@article{af5a3c6583914e13a0bb4fe22b4f6569,
title = "Alternative splicing and translation play important roles in hypoxic germination in rice",
abstract = "Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ∼1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.",
keywords = "Alternative splicing, hypoxia, Oryza sativa, proteogenomics, seed germination, splicing factor, translation initiation",
author = "Chen, {Mo Xian} and Zhu, {Fu Yuan} and Wang, {Feng Zhu} and Ye, {Neng Hui} and Bei Gao and Xi Chen and Zhao, {Shan Shan} and Tao Fan and Cao, {Yun Ying} and Liu, {Tie Yuan} and Su, {Ze Zhuo} and Xie, {Li Juan} and Hu, {Qi Juan} and Wu, {Hui Jie} and Shi Xiao and Jianhua ZHANG and Liu, {Ying Gao}",
note = "Funding Information: This work was supported by the Natural Science Foundation of Guangdong Province (2018A030313030), funds of the Shandong 'Double Top' Program, the China Postdoctoral Science Foundation (2017M622801 and 2018M633162), the Postgraduate Research & Practice Innovative Program of Jiangsu Province (KYCX18_2416), the National Natural Science Foundation of China (31771701, 31701341), Innovative Training Program of Nantong University College Students 2017 (201710304049Z), and Hong Kong Research Grant Council (AoE/M-05/12, AoE/M-403/16, GRF 14122415, 14160516, 14177617). The authors declare no competing fnancial interests. Funding Information: This work was supported by the Natural Science Foundation of Guangdong Province (2018A030313030), funds of the Shandong {\textquoteleft}Double Top{\textquoteright} Program, the China Postdoctoral Science Foundation (2017M622801 and 2018M633162), the Postgraduate Research & Practice Innovative Program of Jiangsu Province (KYCX18_2416), the National Natural Science Foundation of China (31771701, 31701341), Innovative Training Program of Nantong University College Students 2017 (201710304049Z), and Hong Kong Research Grant Council (AoE/M-05/12, AoE/M-403/16, GRF 14122415, 14160516, 14177617).The authors declare no competing financial interests.",
year = "2019",
month = feb,
day = "5",
doi = "10.1093/jxb/ery393",
language = "English",
volume = "70",
pages = "885--895",
journal = "Journal of Experimental Botany",
issn = "0022-0957",
publisher = "Oxford University Press",
number = "3",
}