High levels of RNA-editing site conservation amongst 15 laboratory mouse strains.

ABSTRACT:

Background

Adenosine-to-inosine (A-to-I) editing is a site-selective post-transcriptional alteration of double-stranded RNA by ADAR deaminases that is crucial for homeostasis and development. Recently the Mouse Genomes Project generated genome sequences for 17 laboratory mouse strains and rich catalogues of variants. We also generated RNA-seq data from whole brain RNA from 15 of the sequenced strains.

Results

Here we present a computational approach that takes an initial set of transcriptome/genome mismatch sites and filters these calls taking into account systematic biases in alignment, single nucleotide variant calling, and sequencing depth to identify RNA editing sites with high accuracy. We applied this approach to our panel of mouse strain transcriptomes identifying 7,3

SUBMITTER: Danecek P 

PROVIDER: S-EPMC3446300 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature