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E-GEOD-61066 - ADAR2 reproducibly changes abundance and sequence of mature microRNAs in the mouse brain [RNA-Seq]

Status
Released on 2 October 2014, last updated on 3 October 2014
Organism
Mus musculus
Samples (6)
Protocols (1)
Description
Background: Adenosine deaminases that act on RNA (ADARs) bind to double-stranded and structured RNAs and deaminate adenosines to inosines. This A to I editing is widespread and required for normal life and development. Besides mRNAs and repetitive elements, ADARs can target miRNA precursors. Editing of miRNA precursors can affect processing efficiency and alter target specificity. Interestingly, ADARs can also influence miRNA abundance independent of RNA-editing. In mouse embryos where editing levels are low, ADAR2 was found to be the major ADAR protein that affects miRNA abundance. Here we extend our analysis to adult mouse brains where high editing levels are observed. Results: Using Illumina deep sequencing we compare the abundances of mature miRNAs and editing events within them, between wild-type and ADAR2 knockout mice in the adult mouse brain. Reproducible changes in abundance of specific miRNAs are observed in ADAR2 deficient mice. Most of these quantitative changes seem unrelated to A to I editing events. However, many A to G transitions in cDNAs prepared from mature miRNA sequences, reflecting A to I editing events in the RNA, are observed with frequencies reaching up to 80%. About half of these editing events are primarily caused by ADAR2 while a few miRNAs show increased editing in the absence of ADAR2, suggesting preferential editing by ADAR1. Moreover, novel, previously unknown editing events were identified in several miRNAs. In general 64% of all editing events are located within the seed region of mature miRNAs. In one of these cases retargeting of the edited miRNA could be verified in reporter assays. Also, altered processing efficiency upon editing near a processing site could be experimentally verified. Conclusions: ADAR2 can significantly influence the abundance of certain miRNAs in the brain. Only in a few cases changes in miRNA abundance can be explained by miRNA editing. Thus, ADAR2 binding to miRNA precursors, without editing them, may influence their processing and thereby abundance. ADAR1 and ADAR2 have both overlapping and distinct specificities for editing of miRNA editing sites. Over 60% of editing occurs in the seed region possibly changing target specificities for many edited miRNAs. Examination of the effect of ADAR2 on mature miRNA abundance and sequence in adult mouse brain.
Experiment type
RNA-seq of non coding RNA 
Contacts
Fritz Sedlazeck <fritz.sedlazeck@gmail.com>, Arndt von Haeseler, Cornelia Vesely, Fritz J Sedlazeck, Mansoureh Tajaddod, Michael F Jantsch, Stefanie Tauber
Citation
ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, Haeseler AV, Jantsch MF. , PMID:25260591
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-61066.idf.txt
Sample and data relationshipE-GEOD-61066.sdrf.txt
Additional data (1)E-GEOD-61066.additional.1.zip
Links