Lara Djaković  email
Institute for Virology and Immunobiology

Supervisor:
Prof. Dr. Lars Dölken (Würzburg)
Promotion committee:
Prof. Dr. Lars Dölken (Würzburg)
Prof. Dr. Utz Fischer (Würzburg)
Jun. Prof. Dr. Florian Erhard (Würzburg)

 

 

Functional analysis of HSV-1 induced transcription read-through

Herpes simplex virus 1 (HSV-1) is a large dsDNA virus that efficiently replicates during lytic infection in the cell nucleus by taking over the host cell gene expression machinery thereby causing “host cell shut-off”. It has been shown that lytic HSV-1 infection causes disruption in transcription termination (DoTT) of cellular but not viral genes, resulting in widespread poly(A) read-through for tens-of-thousands of nucleotides commonly ranging into downstream genes. Interestingly, we observed that HSV-1 induced DoTT is accompanied by a substantial increase in accessible chromatin downstream of the affected poly(A) sites and in its kinetics and extent, downstream open chromatin (DOC) essentially matches with the poly(A) read-through transcription. Large regions of DOC indicate impaired histone repositioning when RNA polymerase II (Pol II) transcribes into downstream intergenic regions in HSV‑1 infection.

Therefore, the goal of this research is to investigate the molecular basis of DoTT and DOC regarding changes in the total and phosphorylated RNA Pol II, localization of different histone marks as well as chromatin remodeling factors. To address this question, we are using ChIPmentation, rapid and low-input method that combines chromatin immunoprecipitation with sequencing library preparation by Tn5 transposase (‘tagmentation’) thus allowing adapter ligation directly on bead-bound chromatin.

Altogether, we anticipate this work will provide important insights into the underlying molecular mechanisms involved in a HSV-1 induced DoTT.