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RNA. 2008 Oct;14(10):2074-85. doi: 10.1261/rna.816908. Epub 2008 Sep 4.

Screening of human SNP database identifies recoding sites of A-to-I RNA editing.

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1
Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015-4732, USA.

Abstract

Single nucleotide polymorphisms (SNPs) are DNA sequence variations that can affect the expression or function of genes. As a result, they may lead to phenotypic differences between individuals, such as susceptibility to disease, response to medications, and disease progression. Millions of SNPs have been mapped within the human genome providing a rich resource for genetic variation studies. Adenosine-to-inosine RNA editing also leads to the production of RNA and protein sequence variants, but it acts on the level of primary gene transcripts. Sequence variations due to RNA editing may be misannotated as SNPs when relying solely on expressed sequence data instead of genomic material. In this study, we screened the human SNP database for potential cases of A-to-I RNA editing that cause amino acid changes in the encoded protein. Our search strategy applies five molecular features to score candidate sites. It identifies all previously known cases of editing present in the SNP database and successfully uncovers novel, bona fide targets of adenosine deamination editing. Our approach sets the stage for effective and comprehensive genome-wide screens for A-to-I editing targets.

PMID:
18772245
PMCID:
PMC2553741
DOI:
10.1261/rna.816908
[Indexed for MEDLINE]
Free PMC Article
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