We identified the viral ICP27 protein to be responsible for disruption of transcription termination in HSV-1 infection (Wang et al., Nature commun. 2020). ICP27 directly interacts with the cellular CPSF complex resulting in the formation of a dead-end 3’ processing complex that is unable to cleave the nascent RNA at its 3’-end. Remarkably, ICP27 also acts as a sequence-dependent activator of mRNA 3' processing for viral and a subset of host transcripts by directly binding to the nascent mRNAs.
We found that poly(A) read-through in HSV-1 infection, but not in cellular stress responses, is accompanied by a selective defect in histone repositioning downstream of genes resulting in the formation of extensive open chromatin regions (Hennig et al., PLoS Pathogens 2019). We identified the viral ICP22 protein to be responsible for this effect (Djakovic et al, Nature commun. in revision).
We provided a state-of-the-art reannotation of the HSV-1 genome resulting in the identification of >200 previously unknown viral ORFs and 201 viral transcripts. This include novel viral immediate early proteins and gene products missing in mutant viruses approved for oncolytic therapies.
To study specific changes in RNA polymerase II CTD phosphorylation, we succesfully employed mNET-seq. Integrative analysis with published PRO-seq data revealed unexpected manipulations of promoter-proximal pausing by HSV-1 (manuscript in prep.).
We extensively tested the usefulness of the RNA aptamer Broccoli for live-cell RNA imaging and found it to be not sufficiently stable and bright even upon concatemerization. We found that it is not sufficiently stable and bright to serve as a reliable reporter for single cell analyses.
We pioneered metabolic RNA labeling combined with chemical nucleotide-conversion for single cell RNA sequencing (scSLAM-seq; Erhard et al., Nature 2019). This adds a temporal dimension to single cell RNA sequencing and now facilitates dose-response analyses at single cell level. This was only made possible due to the development of the computational approach GRAND-SLAM, which provides reliable new/total RNA ratios for thousands of genes in individual cells (Jürges et al, Bioinformatics 2018). We filed a patent on GRAND-SLAM.
Exploiting new technologies developed in the frame of this project, we identified miRNA-mediated inhibition of miRNA processing as a so far unknown cellular mechanism by which human herpesvirus 6 disrupts mitochondrial architecture, interferes with intrinsic cellular defense mechanisms and governs the latent-lytic switch (Hennig et al., Nature 2022).
