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The characteristics of mRNA m(6)A methylomes in allopolyploid Brassica napus and its diploid progenitors

Genome duplication events, comprising whole-genome duplication and single-gene duplication, produce a complex genomic context leading to multiple levels of genetic changes. However, the characteristics of m(6)A modification, the most widespread internal eukaryotic mRNA modification, in polyploid spe...

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Autores principales: Li, Zeyu, Li, Mengdi, Wu, Xiaoming, Wang, Jianbo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832873/
https://www.ncbi.nlm.nih.gov/pubmed/36643749
http://dx.doi.org/10.1093/hr/uhac230
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author Li, Zeyu
Li, Mengdi
Wu, Xiaoming
Wang, Jianbo
author_facet Li, Zeyu
Li, Mengdi
Wu, Xiaoming
Wang, Jianbo
author_sort Li, Zeyu
collection PubMed
description Genome duplication events, comprising whole-genome duplication and single-gene duplication, produce a complex genomic context leading to multiple levels of genetic changes. However, the characteristics of m(6)A modification, the most widespread internal eukaryotic mRNA modification, in polyploid species are still poorly understood. This study revealed the characteristics of m(6)A methylomes within the early formation and following the evolution of allopolyploid Brassica napus. We found a complex relationship between m(6)A modification abundance and gene expression level depending on the degree of enrichment or presence/absence of m(6)A modification. Overall, the m(6)A genes had lower gene expression levels than the non-m(6)A genes. Allopolyploidization may change the expression divergence of duplicated gene pairs with identical m(6)A patterns and diverged m(6)A patterns. Compared with duplicated genes, singletons with a higher evolutionary rate exhibited higher m(6)A modification. Five kinds of duplicated genes exhibited distinct distributions of m(6)A modifications in transcripts and gene expression level. In particular, tandem duplication-derived genes showed unique m(6)A modification enrichment around the transcript start site. Active histone modifications (H3K27ac and H3K4me3) but not DNA methylation were enriched around genes of m(6)A peaks. These findings provide a new understanding of the features of m (6)A modification and gene expression regulation in allopolyploid plants with sophisticated genomic architecture.
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spelling pubmed-98328732023-01-12 The characteristics of mRNA m(6)A methylomes in allopolyploid Brassica napus and its diploid progenitors Li, Zeyu Li, Mengdi Wu, Xiaoming Wang, Jianbo Hortic Res Article Genome duplication events, comprising whole-genome duplication and single-gene duplication, produce a complex genomic context leading to multiple levels of genetic changes. However, the characteristics of m(6)A modification, the most widespread internal eukaryotic mRNA modification, in polyploid species are still poorly understood. This study revealed the characteristics of m(6)A methylomes within the early formation and following the evolution of allopolyploid Brassica napus. We found a complex relationship between m(6)A modification abundance and gene expression level depending on the degree of enrichment or presence/absence of m(6)A modification. Overall, the m(6)A genes had lower gene expression levels than the non-m(6)A genes. Allopolyploidization may change the expression divergence of duplicated gene pairs with identical m(6)A patterns and diverged m(6)A patterns. Compared with duplicated genes, singletons with a higher evolutionary rate exhibited higher m(6)A modification. Five kinds of duplicated genes exhibited distinct distributions of m(6)A modifications in transcripts and gene expression level. In particular, tandem duplication-derived genes showed unique m(6)A modification enrichment around the transcript start site. Active histone modifications (H3K27ac and H3K4me3) but not DNA methylation were enriched around genes of m(6)A peaks. These findings provide a new understanding of the features of m (6)A modification and gene expression regulation in allopolyploid plants with sophisticated genomic architecture. Oxford University Press 2022-10-11 /pmc/articles/PMC9832873/ /pubmed/36643749 http://dx.doi.org/10.1093/hr/uhac230 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nanjing Agricultural University. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Li, Zeyu
Li, Mengdi
Wu, Xiaoming
Wang, Jianbo
The characteristics of mRNA m(6)A methylomes in allopolyploid Brassica napus and its diploid progenitors
title The characteristics of mRNA m(6)A methylomes in allopolyploid Brassica napus and its diploid progenitors
title_full The characteristics of mRNA m(6)A methylomes in allopolyploid Brassica napus and its diploid progenitors
title_fullStr The characteristics of mRNA m(6)A methylomes in allopolyploid Brassica napus and its diploid progenitors
title_full_unstemmed The characteristics of mRNA m(6)A methylomes in allopolyploid Brassica napus and its diploid progenitors
title_short The characteristics of mRNA m(6)A methylomes in allopolyploid Brassica napus and its diploid progenitors
title_sort characteristics of mrna m(6)a methylomes in allopolyploid brassica napus and its diploid progenitors
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832873/
https://www.ncbi.nlm.nih.gov/pubmed/36643749
http://dx.doi.org/10.1093/hr/uhac230
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