The pattern of alternative splicing and DNA methylation alteration and their interaction in linseed ( Linum usitatissimum L.) response to repeated drought stresses

Biological Research

article

Wang, Ling¹  Wang, Lei¹  Tan, Meilian¹  Wang, Linhai¹  Zhao, Wei²  You, Jun¹  Wang, Lijun  Yan, Xingchu¹  Wang, Wei¹ 

[1] Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of Chinese Academy of Agricultural Science;Crop Institute, Gansu Academy of Agricultural Sciences

关键词: Drought stresses;    Alternative splicing;    DNA methylation;    Linseed;    Transcriptome;   

DOI  :  10.1186/s40659-023-00424-7

学科分类：社会科学、人文和艺术（综合）

来源: BioMed Central

【 摘 要 】

Drought stress has significantly hampered agricultural productivity worldwide and can also result in modifications to DNA methylation levels. However, the dynamics of DNA methylation and its association with the changes in gene transcription and alternative splicing (AS) under drought stress are unknown in linseed, which is frequently cultivated in arid and semiarid regions. We analysed AS events and DNA methylation patterns in drought-tolerant (Z141) and drought-sensitive (NY-17) linseed under drought stress (DS) and repeated drought stress (RD) treatments. We found that the number of intron-retention (IR) and alternative 3’ splice site (Alt3’SS) events were significantly higher in Z141 and NY-17 under drought stress. We found that the linseed response to the DS treatment was mainly regulated by transcription, while the response to the RD treatment was coregulated by transcription and AS. Whole genome-wide DNA methylation analysis revealed that drought stress caused an increase in the overall methylation level of linseed. Although we did not observe any correlation between differentially methylated genes (DMGs) and differentially spliced genes (DSGs) in this study, we found that the DSGs whose gene body region was hypermethylated in Z141 and hypomethylated in NY-17 were enriched in abiotic stress response Gene Ontology (GO) terms. This finding implies that gene body methylation plays an important role in AS regulation in some specific genes. Our study is the first comprehensive genome-wide analysis of the relationship between linseed methylation changes and AS under drought and repeated drought stress. Our study revealed different interaction patterns between differentially expressed genes (DEGs) and DSGs under DS and RD treatments and differences between methylation and AS regulation in drought-tolerant and drought-sensitive linseed varieties. The findings will probably be of interest in the future. Our results provide interesting insights into the association between gene expression, AS, and DNA methylation in linseed under drought stress. Differences in these associations may account for the differences in linseed drought tolerance.

【 授权许可】

CC BY|CC0