Transposable elements shape the evolution of mammalian innate immunity against pathogens

2023 Fiscal Year Final Research Report

• Project/Area Number: 21K15066
• Research Category: Grant-in-Aid for Early-Career Scientists
• Allocation Type: Multi-year Fund
• Review Section: Basic Section 43050:Genome biology-related
• Research Institution: Kyoto University
• Principal Investigator: CHEN Xun 京都大学, 高等研究院, 特定助教 (30885158)
• Project Period (FY): 2021-04-01 – 2024-03-31
• Keywords: Transposable element / Classification / Annotation / Epigenetics / Infection / Immunity

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.

Free Research Field

Genomics

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.