biostudies-arrayexpressMirko SchmitzHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17158We show strong activation of TEs in the context of DNA virus infection and investigate the molecular mechanisms of how TEs are induced. We demonstrate that herpesvirus infection leads to a robust expression of the MLT and THE1-class of LTR containing retrotransposons as well as a subset of long-interspersed nuclear elements-1 (LINEs), Alu-elements and some HERVs. Mechanistically we demonstrate that this TEs upregulation is induced by two pathways that act synergistically: de-repression of KAP1/TRIM28 mediated by phosphorylation and expression of the pioneer factor double-homeobox 4 (DUX4). Here, we show changes in H3K9me3, H3K14ac and H3K27me3 during two HSV-1 infection timepoints (6h and 14h).biostudies-arrayexpressSequencing - Sequencing was performed using the Illumina NovaSeq 6000 (Homo sapiens)Sample Collection - Primary HFF cells were infected with HSV-1 GFP (MOI of 3) in PBS supplemented with 0.1% Glucose and 1% FCS. The remaining virus was washed away with a low pH buffer (40mM Citric acid, 10mM KCl, 135mM NaCl, pH3) after one hour at 37°C.Library Construction - Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit.Nucleic Acid Extraction - CUT&RUN was performed using the option 1 of the CUT&RUN protocol (v3, dx.doi.org/10.17504/protocols.io.zcpf2vn). 1µg anti-KAP1 Phospho (Ser473) (BioLegend, #644602), H3K9me3 (Abcam) or 1µg rabbit IgG (Cell Signaling Technology) were used accordingly and 5pg Drosophila spike in DNA was added to each sample for normalization.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Sequence reads were mapping to T2T (with Drosophila, dm6 genome, as spike-in) by bowtie2, bigwig files were generated by deeptools. BigWig files of host reads normalized by spike-in were submitted. snakePipes v3.4 was used with the following settings to produce the processed files: DNAmapping: --cutntag --trim --trimmer trimgalore --fastqc ChIPseq: --cutntag --useSpikeInForNorm --getSizeFactorsFrom genomeMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000NEBNext Ultra II DNA Library Prep KitNonesnakePipes 3.4CUT&RUNHomo sapiensFlorian FullMirko SchmitzfalseDNA virus infections shape transposable element activity in vitro and in vivo (HCMV,KSHV,DUX4) - Cut&Run of H3K9me3, H3K14ac and H3K27me3We show strong activation of TEs in the context of DNA virus infection and investigate the molecular mechanisms of how TEs are induced. We demonstrate that herpesvirus infection leads to a robust expression of the MLT and THE1-class of LTR containing retrotransposons as well as a subset of long-interspersed nuclear elements-1 (LINEs), Alu-elements and some HERVs. Mechanistically we demonstrate that this TEs upregulation is induced by two pathways that act synergistically: de-repression of KAP1/TRIM28 mediated by phosphorylation and expression of the pioneer factor double-homeobox 4 (DUX4). Here, we show changes in H3K9me3, H3K14ac and H3K27me3 during two HSV-1 infection timepoints (6h and 14h).2026-06-25T00:00:00Z2026-06-25T01:01:20.196Z2026-06-12T14:51:30.058ZE-MTAB-17158ERP194991EFO_0002944EFO_0009973EFO_0004170EFO_0005518EFO_0003816EFO_0004184