Genome wide analyses uncover allele-specific RNA editing in human and mouse

Nucleic Acids Research
Zhong-Yin ZhouYa-Ping Zhang

Abstract

RNA editing is one of the most common RNA level modifications that potentially generate amino acid changes similar to those resulting from genomic nonsynonymous mutations. However, unlike DNA level allele-specific modifications such as DNA methylation, it is currently unknown whether RNA editing displays allele-specificity across tissues and species. Here, we analyzed allele-specific RNA editing in human tissues and from brain tissues of heterozygous mice generated by crosses between divergent mouse strains and found a high proportion of overlap of allele-specific RNA editing sites between different samples. We identified three allele-specific RNA editing sites cause amino acid changes in coding regions of human and mouse genes, whereas their associated SNPs yielded synonymous differences. In vitro cellular experiments confirmed that sequences differing at a synonymous SNP can have differences in a linked allele-specific RNA editing site with nonsynonymous implications. Further, we demonstrate that allele-specific RNA editing is influenced by differences in local RNA secondary structure generated by SNPs. Our study provides new insights towards a better comprehension of the molecular mechanism that link SNPs with human diseases...Continue Reading

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Apr 24, 2020·Frontiers in Cell and Developmental Biology·Xiaoyan LuHong Wang
Jan 9, 2019·Frontiers in Endocrinology·Che-Pei KungJason D Weber
Dec 19, 2019·Frontiers in Genetics·Ronaldo da Silva Francisco JuniorEnrique Medina-Acosta
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Sep 17, 2021·Functional & Integrative Genomics·Huseyin Avni TacUgur Sezerman

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Datasets Mentioned

BETA
GSE16256
SRP056236
CRA000575

Methods Mentioned

BETA
RNA-seq
DNA-seq
PCR
transfection
electrophoresis

Software Mentioned

Trimmomatic
GATK
Apobec
WASP
RADAR
RNAStructure
Genome Analysis Toolkit ( GATK )
BWA mem
ANNOVAR

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