Functional analysis of downstream open chromatin induced in HSV-1 infection

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Herpes simplex virus 1 (HSV-1) is the causative agent of the common cold sores but also responsible for severe life-threatening diseases including encephalitis, pneumonia, hepatitis and generalized skin infections. Furthermore, HSV-1 is a paradigm for virus-induced host shut-off exerted at RNA level. Recently, we showed that HSV-1 triggers a widespread disruption of transcription termination (DoTT) of cellular but not viral genes, resulting in extensive read-through transcription beyond poly(A) sites. Subsequently, similar observations were also reported in cellular stress responses and cancer. We now found that HSV-1 induced DoTT resembles a cellular stress response and leads to nuclear retention of read-through transcripts, thereby contributing to host shut-off. The focus of the current application is the striking observation that HSV-1-induced DoTT, but not stress-induced read-through transcription, was accompanied by an extensive increase in chromatin accessibility downstream of the affected poly(A) sites. These downstream open chromatin regions (dOCRs) extend for tens-of-thousands of nucleotides and essentially match the region of transcription read-through. In this proposal, we now seek to identify the molecular mechanism responsible for the induction of dOCRs and assess its functional relevance for productive HSV-1 infection. The proposed project combines wet-lab work and bioinformatics analyses to test our hypothesis that: (i) dOCRs in HSV-1 infection arise from an impairment in histone repositioning upon Pol II transcription into genomic regions outside of genes; (ii) histone release during dOCR formation explains the previously reported increase in the pool of free nucleoplasmic histones; (iii) the associated increase in histone mobility facilitates chromatinization of the replicating viral DNA. Results obtained from this work will detail how an important human pathogen manipulates the transcriptional machinery to promote productive viral replication. In addition, it will pioneer a fascinating new model for studying the molecular mechanisms orchestrating gene expression and chromatin architecture in human cells.