| Project/Area Number |
20F20395
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| Research Category |
Grant-in-Aid for JSPS Fellows
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| Allocation Type | Single-year Grants |
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| Section | 外国 |
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| Review Section |
Basic Section 40040:Aquatic life science-related
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| Research Institution | The University of Tokyo |
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Principal Investigator |
浅川 修一 東京大学, 大学院農学生命科学研究科(農学部), 教授 (30231872)
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| Co-Investigator(Kenkyū-buntansha) |
HUANG SONGQIAN 東京大学, 農学生命科学研究科, 外国人特別研究員
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| Project Period (FY) |
2020-11-13 – 2023-03-31
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| Project Status |
Granted (Fiscal Year 2022)
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| Budget Amount *help |
¥2,200,000 (Direct Cost: ¥2,200,000)
Fiscal Year 2022: ¥400,000 (Direct Cost: ¥400,000)
Fiscal Year 2021: ¥1,100,000 (Direct Cost: ¥1,100,000)
Fiscal Year 2020: ¥700,000 (Direct Cost: ¥700,000)
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| Keywords | piRNA / biogenesis / exosome / small RNA / evolution / molluscan / metazoans / RNA function / miRNA / sRNA-seq / Computational genomics / Bioinformatic analysis / Functional analysis / Somatic piRNA / Mollusca |
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| Outline of Research at the Start |
Complete genome sequences of 30 mollusks are downloaded from public databases to identify piRNA biogenesis factor genes, and then performed evolutionary analysis. The data analysis of small RNA is according to the previous procedures using in P. fucata small RNA data analysis, including data quality check and length distribution filtering, genome mapping, Rfam and other known RNA mapping. piRNA biogenesis factor genes will be examined by real-time PCR. The consensus sequences of transposon elements are obtained based on the REPCLASS and TEclass integration results.
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| Outline of Annual Research Achievements |
We aimed to reveal the sncRNAs involved in the immune response during grafting transplantation by the pearl oyster Pinctada fucata. Exosomes were successfully extracted from the P. fucata haemolymph during graft transplantation. The expression patterns of the miRNAs and piRNAs at the grafting and initial stages were not substantially different, but varied significantly between the initial and later stages. Target prediction and functional analysis indicate that these miRNAs and piRNAs are related to immune response upon grafting transplantation, whereas piRNAs may also be associated with transposon silencing by targeting with genome transposon elements. This work provides the basis for a functional understanding of exosome-derived sncRNAs and helps to gain further insight into the PIWI/piRNA pathway function outside of germline cells in molluscs.
Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The dual functions of piRNA were examined in P. fucata somatic and gonadal tissues. The results indicated that piRNAs from somatic tissues may be related to gene regulation, whereas piRNAs from gonadal tissues are more closely associated to transposon silencing. This study will enhance our understanding of the role of piRNAs in mollusks, transposon silencing, and the regulatory function of the PIWI/piRNA pathway on protein-coding genes outside of germ line cells in invertebrates.
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| Current Status of Research Progress |
Current Status of Research Progress
1: Research has progressed more than it was originally planned.
Reason
As a newly discovered class of non-coding small molecule RNAs, piRNAs are mostly found in the vertebrate germ lines and play a role in suppressing genomic transposon activity and maintaining genomic stability. Based on the functional and evolutionary studies of piRNAs in mollusks, this study analyzed the spatial and temporal expression of small molecule RNAs in nine species of mollusks, breaking through the prior knowledge of germ line specific expression of piRNAs and further expanding the expression and function of piRNAs outside the gonads. Meanwhile, the mechanism of exosomal small molecule RNA-mediated maintenance of homeostasis in aquatic animals under environmental stress has been deeply analyzed, and we found that exosomes are rich in small molecule RNAs, among which miRNAs and piRNAs are involved in cellular immune response, and exosomal piRNAs are also involved in transposon silencing. This further expanded the functional scope of piRNAs in molluscan somatic cells and helped to further understand the new functions of piRNAs beyond molluscan germ cells. Subsequently, the piRNA study was expanded to include the analysis of piRNAs from 115 animal species in 14 animal phyla. The series of studies on piRNAs enriched the species and functional scope of metazoans small molecule RNAs and broke the prior knowledge of piRNA germ line specific expression. The related results were published in Open Biology, RNA Biology, Int J Mol Sci, Front M
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| Strategy for Future Research Activity |
Currently, there is a debated about their biogenesis and function, especially in non-model animals. A meta-analysis of more than thousand small RNA sequencing libraries have revealed that piRNAs are ubiquitously expressed in almost all domains of life (nematode to humans), but limit to germ line in vertebrates. piRNAs biogenesis is differ from miRNA biogenesis pathway. In my analysis of the piRNA pathway genes reveled that piRNA biogenesis genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. The evolution status of piRNA biogenesis genes will be evaluate both in invertebrates and vertebrates.
In the previous meta-analysis of piRNA in 115 animals but not include crustaceans. It is necessary to investigate the situation of piRNAs in aquatic crustaceans for a comprehensive analysis of the piRNAs evolution in aquatic animals. From the above shrimp small RNA, I found that piRNAs were highly expressed at the early embryonic development stage, while the abundance of piRNA decreased as the embryonic developmental stage continued. In addition, two distinct piRNAs discovered in somatic and gonadal tissues, which was not the same in other animals. It is necessary to carry out research on shrimp piRNA, especially its role in embryonic development. So far, the role of piRNA in embryonic development has not been developed in invertebrates. The shrimp tissues and embryos were sampled for small RNA sequencing to expand the functional evolution of piRNAs in animal evolution, especially in invertebrates.
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