文献类型： 外文期刊

作者： Zhou, Qian ¹ ; Fu, Haihui ¹ ; Yang, Dewei ³ ; Ye, Congting ¹ ; Zhu, Sheng ⁴ ; Lin, Juncheng ¹ ; Ye, Wenbin ⁴ ; Ji, Guoli; ¹ ;

作者机构： 1.Xiamen Univ, Coll Environm & Ecol, Minist Educ Coastal & Wetland Ecosyst, Key Lab, Xiamen 361102, Fujian, Peoples R China

2.Western Univ Hlth Sci, Grad Coll Biomed Sci, Pomona, CA 91766 USA

3.Fujian Acad Agr Sci, Rice Res Inst, Fuzhou 350003, Fujian, Peoples R China

4.Xiamen Univ, Dept Automat, Xiamen 361005, Fujian, Peoples R China

5.Fudan Univ, Sch Life Sci, Collaborat Innovat Ctr Genet & Dev, State Key Lab Genet Engn, Shanghai 200438, Peoples R China

6.Fudan Univ, Sch Life Sci, Collaborat Innovat Ctr Genet & Dev, MOE Key Lab Contemporary Anthropol, Shanghai 200438, Peoples R China

7.Fudan Univ, Shanghai Canc Ctr, Shanghai 200438, Peoples R China

关键词： alternative polyadenylation; 3 ' end formation; environmental adaptation; post-transcriptional regulation; rice subspecies; RNA processing; transcriptome analysis

期刊名称：PLANT JOURNAL （ 影响因子：6.417； 五年影响因子：7.627 ）

ISSN： 0960-7412

年卷期： 2019 年 98 卷 2 期

页码：

收录情况： SCI

摘要： Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica. Using a poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage between indica and japonica, and extensive differentiation in APA profiles was detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance of indica and cold-stress tolerance of japonica. In most tissues, differential usage of APA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of the booting stage, APA site-switching genes displayed global shortening of 3 ' untranslated regions with increased expression in indica compared with japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis in indica than in japonica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits.