Epigenetics of Alternative Splicing in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (15 February 2022) | Viewed by 2823

Special Issue Editors

School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, UK
Interests: alternative splcing and abiotic stress tolerance; epigenetics of alternative splicing; heterosis
Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
Interests: epigenomics; abiotic stress; alternative splicing; gene regulation; epiRILs.
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Special Issue Information

Dear Colleagues, 

Alternative splicing (AS) is widespread in humans and plants. Recent evidence suggests that the process of splicing is largely co-transcriptional, and introns are spliced when pre-mRNA is still attached to DNA by RNA polymerase II (RNAPII). Since DNA is packaged into chromatin, it provides a natural barrier to the advancing RNAPII and influences the splicing process. Exons are usually GC-rich (nucleosome-rich compared to GC-poor introns), and transcription through nucleosome-rich regions with compact chromatin tends to be slower. Nucleosome occupancy is also lower in alternatively spliced exons compared to those that are constitutively spliced. DNA methylation affects exon recognition and is influenced by the GC architecture of exons and flanking introns in humans. Recent evidence suggests that histone modifications also directly affect AS in humans. Such evidence in plants is lacking; however, similar mechanisms may be involved, as the majority of Arabidopsis genes exhibit similar gene body methylation to other organisms. Not surprisingly, novel findings in plants have shown that the process of splicing is indeed predominantly co-transcriptional in plants; however, the mechanistic details remain to be elucidated. Therefore, this Special Issue aims to address how differences in DNA methylation, chromatin architecture, histone modification and RNA modifications influence splicing.

Dr. Naeem Hasan Syed
Dr. Saurabh Chaudhary
Guest Editors

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Keywords

  • epigenetics
  • DNA-methylation
  • chromatin structure
  • alternative splicing
  • gene regulation

Published Papers (1 paper)

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Research

19 pages, 3734 KiB  
Article
Stochastic Variation in DNA Methylation Modulates Nucleosome Occupancy and Alternative Splicing in Arabidopsis thaliana
Plants 2022, 11(9), 1105; https://doi.org/10.3390/plants11091105 - 19 Apr 2022
Cited by 2 | Viewed by 2142
Abstract
Plants 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 [...] Read more.
Plants 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. Full article
(This article belongs to the Special Issue Epigenetics of Alternative Splicing in Plants)
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