISEs. We conclude that studies of genetic variation can successfully discriminate and identify functional elements in noncoding regions. As more noncoding sequence data become available, the methods employed here can be utilized to identify additional functional elements in the human genome and provide possible explanations for phenotypic associations.
Footnotes
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↵6 Corresponding author.
E-mail david.lomelin{at}ucsf.edu; fax (858) 754-2988.
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[Supplemental material is available online at http://www.genome.org.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.094151.109.
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- Received March 20, 2009.
- Accepted December 17, 2009.
- Copyright © 2010 by Cold Spring Harbor Laboratory Press
