| Project/Area Number |
21K15066
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| Research Category |
Grant-in-Aid for Early-Career Scientists
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| Allocation Type | Multi-year Fund |
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| Review Section |
Basic Section 43050:Genome biology-related
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| Research Institution | Kyoto University |
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Principal Investigator |
CHEN Xun 京都大学, 高等研究院, 特定助教 (30885158)
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| Project Period (FY) |
2021-04-01 – 2024-03-31
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| Project Status |
Completed (Fiscal Year 2023)
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| Budget Amount *help |
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2023: ¥130,000 (Direct Cost: ¥100,000、Indirect Cost: ¥30,000)
Fiscal Year 2022: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2021: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
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| Keywords | Transposable element / Classification / Annotation / Epigenetics / Infection / Immunity / pathogen-specific / transposable elements / immune cells / transcriptome / evolution / Immune cells / Evolution / Macrophages / Immunology / Comparative epigenomics |
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| Outline of Research at the Start |
In this project, I propose to perform the comparative epigenomic analysis to understand how do TE-derived regulatory elements shape the evolution of immune transcriptional network against different pathogens. The results will expand the understanding of the evolution of immunity.
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| Outline of Final Research Achievements |
We examined transposable elements that were up-regulated upon the infection of different pathogens. We identified many LTR subfamilies that were significantly activated following Salmonella infection; we found another set of LTR subfamilies that were activated following influenza infection. These pathogen-specific subfamilies were mostly integrated before primates during evolution.
After we look into the candidate TE subfamilies, we found that many instances from these subfamilies were mis-annotated. We then performed the phylogenetic analysis to re-annotate instances from relatively young subfamilies. In the end, we validated that the new annotation that we achieved have a high sequence, epigenetics, and functional specificity validated by using the massive parallel reporter assay.
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| Academic Significance and Societal Importance of the Research Achievements |
We revealled many pathogen specific TE subfamilies indicating their potential important functions during infection. We also found many young subfamilies were misannotated. We then proposed a new classification and annotation approach, which is key to resolve the role of TEs played during infection.
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