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Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells (CUT&RUN)

ABSTRACT: Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells (CUT&RUN)

PROVIDER: PRJNA826886 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18761414_1.fastq.gz	Fastqsanger.gz
	SRR18761414_2.fastq.gz	Fastqsanger.gz
	SRR18761415_1.fastq.gz	Fastqsanger.gz
	SRR18761415_2.fastq.gz	Fastqsanger.gz
	SRR18761416_1.fastq.gz	Fastqsanger.gz

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Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells (CUT&RUN)

Project description: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.

2022-04-21 | GSE200831 | GEO