Identification of RNA editing sites in the SNP database.
The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications.
Eisenberg
Eli
E
School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, TAU, Tel Aviv 69978, Israel.
Adamsky
Konstantin
K
Cohen
Lital
L
Amariglio
Ninette
N
Hirshberg
Abraham
A
Rechavi
Gideon
G
Levanon
Erez Y
EY
D001483:Base Sequence; D030561:Databases, Nucleic Acid; D039642:Eukaryotic Initiation Factors / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017393:RNA Editing; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism
D039642:Eukaryotic Initiation Factors; D012269:Ribosomal Proteins; C040343:ribosomal protein S19