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Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells

View ORCID ProfileGiulia Irene Maria Pasquesi, Conor J. Kelly, Andrea D. Ordonez, View ORCID ProfileEdward B. Chuong
doi: https://doi.org/10.1101/2022.04.18.488675
Giulia Irene Maria Pasquesi
1BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder
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  • ORCID record for Giulia Irene Maria Pasquesi
Conor J. Kelly
1BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder
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Andrea D. Ordonez
1BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder
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Edward B. Chuong
1BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder
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  • ORCID record for Edward B. Chuong
  • For correspondence: edward.chuong@colorado.edu
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ABSTRACT

Background Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN- stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat (Myotis lucifugus) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN.

Results We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional induction in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NLRC5, SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN.

Conclusion Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting candidate loci that may contribute to bat-specific immune function.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 18, 2022.
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Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells
Giulia Irene Maria Pasquesi, Conor J. Kelly, Andrea D. Ordonez, Edward B. Chuong
bioRxiv 2022.04.18.488675; doi: https://doi.org/10.1101/2022.04.18.488675
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Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells
Giulia Irene Maria Pasquesi, Conor J. Kelly, Andrea D. Ordonez, Edward B. Chuong
bioRxiv 2022.04.18.488675; doi: https://doi.org/10.1101/2022.04.18.488675

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