E-GEOD-47997 - Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) [RNA-seq]

Status
Released on 17 June 2013, last updated on 3 May 2014
Organism
Homo sapiens
Samples (4)
Protocols (4)
Description
Alternative mRNA splicing is a major mechanism for gene regulation and transcriptome diversity. Despite the extent of the phenomenon, the regulation and specificity of the splicing machinery are only partially understood. Adenosine-to-inosine (A-to-I) RNA editing of pre-mRNA by ADAR enzymes has been linked to splicing regulation in several cases. Here we used bioinformatics approaches, RNA-seq and exon-specific microarray of ADAR knockdown cells to globally examine how ADAR and its A-to-I RNA editing activity influence alternative mRNA splicing. Although A-to-I RNA editing only rarely targets canonical splicing acceptor, donor, and branch sites, it was found to affect splicing regulatory elements (SREs) within exons. Cassette exons were found to be significantly enriched with A-to-I RNA editing sites compared with constitutive exons. RNA-seq and exon-specific microarray revealed that ADAR knockdown in hepatocarcinoma and myelogenous leukemia cell lines leads to global changes in gene expression, with hundreds of genes changing their splicing patterns in both cell lines. This global change in splicing pattern cannot be explained by putative editing sites alone. Genes showing significant changes in their splicing pattern are frequently involved in RNA processing and splicing activity. Analysis of recently published RNA-seq data from glioblastoma cell lines showed similar results. Our global analysis reveals that ADAR plays a major role in splicing regulation. Although direct editing of the splicing motifs does occur, we suggest it is not likely to be the primary mechanism for ADAR-mediated regulation of alternative splicing. Rather, this regulation is achieved by modulating trans-acting factors involved in the splicing machinery. HepG2 and K562 cell lines were stably transfected with plasmids containing siRNA designed to specifically knock down ADAR expression (ADAR KD). This in order to examine how ADAR affects alternative splicing globally.
Experiment type
RNA-seq of coding RNA 
Contacts
jasmine jacob <j-jacob@sheba.health.gov.il>, Eran Eyal, Gideon Rechavi, Jasmine Jacob-Hirsch, Karen Cesarkas, Michal Safran, Naamit Deshet-Unger, Ninette Amariglio, Oz Solomon, Pinchas Akiva, Reut Kabesa, Ron Unger, Shirely Oren
Citation
Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). Solomon O, Oren S, Safran M, Deshet-Unger N, Akiva P, Jacob-Hirsch J, Cesarkas K, Kabesa R, Amariglio N, Unger R, Rechavi G, Eyal E. , Europe PMC 23474544
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-47997.idf.txt
Sample and data relationshipE-GEOD-47997.sdrf.txt
Links