2020 Fiscal Year Annual Research Report
Elucidation of the function of piRNAs ubiquitously expressed in mollusks
| Project/Area Number |
20F20395
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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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| Keywords | miRNA / piRNA / sRNA-seq / Computational genomics / Bioinformatic analysis / Functional analysis / Somatic piRNA / Mollusca |
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| Outline of Annual Research Achievements |
We performed a persistent research of small RNA in molluscs, more specifically on 1) classification, identification, expression and target prediction of miRNAs, and 2) piRNA identification, expression and biogenesis analysis. In miRNAs, 186 known and 42 novel miRNAs were identified in Pinctada fucata. Target prediction was performed in biomineralization related genes to improve the understanding of miRNAs in biomineralization. In case of piRNA analysis, we firstly found that piRNAs were ubiquitously expressed in somatic and gonad tissues in P. fucata. Different populations of piRNAs participate in the ping-pong amplification loop in a tissular specific manner in P. fucata. The expression patterns and characteristics of piRNAs reveal a fascinating and unanticipated dimension of P. fucata biology. A genome-wide computational prediction of miRNAs was also performed to improve the understanding of miRNA observation and function in molluscs. Hundreds of conserved miRNAs were predicted in 35 species of molluscs through genome scanning. The miRNAs’ population, isoforms, organization, and function were characterized in detail. Key miRNA biogenesis factors, including AGO2, DGCR8, DICER, DROSHA, TRABP2, RAN, and XPO5, were elucidated based on homologue sequence searching. the miRNAs’ function in biomineralization, immune and stress response, as well as growth and development We also summarzed in molluscs. The study will provide insight into miRNA biogenesis and function in molluscs, as well as other invertebrates.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
PIWI/piRNA suppress transposon activity in animals, thereby safeguarding the genome from detrimental insertion mutagenesis. Recently, evidence revealed additional piRNA targets and functions in various animals. Bioinformatic analyses suggested that different piRNA populations participate in the ping-pong amplification loop in a tissue-specific manner. While the role of somatic and gonadal piRNA is not well-characterized in P. fucata. Transcriptome analysis was performed to unraveled the piRNA biogenesis and piRNA-mediated gene regulation in P. fucata. These findings have improved our knowledge of the role of piRNA in mollusks, and provided evidence to understand the regulatory function of the PIWI/piRNA pathway on protein-coding genes outside of germline cells. Since the discovery of somatic piRNA in P. fucata, we are planning to scan more molluscs. We sequenced 100 libraries from ten more molluscs species and collected 171 sRNA-seq data from 24 Mollusca species from public database for piRNA discovery profiling. We found that ubiquitously expressed piRNA molecules in the soma of molluscs. Furthermore, we are planning to scan the animal's somatic piRNA during the entire animal evolution process. sRNA-seq data from different different animal phyla were download for piRNA discovery. The expression and function research of piRNA in invertebrate soma needs to attract more attention to expand the function research of piRNA in Metazoan, which suggest diversity function of piRNA outside of germline in invertebrates. As described above, our research has made great progress.
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| Strategy for Future Research Activity |
Since we focus on the expression and function of PIWI/piRNA in Mollusca species, we are planning to collect ten more Mollusca species for sRNA-seq. The somatic and gonad tissues will dissected for total RNA isolation and small RNA sequencing. The genome sequence of the involved animal species will be used for transposon element analysis to further understand the piRNA-mediated TEs silencing in Mollusca. In addition, more than 1500 available small RNA sequencing data will be download from public database for piRNA discovery in animals, including Protozoa, Nematoda, Porifera, Platyhelminthes, Annelida, Cnidaria, Echinodermata, Mollusca, Crustacea, Arthropoda, Teleostean, Chondrichthyes, Amphibian, Reptilia, Aves and Mammal. Our research has initially found that: 1) Invertebrate soma retain the original ancestral function of piRNA, while lost in vertebrates; 2) piRNA play a vital role in the early embryonic developmental stage of all animals, possibly by inhibiting the activity of transposon elements to safeguard the genome; 3) piRNA clusters in vertebrate and invertebrate genomes are significantly different, clustering into two categories. After analyzed of these piRNA in animals, we will firstly report the discovery of somatic piRNA in invertebrates by small RNA sequencing, which were neglected by most researchers. In addition, we will make a piRNA database for all performed organisms which discovery from sRNA-seq.
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