Cells respond to DNA double-strand breaks (DSBs) by suppressing transcriptional activities on the damaged chromatin, an emerging DNA Damage Response (DDR) that underlies effective DNA repair and maintenance of genome stability. However, the molecular bases that actively restart transcriptional processes following DSB repair remain poorly defined. Importantly, failing to timely resume gene expression can compromise transcriptome signature and regulation, and can impose deleterious consequence on cell identity and cell fate.

We previously uncovered a DYRK1B-dependent pathway that actively inhibits local transcription on the damaged chromatin (PNAS 2020; Nucleic Acids Res 2021), a DDR accomplished, in part, by enforcing DSB accumulation of the histone methyltransferase EHMT2. Consistent with established role of EHMT2 in depositing the transcription repressive mark H3K9me2, we showed that DNA damage triggered DYRK1B/EHMT2-dependent H3K9 dimethylation on the DSB-flanking chromatin. In line with a role of H3K9me2 in DSB-induced transcription silencing in cis (DISC), counteracting H3K9me2 by forced expression of H3K9 demethylases (e.g. PHF8, JMJD2A) effectively compromised DISC. Conversely, perturbating H3K9 demethylation led to delayed recovery of transcription following DSB repair. Importantly, mechanistically how H3K9me2 demethylating activities are tempo-spatially coupled to DSB repair remains enigmatic.

To understand how the dynamic regulation of H3K9me2 coordinates local transcription with DSB repair processes, we will chart H3K9 methylation status at DSB-flanking chromatin domains, and will perform global transcriptome analyses following induction and repair of sequence-specific DSBs. We will determine the genetic requirements that license docking of H3K9me2 demethylating activities at DSB-flanking chromatin domains, will profile their occupancies surrounding annotated DSBs, and will examine how different H3K9 demethylases may support timely recovery of transcriptional activities following DNA repair. Finally, we will define how perturbing H3K9me2 may impact gene expression programmes, and will explore how restoration of DSB-associated histone marks underlies cell identity maintenance.

This study builds on our existing strength and represents an exciting initiative to define the molecular bases that tempo-spatially couple transcription recovery and DSB repair, and will shed mechanistic light to advance our understanding of transcriptional control on the damaged chromatin. Our characterisation of druggable DDR factors also rationalises and provides insight towards the development of potential therapeutic interventions for the treatment and management of genome instability-associated diseases.