title: Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR).
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.
authors.affiliation: Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Ramat Gan, Israel.
authors.forename: Oz
authors.initials: O
authors.lastname: Solomon
authors.forename: Shirley
authors.initials: S
authors.lastname: Oren
authors.forename: Michal
authors.initials: M
authors.lastname: Safran
authors.forename: Naamit
authors.initials: N
authors.lastname: Deshet-Unger
authors.forename: Pinchas
authors.initials: P
authors.lastname: Akiva
authors.forename: Jasmine
authors.initials: J
authors.lastname: Jacob-Hirsch
authors.forename: Karen
authors.initials: K
authors.lastname: Cesarkas
authors.forename: Reut
authors.initials: R
authors.lastname: Kabesa
authors.forename: Ninette
authors.initials: N
authors.lastname: Amariglio
authors.forename: Ron
authors.initials: R
authors.lastname: Unger
authors.forename: Gideon
authors.initials: G
authors.lastname: Rechavi
authors.forename: Eran
authors.initials: E
authors.lastname: Eyal
mesh_terms: D000241:Adenosine / Q000235:genetics / Q000378:metabolism; D000243:Adenosine Deaminase / Q000235:genetics* / Q000378:metabolism; D017398:Alternative Splicing / Q000235:genetics*; D001483:Base Sequence; D045744:Cell Line, Tumor; D005091:Exons / Q000235:genetics; D005786:Gene Expression Regulation; D006801:Humans; D007288:Inosine / Q000235:genetics; D017393:RNA Editing / Q000235:genetics; D012322:RNA Precursors / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D016601:RNA-Binding Proteins
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D007288:Inosine; C567955:ADARB1 protein, human; D000243:Adenosine Deaminase; D000241:Adenosine