Fig. 1

Experimental design. A Myotis lucifugus embryonic fibroblast primary cells were treated for 24 hours (24 h) and for 4 hours (4 h) with 1000 U/ml of universal IFNa (+IFNa) or matched volume of DPBS (−IFNa). Total RNA at both time points was extracted and used as input for RNA library preparation and sequencing to identify differentially expressed genes and transposable elements (TEs). To characterize changes in chromatin accessibility upon IFN treatment, cells were similarly treated for 4 h, and subjected to the CUT&RUN protocol on H3K27ac, POLR2A, and STAT1. B The chromosome-level genome assembly for Myotis lucifugus was used as reference to perform de novo repeat element identification and annotation. Combined with genome guided transcriptome assembly of our RNA-seq datasets, the custom repeat element annotation was used to identify TE-derived and virus-derived isoforms and transcription start sites (TSS)