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Evolution of the RNA N6-Methyladenosine Methylome Mediated by Genomic Duplication

Evolution of the RNA N6-Methyladenosine Methylome Mediated by Genomic Duplication

Authors :
Zhaoxue Han
Jie Song
Chuang Ma
Yuhong Qi
Zhenyan Miao
Ting Zhang
Source :
Plant Physiology. 182:345-360
Publication Year :
2019
Publisher :
Oxford University Press (OUP), 2019.

Abstract

RNA N6-methyladenosine (m6A) modification is the most abundant form of RNA epigenetic modification in eukaryotes. Given that m6A evolution is associated with the selective constraints of nucleotide sequences in mammalian genomes, we hypothesize that m6A evolution can be linked, at least in part, to genomic duplication events in complex polyploid plant genomes. To test this hypothesis, we presented the maize (Zea mays) m6A modification landscape in a transcriptome-wide manner and identified 11,968 m6A peaks carried by 5,893 and 3,811 genes from two subgenomes (maize1 and maize2, respectively). Each of these subgenomes covered over 2,200 duplicate genes. Within these duplicate genes, those carrying m6A peaks exhibited significant differences in retention rate. This biased subgenome fractionation of m6A-methylated genes is associated with multiple sequence features and is influenced by asymmetric evolutionary rates. We also characterized the coevolutionary patterns of m6A-methylated genes and transposable elements, which can be mediated by whole genome duplication and tandem duplication. We revealed the evolutionary conservation and divergence of duplicated m6A functional factors and the potential role of m6A modification in maize responses to drought stress. This study highlights complex interplays between m6A modification and gene duplication, providing a reference for understanding the mechanisms underlying m6A evolution mediated by genome duplication events.

Details

ISSN :
15322548 and 00320889
Volume :
182
Database :
OpenAIRE
Journal :
Plant Physiology
Accession number :
edsair.doi...........d6ba635c1a64da5cc178ac397760030d
Full Text :
https://doi.org/10.1104/pp.19.00323