Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis

Hua Zhou, Haiyue Zeng, Tingting Yan, Sunlu Chen, Ying Fu, Guochen Qin, Xianhai Zhao, Yueqin Heng, Jian Li, Fang Lin, Dongqing Xu, Ning Wei and Xing Wang Deng ()
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Hua Zhou: Southern University of Science and Technology
Haiyue Zeng: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Tingting Yan: Southern University of Science and Technology
Sunlu Chen: Nanjing Agricultural University
Ying Fu: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Guochen Qin: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Xianhai Zhao: Southern University of Science and Technology
Yueqin Heng: Southern University of Science and Technology
Jian Li: Southern University of Science and Technology
Fang Lin: Lanzhou University
Dongqing Xu: Nanjing Agricultural University
Ning Wei: Southwest University
Xing Wang Deng: Southern University of Science and Technology

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Intron retention (IR) is the most common alternative splicing event in Arabidopsis. An increasing number of studies have demonstrated the major role of IR in gene expression regulation. The impacts of IR on plant growth and development and response to environments remain underexplored. Here, we found that IR functions directly in gene expression regulation on a genome-wide scale through the detainment of intron-retained transcripts (IRTs) in the nucleus. Nuclear-retained IRTs can be kept away from translation through this mechanism. COP1-dependent light modulation of the IRTs of light signaling genes, such as PIF4, RVE1, and ABA3, contribute to seedling morphological development in response to changing light conditions. Furthermore, light-induced IR changes are under the control of the spliceosome, and in part through COP1-dependent ubiquitination and degradation of DCS1, a plant-specific spliceosomal component. Our data suggest that light regulates the activity of the spliceosome and the consequent IRT nucleus detainment to modulate photomorphogenesis through COP1.

Date: 2024
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DOI: 10.1038/s41467-024-49571-9

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