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Genome Biol. 2017 Jul 28;18(1):143. doi: 10.1186/s13059-017-1270-7.

Population and allelic variation of A-to-I RNA editing in human transcriptomes.

Author information

1
Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
2
Department of Microbiology & Parasitology, Medical School of Hebei University, Baoding, Hebei Province, 071002, China.
3
Department of Statistics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
4
Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA. yxing@ucla.edu.

Abstract

BACKGROUND:

A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing.

RESULTS:

In order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis. We identify 1054 RNA editing events associated with cis genetic polymorphisms. Additionally, we find that a subset of these polymorphisms is linked to genome-wide association study signals of complex traits or diseases. Finally, compared to random cis polymorphisms, polymorphisms associated with RNA editing variation are located closer spatially to their respective editing sites and have a more pronounced impact on RNA secondary structure.

CONCLUSIONS:

Our study reveals widespread cis variation in RNA editing among genetically distinct individuals and sheds light on possible phenotypic consequences of such variation on complex traits and diseases.

KEYWORDS:

GWAS; Genetic variation; RNA editing; RNA-seq; Transcriptome

PMID:
28754146
PMCID:
PMC5532815
DOI:
10.1186/s13059-017-1270-7
[Indexed for MEDLINE]
Free PMC Article

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