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| Status |
Public on Apr 21, 2022 |
| Title |
Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells (CUT&RUN) |
| Organism |
Myotis lucifugus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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. We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional upregulation in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NRLC5, 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. Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting potential candidate loci that contribute to bat-specific immune function.
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| Overall design |
Epigenomic (CUT&RUN) profiling of bat embryonic fibroblast cells that were either untreated or stimulated with 1000U/mL universal interferon alfa (IFNa) for 4hrs.
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| Contributor(s) |
Pasquesi GM, Chuong EB |
| Citation missing |
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| Submission date |
Apr 14, 2022 |
| Last update date |
Apr 23, 2022 |
| Contact name |
Edward B Chuong |
| E-mail(s) |
edward.chuong@colorado.edu
|
| Organization name |
University of Colorado Boulder
|
| Department |
Molecular, Cellular and Developmental Biology
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| Lab |
Chuong Lab
|
| Street address |
3415 Colorado Ave., room E251
|
| City |
Boulder |
| State/province |
Colorado |
| ZIP/Postal code |
80303 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL32169 |
Illumina NovaSeq 6000 (Myotis lucifugus) |
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| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE200833 |
Transcriptomic and epigenomic profiling of Myotis lucifugus embryonic fibroblast cells |
|
| Relations |
| BioProject |
PRJNA826886 |
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