{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Mirko Schmitz"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17158"],"description":["We 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)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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 genome"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","NEBNext Ultra II DNA Library Prep Kit","None","snakePipes 3.4"],"study_type":["CUT&RUN"],"species":["Homo sapiens"],"pubmed_authors":["Florian Full","Mirko Schmitz"],"additional_accession":[]},"is_claimable":false,"name":"DNA virus infections shape transposable element activity in vitro and in vivo (HCMV,KSHV,DUX4) - Cut&Run of H3K9me3, H3K14ac and H3K27me3","description":"We 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).","dates":{"release":"2026-06-25T00:00:00Z","modification":"2026-06-25T01:01:20.196Z","creation":"2026-06-12T14:51:30.058Z"},"accession":"E-MTAB-17158","cross_references":{"ENA":["ERP194991"],"EFO":["EFO_0002944","EFO_0009973","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0004184"]}}