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Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana
Author(s) -
Jabre Ibtissam,
Chaudhary Saurabh,
Guo Wenbin,
Kalyna Maria,
Reddy Anireddy S. N.,
Chen Weizhong,
Zhang Runxuan,
Wilson Cornelia,
Syed Naeem H.
Publication year - 2021
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.17062
Subject(s) - nucleosome , chromatin , biology , intron , rna splicing , arabidopsis , swi/snf , arabidopsis thaliana , histone , genetics , transcriptome , alternative splicing , gene , computational biology , exon , microbiology and biotechnology , rna , gene expression , mutant
Summary 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.