Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana.

Journal article

Chaudhary, Saurabh, Jabre, Ibtissam and Syed, Naeem 2021. Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana. Genomics. 113 (6), pp. 3476-3486. https://doi.org/S0888-7543(21)00312-8
AuthorsChaudhary, Saurabh, Jabre, Ibtissam and Syed, Naeem
AbstractHow stable and temperature-dependent variations in DNA methylation and nucleosome occupancy influence alternative splicing (AS) remains poorly understood in plants. To answer this, we generated transcriptome, whole-genome bisulfite, and MNase sequencing data for an epigenetic Recombinant Inbred Line (epiRIL) of A. thaliana at normal and cold temperature. For comparative analysis, the same data sets for the parental ecotype Columbia (Col-0) were also generated, whereas for DNA methylation, previously published high confidence methylation profiles of Col-0 were used. Significant epigenetic differences in an identical genetic background were observed between Col-0 and epiRIL lines under normal and cold temperatures. Our transcriptome data revealed that differential DNA methylation and nucleosome occupancy modulate expression levels of many genes and AS in response to cold. Collectively, DNA methylation and nucleosome levels exhibit characteristic patterns around intron-exon boundaries at normal and cold conditions, and any perturbation in them, in an identical genetic background is sufficient to modulate AS in Arabidopsis. [Abstract copyright: Crown Copyright © 2021. Published by Elsevier Inc. All rights reserved.]
KeywordsepiRILs; Nucleosome occupancy; Alternative splicing; DNA-methylation; Cold stress; Arabidopsis
Year2021
JournalGenomics
Journal citation113 (6), pp. 3476-3486
PublisherElsevier
ISSN1089-8646
Digital Object Identifier (DOI)https://doi.org/S0888-7543(21)00312-8
https://doi.org/10.1016/j.ygeno.2021.08.006
Official URLhttps://www.sciencedirect.com/science/article/pii/S0888754321003128
Publication dates
Online12 Aug 2021
Publication process dates
Accepted10 Aug 2021
Deposited04 Jul 2024
Publisher's version
File Access Level
Open
Output statusPublished
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0888-7543/Crown Copyright © 2021 Published by Elsevier Inc. This article is made available under the Elsevier license (http://www.elsevier.com/openaccess/userlicense/1.0/).

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