PT  - JOURNAL ARTICLE
AU  - Mo-Xian Chen
AU  - Fu-Yuan Zhu
AU  - Feng-Zhu Wang
AU  - Neng-Hui Ye
AU  - Bei Gao
AU  - Xi Chen
AU  - Shan-Shan Zhao
AU  - Tao Fan
AU  - Yun-Ying Cao
AU  - Tie-Yuan Liu
AU  - Ze-Zhuo Su
AU  - Li-Juan Xie
AU  - Qi-Juan Hu
AU  - Hui-Jie Wu
AU  - Shi Xiao
AU  - Jianhua Zhang
AU  - Ying-Gao Liu
TI  - Alternative splicing and translation play important roles in parallel with transcriptional regulation during rice hypoxic germination
AID  - 10.1101/371583
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 371583
4099  - http://biorxiv.org/content/early/2018/07/18/371583.short
4100  - http://biorxiv.org/content/early/2018/07/18/371583.full
AB  - Post-transcriptional mechanisms, including alternative splicing (AS) and alternative translation initiation (ATI), have been used to explain the protein diversity involved in plant developmental processes and stress responses. Rice germination under hypoxia conditions is a classical model system for the study of low oxygen stress. It is known that there is transcriptional regulation during rice hypoxic germination, but the potential roles of AS and ATI in this process are not well understood. In this study, a proteogenomic approach was used to integrate the data from RNA sequencing, qualitative and quantitative proteomics to discover new players or pathways in the response to hypoxia stress. The improved analytical pipeline of proteogenomics led to the identification of 10,253 intron-containing genes, 1,729 of which were not present in the current annotation. Approximately 1,741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds in comparison to controls. Over 95% of these were not present in the list of differentially expressed genes (DEG). In particular, regulatory pathways such as spliceosome, ribosome, ER 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 traditional transcriptional regulation. Massive AS changes were identified, including the preference usage of certain non-conventional splice sites and enrichment of splicing factors in the DAS datasets. In addition, using self-constructed protein libraries by 6-frame translation, thousands of novel proteins/peptides contributed by ATI were identified. In summary, these results provide deeper insights towards understanding the underlying mechanisms of AS and ATI during rice hypoxic germination.