Stochastic variation in DNA methylation modulates nucleosome occupancy and alternative splicing in Arabidopsis thaliana

Journal article

Jabre, Ibtissam, Chaudhary, S., Wilson, C., Staiger, D. and Syed, N. 2022. Stochastic variation in DNA methylation modulates nucleosome occupancy and alternative splicing in Arabidopsis thaliana. Plants. 11 (9), p. 1105. https://doi.org/10.3390/plants11091105
AuthorsJabre, Ibtissam, Chaudhary, S., Wilson, C., Staiger, D. and Syed, N.
AbstractPlants use complex gene regulatory mechanisms to overcome diverse environmental challenges. For instance, cold stress induces rapid and massive transcriptome changes via alternative splicing (AS) to confer cold tolerance in plants. In mammals, mounting evidence suggests chromatin structure can regulate co-transcriptional AS. Recent evidence also supports co-transcriptional regulation of AS in plants, but how dynamic changes in DNA methylation and the chromatin structure influence the AS process upon cold stress remains poorly understood. In this study, we used the DNA methylation inhibitor 5-Aza-2′-Deoxycytidine (5-aza-dC) to investigate the role of stochastic variations in DNA methylation and nucleosome occupancy in modulating cold-induced AS, in Arabidopsis thaliana (Arabidopsis). Our results demonstrate that 5-aza-dC derived stochastic hypomethylation modulates nucleosome occupancy and AS profiles of genes implicated in RNA metabolism, plant hormone signal transduction, and of cold-related genes in response to cold stress. We also demonstrate that cold-induced remodelling of DNA methylation regulates genes involved in amino acid metabolism. Collectively, we demonstrate that sudden changes in DNA methylation via drug treatment can influence nucleosome occupancy levels and modulate AS in a temperature-dependent manner to regulate plant metabolism and physiological stress adaptation.
KeywordsArabidopsis thaliana; Alternative splicing; Cold stress; Co-transcriptional Alternative Splicing; Stochastic Dna Methylation
Year2022
JournalPlants
Journal citation11 (9), p. 1105
PublisherMDPI AG
ISSN2223-7747
Digital Object Identifier (DOI)https://doi.org/10.3390/plants11091105
Official URLhttps://www.mdpi.com/2223-7747/11/9/1105
Publication dates
Print01 Apr 2022
Online19 Apr 2022
Publication process dates
Deposited20 Apr 2022
Accepted07 Apr 2022
Publisher's version
Output statusPublished
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