Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

Ibtissam Jabre, Saurabh Chaudhary, Wenbin Guo, Maria Kalyna, Anireddy S. N. Reddy, Weizhong Chen, Runxuan Zhang, Cornelia Wilson, Naeem H. Syed (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

21 Citations (Scopus)
80 Downloads (Pure)


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.

Original languageEnglish
Pages (from-to)1937-1945
Number of pages9
JournalNew Phytologist
Issue number4
Early online date1 Nov 2020
Publication statusPublished - Feb 2021


  • Arabidopsis thaliana
  • alternative splicing
  • co-transcriptional splicing
  • cold stress
  • exitrons
  • nucleosome positioning

ASJC Scopus subject areas

  • Physiology
  • Plant Science


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