2022 Fiscal Year Research-status Report
Transposable elements shape the evolution of mammalian innate immunity against pathogens
| Project/Area Number |
21K15066
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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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| Keywords | pathogen-specific / transposable elements / immune cells / transcriptome / evolution |
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| Outline of Annual Research Achievements |
We have identified transposable elements (TEs) that are induced by salmonella but not by influenza virus infection in human macrophages last year. We further collected available RNA-seq datasets in immune cells following different pathogen infection separately.
This year, We further identified 34 TE families that are highly activated following ebolavirus infection and 43 TE families are activated following influenza infection. They were consistently highly activated in multiple immune cells compared to other pathogens. We also found that these pathogen-specific families are mostly integrated before primates during evolution.
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| Current Status of Research Progress |
Current Status of Research Progress
3: Progress in research has been slightly delayed.
Reason
After we found the pathogen-specific TE families, we are particulally interested in these differentially activated TEs upon pathogen infection.
We have carefully examine the TE families we found in multiple immune cells.
We have also found that these families are shared between primates while some of them are absent in mouse genome.
We then want to look at whether these TE families shape the evolution of the immune response to different pathogens by epigenetically regulating their ajacent immune-related genes.
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| Strategy for Future Research Activity |
To achieve our goals, we have purchased the human macrophage cell line THP-1 for the planed epigenetic profiles to functinonally validate the regulation of activated endogenous retrovirus families.
We also plan to use the Massively Parallel Reporter Assay to validate the regulatory activity of these families in THP-1 cell line following different pathogen infection.
We will also compare the results in THP-1 cell line with human primary macrophages to examine their functionality in primary cells.
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| Causes of Carryover |
As we planned, we will perform additional RNA-seq, ATAC-seq, and Chip-seq sequencing experiment of the THP-1 cell line following infection in this year.
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