Human genetic variation recognizes functional elements in noncoding sequence

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.

Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy

“…using RepeatMasker, and species-specific collection of repeat sequences from the latest Repbase-Update (35). A variety of complementary approaches were used to search for exons and regulatory elements (36): GENSCAN and ExonScan Web Server to identify ab initio exons; Expasy Translate tool to search for potential ORFs checked for homology with BLASTP against Swiss-Prot and PDB-databases; BLASTN (37) against mRNA (expressed sequence tag or cDNA) sequences from GenBank (release 123); the Rfam database (v10.1) (http:// rfam.sanger.ac.uk/); tRNAscan-SE (38); the fRNA database (v3.4) (39); and support vector machine-based algorithms to search for real miRNA hairpins (40,41) (Table S2). …”

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

“…Introns probably represent substantially larger targets for functional mutations than has hitherto been recognized [Lynch, 2010] on account of their harboring a multiplicity of functional elements including intron splice enhancers and silencers, cis-acting RNA elements that regulate alternative splicing [Tress et al, 2007;Wang et al, 2009a], and potentially also trans-splicing elements [Akiva et al, 2006;Gingeras 2009;Shao et al, 2006], as well as other regulatory elements some of which may be deeply embedded within very large introns [Solis et al, 2008]. In terms of identifying intronic functional elements, it may be helpful that they are often characterized by a reduced level of genetic variation [Lomelin et al, 2010].…”

Novel mutation and three other sequence variants segregating with phenotype at keratoconus 13q32 susceptibility locus

“…The non-coding regions of genes, including introns, contain many regulatory elements, 52 and intronic alterations, that is, single-nucleotide changes, can result in deleterious effect on pre-messenger RNA splicing. 53 Identification of these sequence variants could be non-accidental, and they could have a role in the KTCN etiology.…”