Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

Journal article

Jabre, I., Chaudhary, S., Guo, W., Kalyna, M., Reddy, A. S. N., Chen, W., Zhang, R., Wilson, C. and Syed, N. 2020. Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana. New Phytologist. https://doi.org/10.1111/nph.17062
AuthorsJabre, I., Chaudhary, S., Guo, W., Kalyna, M., Reddy, A. S. N., Chen, W., Zhang, R., Wilson, C. and Syed, N.
Abstract

• Alternative splicing (AS) is a major gene regulatory mechanism in plants. Recent evidence supports co-transcriptional splicing in plants, hence the chromatin state can impact AS. However, how dynamic changes in the chromatin state such as nucleosome occupancy influence the cold-induced AS remains poorly understood.
• Here, we generated transcriptome (RNA-Seq) and nucleosome positioning (MNase-Seq) data for Arabidopsis thaliana to understand how nucleosome positioning modulates cold-induced AS.
• Our results show that characteristic nucleosome occupancy levels are strongly associated with the type and abundance of various AS events under normal and cold temperature conditions in Arabidopsis. Intriguingly, exitrons, alternatively spliced internal regions of protein-coding exons, exhibit distinctive nucleosome positioning pattern compared to other alternatively spliced regions. Likewise, nucleosome patterns differ between exitrons and retained introns pointing to their distinct regulation.
• Collectively, our data show that characteristic changes in nucleosome positioning modulate AS in plants in response to cold.

KeywordsAlternative Splicing; Arabidopsis thaliana; Cold stress; Co-transcriptional Splicing; Exitrons; Nucleosome Positioning
Year2020
JournalNew Phytologist
PublisherWiley
ISSN0028-646X
1469-8137
Digital Object Identifier (DOI)https://doi.org/10.1111/nph.17062
Official URLhttps://doi.org/10.1111/nph.17062
Publication dates
Online01 Nov 2020
Publication process dates
Accepted24 Oct 2020
Deposited29 Oct 2020
Accepted author manuscript
File Access Level
Open
Output statusPublished
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