Alternative splicing and translation play important roles in hypoxic germination in rice

Mo Xian Chen, Fu Yuan Zhu, Feng Zhu Wang, Neng Hui Ye, Bei Gao, Xi Chen, Shan Shan Zhao, Tao Fan, Yun Ying Cao, Tie Yuan Liu, Ze Zhuo Su, Li Juan Xie, Qi Juan Hu, Hui Jie Wu, Shi Xiao, Jianhua ZHANG, Ying Gao Liu*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

49 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)885-895
Number of pages11
JournalJournal of Experimental Botany
Issue number3
Publication statusPublished - 5 Feb 2019

Scopus Subject Areas

  • Physiology
  • Plant Science

User-Defined Keywords

  • Alternative splicing
  • hypoxia
  • Oryza sativa
  • proteogenomics
  • seed germination
  • splicing factor
  • translation initiation


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