Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

Jabre, Ibtissam, Chaudhary, Saurabh, Guo, Wenbin, Kalyna, Maria, Reddy, Anireddy S. N., Chen, Weizhong, Zhang, Runxuan, Wilson, Cornelia and Syed, Naeem H. 2021. Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana. New Phytologist 229 (4) , pp. 1937-1945. 10.1111/nph.17062

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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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences
Additional Information:	The definitive version is available at http://online↲ library.wiley.com/journal/10.1111/(ISSN)1469-8137
Publisher:	Wiley
ISSN:	0028-646X
Date of First Compliant Deposit:	7 December 2020
Date of Acceptance:	24 October 2020
Last Modified:	05 May 2023 07:25
URI:	https://orca.cardiff.ac.uk/id/eprint/136834

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