Seeing the unseen in characterizing RNA editome during rice endosperm development
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...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-10-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-024-07032-5 |
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| author | 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_facet | 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_sort | Ming Chen |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-4bc6f56aeae64f83b810d865883fef5c |
| institution | OA Journals |
| issn | 2399-3642 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-4bc6f56aeae64f83b810d865883fef5c2025-08-20T02:17:53ZengNature PortfolioCommunications Biology2399-36422024-10-017111310.1038/s42003-024-07032-5Seeing the unseen in characterizing RNA editome during rice endosperm developmentMing Chen0Lin Xia1Xinyu Tan2Shenghan Gao3Sen Wang4Man Li5Yuansheng Zhang6Tianyi Xu7Yuanyuan Cheng8Yuan Chu9Songnian Hu10Shuangyang Wu11Zhang Zhang12National Genomics Data Center, China National Center for BioinformationNational Genomics Data Center, China National Center for BioinformationBeijing Institute of Genomics, Chinese Academy of SciencesBeijing Institute of Genomics, Chinese Academy of SciencesBeijing Institute of Genomics, Chinese Academy of SciencesNational Genomics Data Center, China National Center for BioinformationNational Genomics Data Center, China National Center for BioinformationNational Genomics Data Center, China National Center for BioinformationNational Genomics Data Center, China National Center for BioinformationNational Genomics Data Center, China National Center for BioinformationBeijing Institute of Genomics, Chinese Academy of SciencesBeijing Institute of Genomics, Chinese Academy of SciencesNational Genomics Data Center, China National Center for BioinformationAbstract 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.https://doi.org/10.1038/s42003-024-07032-5 |
| spellingShingle | 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 Seeing the unseen in characterizing RNA editome during rice endosperm development Communications Biology |
| title | Seeing the unseen in characterizing RNA editome during rice endosperm development |
| title_full | Seeing the unseen in characterizing RNA editome during rice endosperm development |
| title_fullStr | Seeing the unseen in characterizing RNA editome during rice endosperm development |
| title_full_unstemmed | Seeing the unseen in characterizing RNA editome during rice endosperm development |
| title_short | Seeing the unseen in characterizing RNA editome during rice endosperm development |
| title_sort | seeing the unseen in characterizing rna editome during rice endosperm development |
| url | https://doi.org/10.1038/s42003-024-07032-5 |
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