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Series GSE47945 Query DataSets for GSE47945
Status Public on Jun 15, 2013
Title Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) [expression]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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.
Overall design 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.
Contributor(s) 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
Citation(s) 23474544
Submission date Jun 14, 2013
Last update date Oct 25, 2022
Contact name jasmine Jacob
Phone 0523790500
Organization name Sheba Medical Center at Tel HaShomer
Street address haChevel 33
City Shoham
State/province -Select-
ZIP/Postal code 60850
Country Israel
Platforms (1)
GPL5175 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
Samples (4)
GSM1163066 B637_HEPG2_SCR
GSM1163067 B638_HEPG2_1105
GSM1163068 B640_K562_SCR
This SubSeries is part of SuperSeries:
GSE47998 Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR)
BioProject PRJNA208432

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE47945_RAW.tar 83.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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