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Oct 13, 2024;7 (1): 1314.

Seeing the unseen in characterizing RNA editome during rice endosperm development.

Ming Chen, Lin Xia, Xinyu Tan, Shenghan Gao, Sen Wang, Man Li, Yuansheng Zhang, Tianyi Xu, Yuanyuan Cheng, Yuan Chu, Songnian Hu, Shuangyang Wu, Zhang Zhang
Author Information
  1. Ming Chen: National Genomics Data Center, China National Center for Bioinformation, Beijing, China. ORCID
  2. Lin Xia: National Genomics Data Center, China National Center for Bioinformation, Beijing, China.
  3. Xinyu Tan: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  4. Shenghan Gao: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. ORCID
  5. Sen Wang: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  6. Man Li: National Genomics Data Center, China National Center for Bioinformation, Beijing, China.
  7. Yuansheng Zhang: National Genomics Data Center, China National Center for Bioinformation, Beijing, China.
  8. Tianyi Xu: National Genomics Data Center, China National Center for Bioinformation, Beijing, China. ORCID
  9. Yuanyuan Cheng: National Genomics Data Center, China National Center for Bioinformation, Beijing, China.
  10. Yuan Chu: National Genomics Data Center, China National Center for Bioinformation, Beijing, China.
  11. Songnian Hu: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. husn@im.ac.cn. ORCID
  12. Shuangyang Wu: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. shuangyang.wu@gmi.oeaw.ac.at. ORCID
  13. Zhang Zhang: National Genomics Data Center, China National Center for Bioinformation, Beijing, China. zhangzhang@big.ac.cn. ORCID
PMID: 39397073 DOI: 10.1038/s42003-024-07032-5

Abstract

Rice (Oryza sativa L.) endosperm is essential to provide nutrients for seed germination and determine grain yield. RNA editing, a post-transcriptional modification essential for plant development, unfortunately, is not fully characterized during rice endosperm development. Here, we perform systematic analyses to characterize RNA editome during rice endosperm development. We find that most editing sites are C-to-U CDS-recoding in mitochondria, leading to increased hydrophobic amino acids and changed structures of mitochondrial proteins. Comparative analysis of RNA editome reveals that CDS-recoding sites present higher editing frequencies with lower variabilities and their resultant recoded amino acids tend to exhibit stronger evolutionary conservation across many land plants. Furthermore, we classify mitochondrial genes into three groups, presenting distinct patterns in terms of CDS-recoding events. Besides, we conduct genome-wide screening to detect pentatricopeptide repeat (PPR) proteins and construct PPR-RNA binding profiles, yielding candidate PPR editing factors related to rice endosperm development. Taken together, our findings provide valuable insights for deciphering fundamental mechanisms of rice endosperm development underlying RNA editing machinery.

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Grants

  1. 32030021/National Natural Science Foundation of China (National Science Foundation of China)

MeSH Term

Oryza
Endosperm
RNA Editing
RNA, Plant
Gene Expression Regulation, Plant
Plant Proteins
Mitochondria

Chemicals

RNA, Plant
Plant Proteins
Journal Article

Links to CNCB-NGDC Resources

GSA: CRA008750 (The whole genome re-sequencing and RNA-Seq raw data of Oryza sativa cv. Nipponbare)

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