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Alternative splicing of lncRNA LAIR fine-tunes the regulation of neighboring yield-related gene LRK1 expression in rice

文献类型： 外文期刊

作者： Wang, Ying 1 ; Cao, Liming 5 ; Liu, Mingyu 1 ; Yan, Peiwen 1 ; Niu, Fuan 1 ; Dong, Shiqing 1 ; Ma, Fuying 1 ; Lan, Dengyong 1 ; Zhang, Xinwei 1 ; Hu, Jian 1 ; Xin, Xiaoyun 1 ; Yang, Jinshui 1 ; Luo, Xiaojin 1 ;

作者机构： 1.Fudan Univ, State Key Lab Genet Engn, Key Lab Biodivers Sci & Ecol Engn, Minist Educ,Inst Plant Biol,Sch Life Sci, Shanghai 200438, Peoples R China

2.Fudan Univ, Sch Life Sci, MOE Engn Res Ctr Gene Technol, Shanghai 200438, Peoples R China

3.Fudan Zhangjiang Inst, Res Ctr Ecol Sci & Technol, 351 Guoshoujing Rd, Shanghai 201203, Peoples R China

4.Fudan Univ, Natl Sci Pk, Shanghai 200433, Peoples R China

5.Shanghai Acad Agr Sci, Inst Crop Breeding & Cultivat, Shanghai 201403, Peoples R China

6.Huaiyin Normal Univ, Sch Life Sci, Jiangsu Key Lab Ecoagr Biotechnol Hongze Lake, Huaian 223300, Peoples R China

关键词： long noncoding RNA; LAIR; alternative splicing; LRK gene cluster; fine-tuning regulation; rice yield; stress response; molecular polymorphism breeding

期刊名称：PLANT JOURNAL （ 影响因子：6.2； 五年影响因子：7.1 ）

ISSN： 0960-7412

年卷期： 2024 年 119 卷 4 期

页码：

收录情况： SCI

摘要： The diversity in alternative splicing of long noncoding RNAs (lncRNAs) poses a challenge for functional annotation of lncRNAs. Moreover, little is known on the effects of alternatively spliced lncRNAs on crop yield. In this study, we cloned nine isoforms resulting from the alternative splicing of the lncRNA LAIR in rice. The LAIR isoforms are generated via alternative 5 '/3 ' splice sites and different combinations of specific introns. All LAIR isoforms activate the expression of the neighboring LRK1 gene and enhance yield-related rice traits. In addition, there are slight differences in the binding ability of LAIR isoforms to the epigenetic modification-related proteins OsMOF and OsWDR5, which affect the enrichment of H4K16ac and H3K4me3 at the LRK1 locus, and consequently fine-tune the regulation of LRK1 expression and yield-related traits. These differences in binding may be caused by polymorphic changes to the RNA secondary structure resulting from alternative splicing. It was also observed that the composition of LAIR isoforms was sensitive to abiotic stress. These findings suggest that the alternative splicing of LAIR leads to the formation of a functional transcript population that precisely regulates yield-related gene expression, which may be relevant for phenotypic polymorphism-based crop breeding under changing environmental conditions.

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