Periodic Reporting for period 1 - TranscriptStress (The transcriptional response to oxidative stress)
Okres sprawozdawczy: 2023-07-01 do 2025-12-31
Environmental stress triggers a cellular response to promote adaptation and survival, typically through activation of stress genes. What is less appreciated is that various types of cellular stress at the same time induce widespread transcriptional repression at most other genes. Although such transcriptional reprogramming is common to various kinds of cellular stress, recent evidence suggests it is governed by different stress-specific mechanisms. A brief exposure to oxidative stress leads to a rapid and transient global repression of transcription. However, our current knowledge about the oxidative stress response is extremely limited. With this project we aim to understand the transcriptional response to oxidative stress, both in terms of regulation of transcription elongation as well as termination and that these are connected to post-translational modifications of RNA polymerase II (RNAPII) itself.
To address the transcriptional response to oxidative stress we will investigate the cause and consequences of the transcriptome-wide oxidative stress induce by a brief sublethal dose of hydrogen peroxide or menadione in human cells and following physiologically induced oxidative stress in mice. To this end, we will use a combination of state-of-the art sequencing techniques coupled with time-resolved proteomics and a novel screening approach. Together, we expect our work to provide important new knowledge about the transcriptional response to oxidative stress and the factors involved – in an area that is currently not well understood. Such knowledge is also crucial to understand the fundamental mechanisms allowing RNAPII to stop transcribing and restart again. Finally, we will investigate how factors involved in the transcriptional response influence transcription-associated genome instability and cell identity. This will be relevant for diseases in which oxidative stress has been implicated, such as neurological disorders and cancer.
To address the transcriptional response to oxidative stress we will investigate the cause and consequences of the transcriptome-wide oxidative stress induce by a brief sublethal dose of hydrogen peroxide or menadione in human cells and following physiologically induced oxidative stress in mice. To this end, we will use a combination of state-of-the art sequencing techniques coupled with time-resolved proteomics and a novel screening approach. Together, we expect our work to provide important new knowledge about the transcriptional response to oxidative stress and the factors involved – in an area that is currently not well understood. Such knowledge is also crucial to understand the fundamental mechanisms allowing RNAPII to stop transcribing and restart again. Finally, we will investigate how factors involved in the transcriptional response influence transcription-associated genome instability and cell identity. This will be relevant for diseases in which oxidative stress has been implicated, such as neurological disorders and cancer.
Research from this project has uncovered a rapid and widespread cessation of global transcription following oxidative DNA base damage. By monitoring genomic RNA polymerase II (RNAPII) occupancy and elongation dynamics, we have established that transient oxidative stress arrests the progression of RNAPII elongation complexes in the gene body and temporarily halts new initiation. We found that this occurs in a unique and transient manner characterised by abrupt stalling of RNAPII, dead-in-its track, through a mechanism distinct from UV-induced RNAPII stalling or heat shock induced transcriptional attenuation. The transient RNAPII arrest is followed by a rapid elongation complex recovery when the lesions are repaired, allowing RNAPII to resume transcription from within the gene body. We find that the restriction of initiation and early elongation complexes is controlled by PARylation, while the recovery of RNAPII arrested in the gene body requires DNA repair mediated the base excision repair and single stranded break repair pathways.
We expect our results that the transcriptional response to oxidative damage is largely tied to DNA damage repair will lead to new areas of research into how PARylation affects RNAPII stalling early in the gene body and the role of oxidative damage as an impairment for RNAPII elongation.