Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) (original) (raw)
- Shirley Oren1,3,
- Michal Safran1,
- Naamit Deshet-Unger1,
- Pinchas Akiva1,3,
- Jasmine Jacob-Hirsch1,
- Karen Cesarkas1,
- Reut Kabesa2,
- Ninette Amariglio1,
- Ron Unger2,
- Gideon Rechavi1,3 and
- Eran Eyal1,4
- 1Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Ramat Gan, Israel
- 2The Everard & Mina Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
- 3Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
Abstract
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.
- RNA editing
- alternative splicing
- all exon microarray
- ADAR
- RNA-seq
- massively parallel sequencing (MPS)
Footnotes
↵4 Corresponding author
E-mail eran.eyal{at}sheba.health.gov.ilReceived December 26, 2012.
Accepted February 13, 2013.
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