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The chromatin remodeler ZmCHB101 impacts alternative splicing contexts in response to osmotic stress

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Abstract

Key message

Maize SWI3-type chromatin remodeler impacts alternative splicing contexts in response to osmotic stress by altering nucleosome density and affecting transcriptional elongation rate.

Abstract

Alternative splicing (AS) is commonly found in higher eukaryotes and is an important posttranscriptional regulatory mechanism to generate transcript diversity. AS has been widely accepted as playing essential roles in different biological processes including growth, development, signal transduction and responses to biotic and abiotic stresses in plants. However, whether and how chromatin remodeling complex functions in AS in plant under osmotic stress remains unknown. Here, we show that a maize SWI3D protein, ZmCHB101, impacts AS contexts in response to osmotic stress. Genome-wide analysis of mRNA contexts in response to osmotic stress using ZmCHB101-RNAi lines reveals that ZmCHB101 impacts alternative splicing contexts of a subset of osmotic stress-responsive genes. Intriguingly, ZmCHB101-mediated regulation of gene expression and AS is largely uncoupled, pointing to diverse molecular functions of ZmCHB101 in transcriptional and posttranscriptional regulation. We further found ZmCHB101 impacts the alternative splicing contexts by influencing alteration of chromatin and histone modification status as well as transcriptional elongation rates mediated by RNA polymerase II. Taken together, our findings suggest a novel insight of how plant chromatin remodeling complex impacts AS under osmotic stress .

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Acknowledgements

The authors would like to thank Dr. Shucai Wang for critical reading of the manuscript and helpful discussions.

Funding

The research was supported by the National Natural Science Foundation of China (#31601311 to Z.-Y.X. and #31471565 to X.Q.), Natural Science Foundation of Jilin Province of China (#20180101233JC to Z.-Y.X.) and the Fundamental Research Fund for the Central Universities (#2412018BJ002 to Z.-Y.X.).

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  1. Xutong Wang

    Present address: Department of Agronomy, Purdue University, West Lafayette, USA

Authors and Affiliations

  1. School of Agronomy, Jilin Agricultural Science and Technology University, Jilin, 132301, People’s Republic of China

    Xiaoming Yu

  2. Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People’s Republic of China

    Xiaoming Yu, Xinchao Meng, Yutong Liu, Xutong Wang, Tian-Jing Wang, Ai Zhang, Ning Li, Bao Liu & Zheng-Yi Xu

  3. Department of Agronomy, Jilin Agricultural University, Changchun, 130118, People’s Republic of China

    Xin Qi

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Yu, X., Meng, X., Liu, Y. et al. The chromatin remodeler ZmCHB101 impacts alternative splicing contexts in response to osmotic stress. Plant Cell Rep 38, 131–145 (2019). https://doi.org/10.1007/s00299-018-2354-x

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