The pattern of DNA methylation alteration, and its association with the expression changes of non-coding RNAs and mRNAs in Moso bamboo under abiotic stress

Yiqian Ding; Long-Hai Zou; Jiajun Wu; Muthusamy Ramakrishnan; Yubang Gao; Liangzhen Zhao; Mingbing Zhou

doi:10.1016/j.plantsci.2022.111451

The pattern of DNA methylation alteration, and its association with the expression changes of non-coding RNAs and mRNAs in Moso bamboo under abiotic stress

Plant Sci. 2022 Dec:325:111451. doi: 10.1016/j.plantsci.2022.111451. Epub 2022 Sep 6.

Authors

Yiqian Ding¹, Long-Hai Zou², Jiajun Wu¹, Muthusamy Ramakrishnan¹, Yubang Gao¹, Liangzhen Zhao³, Mingbing Zhou⁴

Affiliations

¹ The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
² The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China. Electronic address: zoulonghai@zafu.edu.cn.
³ The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
⁴ The State Key Laboratory of Subtropical Silviculture; Institute of Bamboo, Zhejiang A&F University, Lin'an, Hangzhou 311300, China. Electronic address: zhoumingbing@zafu.edu.cn.

PMID: 36075278
DOI: 10.1016/j.plantsci.2022.111451

Abstract

Epigenetic changes play an important role in plant growth and development and in stress response. However, DNA methylation pattern and its relationship with the expression changes of non-coding RNAs and mRNAs of Moso bamboo in response to abiotic stress is still largely unknown. In this work, we used whole-genome bisulfite sequencing in combination with whole-transcriptome sequencing to analyze the DNA methylation and transcription patterns of mRNAs and non-coding RNAs in Moso bamboo under abiotic stresses such as cold, heat, ultraviolet (UV) and salinity. We found that CHH methylation in the promoter region was positively correlated with gene expression, while CHG and CHH methylations in the gene body regions were negatively associated with gene expression. Moreover, CG and CHG methylations in the promoter regions were negatively correlated with the transcript abundance of long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs). Similarly, the methylation levels of three contexts in the genic regions were negatively correlated with the transcript abundance of lncRNAs and miRNAs but positively correlated with that of circRNAs. In addition, we suggested that the reduction of 21-nt and 24-nt small interfering RNA (siRNA) expression tended to increase methylation levels in the genic regions. We found that stress-responsive genes such as CRPK1, HSFB2A and CIPK were differentially methylated and expressed. Our results also proposed that DNA methylation may regulate the expression of the transcription factors (TFs) and plant hormone signalling genes such as IAA9, MYC2 and ERF110 in response to abiotic stress. This study firstly reports the abiotic stress-responsive DNA methylation pattern and its involvement of expression of coding RNAs and non-coding RNAs in Moso bamboo. The results expand the knowledge of epigenetic mechanisms in Moso bamboo under abiotic stress and support in-depth deciphering of the function of specific non-coding RNAs in future studies.

Keywords: Abiotic stress; DNA methylation; Non-coding RNAs; Phyllostachys edulis; Transcription patterns.

MeSH terms

DNA Methylation / genetics
Gene Expression Regulation, Plant / genetics
MicroRNAs*
Poaceae / genetics
RNA, Circular
RNA, Long Noncoding*
RNA, Messenger / genetics
Stress, Physiological / genetics

Substances

RNA, Circular
RNA, Long Noncoding
RNA, Messenger
MicroRNAs