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CC BY-NC-ND V4.0, Open Access
Journal article
Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut
Plant biotechnology journal, Vol.22(6), pp.1681-1702
2024
PMID: 38294334
Abstract
Alternative splicing (AS), an important post‐transcriptional regulation mechanism in eukaryotes, can significantly increase transcript diversity and contribute to gene expression regulation and many other complicated developmental processes. While plant gene AS events are well described, few studies have investigated the comprehensive regulation machinery of plant AS. Here, we use multi‐omics to analyse peanut AS events. Using long‐read isoform sequencing, 146 464 full‐length non‐chimeric transcripts were obtained, resulting in annotation corrections for 1782 genes and the identification of 4653 new loci. Using Iso‐Seq RNA sequences, 271 776 unique splice junctions were identified, 82.49% of which were supported by transcriptome data. We characterized 50 977 polyadenylation sites for 23 262 genes, 12 369 of which had alternative polyadenylation sites. AS allows differential regulation of the same gene by miRNAs at the isoform level coupled with polyadenylation. In addition, we identified many long non‐coding RNAs and fusion transcripts. There is a suppressed effect of 6mA on AS and gene expression. By analysis of chromatin structures, the genes located in the boundaries of topologically associated domains, proximal chromosomal telomere regions, inter‐ or intra‐chromosomal loops were found to have more unique splice isoforms, higher expression, lower 6mA and more transposable elements (TEs) in their gene bodies than the other genes, indicating that chromatin interaction, 6mA and TEs play important roles in AS and gene expression. These results greatly refine the peanut genome annotation and contribute to the study of gene expression and regulation in peanuts. This work also showed AS is associated with multiple strategies for gene regulation.
Details
- Title
- Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut
- Authors/Creators
- Lihui Wang - Fujian Agriculture and Forestry UniversityHua Chen - Fujian Agriculture and Forestry UniversityYuhui Zhuang - Fujian Agriculture and Forestry UniversityKun Chen - Fujian Agriculture and Forestry UniversityChong Zhang - Fujian Agriculture and Forestry UniversityTiecheng Cai - Fujian Agriculture and Forestry UniversityQiang Yang - Fujian Agriculture and Forestry UniversityHuiwen Fu - Fujian Agriculture and Forestry UniversityXiangyu Chen - Fujian Academy of Agricultural SciencesAnnapurna Chitkineni - Murdoch UniversityXiyin Wang - North China University of Science and TechnologyRajeev K. Varshney - Murdoch University, Food Futures InstituteWeijian Zhuang - Fujian Agriculture and Forestry University
- Publication Details
- Plant biotechnology journal, Vol.22(6), pp.1681-1702
- Publisher
- Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
- Identifiers
- 991005637069807891
- Copyright
- © 2024 The Authors.
- Murdoch Affiliation
- Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.100 Epigenetic Regulation
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science