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E-GEOD-70588 - ADAR2 affects mRNA coding sequence edits but not gene expression or splicing in vivo

Status
Released on 3 July 2016, last updated on 28 December 2016
Organism
Mus musculus
Samples (12)
Protocols (2)
Description
Adenosine deaminases (ADARs) are RNA binding proteins that bind to double stranded RNA and convert adenosine to inosine. Editing creates multiple isoforms of neurotransmitter receptors, including AMPA-subtype Glutamate channels such as Gria2 that is edited to introduce a Q to R amino acid change. Adar2 knock out mice die of seizures shortly after birth, but if the Gria2 Q/R editing site is mutated to mimic the edited version then the animals are viable. We performed RNA-Seq on the frontal cortices of Adar2-/- Gria2R/R mice and their Adar2+/+ Gria2R/R littermates, quantifying overall gene expression, splicing, and A to I editing in a transcriptome-wide fashion. We found 56 editing sites whose level of editing was significantly diminished in the Adar2 deficient animals. The majority of Adar2 responsive editing sites were in the coding regions of genes. Interestingly, other than Adar2 expression, there were only two additional statistically significant differentially expressed genes, Flnb and Cdh13. There were also only three exons that showed statistically significant differences in expression levels between the two genotypes. This work illustrates that ADAR2 is important in site-specific changes of protein coding sequences but has only modest effects on gene expression or splicing in vivo. 6 ADAR2 Knock out frontal cortices and 6 litter mate control frontal cortices from male mice
Experiment type
RNA-seq of coding RNA 
Contacts
Allissa A Dillman <allissa.dillman@nih.gov>, Dagmar Galter, Mark R Cookson
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-70588.idf.txt
Sample and data relationshipE-GEOD-70588.sdrf.txt
Additional data (1)E-GEOD-70588.additional.1.zip
Links