Elise Fouquerel, Ph.D.

The overarching goal of my research is to (i) understand how DNA-dependent ADP-Ribose Transferase (ART; PARP) enzymatic activities orchestrate the preservation of genomic stability, and (ii) define the PARP-dependent mechanisms preventing tumorigenesis and aging related diseases. Our lab’s research efforts is focused on 3 main projects.

Project 1: PARP1 in the orchestration of R-loop resolution. Transcription is a fundamental cellular process. Yet, it can threaten genome stability via the formation of R-loops. R-loops are three-stranded nucleic acid structures composed of an RNA-DNA hybrid and a displaced non-template DNA strand. They can be found at gene promoters, termination regions, and gene bodies, where they play various physiological roles. Yet, their unrestrained formation or defective resolution can lead to DNA damage and genome instability, particularly in cells undergoing replication due to collisions between the transcription and replication complexes. Accordingly, unwarranted R-loops accumulation has been tightly associated with tumorigenesis. Elucidating the molecular mechanisms of R-loop formation and resolution is therefore crucial to gaining a deeper understanding of genomic instability associated with cancer and etiology of cancer. Our laboratory has recently demonstrated that the DNA repair enzyme PARP1 can bind to R-loops in vitro and in cells, leading to the activation of its ADP-ribosylation activity (Laspata et al., 2023 NAR). We are now pursuing our research effort following 3 main goals:

- Determine the mechanisms underpinning the binding of PARP1 to R-loops and its subsequent activation.

- Identifying the R-loop resolution factors whose recruitment depends on PARP1

- Define the role of PARP1 and DHX9 helicase interaction in the R-loop resolution process. These projects involve the use of molecular and cellular biology techniques including CUT&RUN sequencing and mass spectrometry combined with fluorescence high resolution microscopy and single molecule assays (AFM, C-trap).

Project 2: Determining the impact of oxidative DNA lesion induction at centromeres on genome stability. Faithful division of chromosomes is ensured by the presence of specific loci called centromeres. By mediating kinetochore assembly and subsequent chromosome segregation, centromeres ensure proper cell division and stable transmission of the genome. Centromere dysfunction is associated with aneuploidy, DNA translocations, rearrangements, and loss of genetic material through micronuclei formation, that are hallmarks of chromosomal instability (CIN) and features of cancer cells. Thus, understanding the mechanisms that preserve centromere integrity, especially upon DNA damage, is crucial for human health. Several epidemiological studies on chronic human illnesses and tumorigenesis, have linked centromere-induced CIN to chronic exposure to oxidative stress (OS). However, the mechanisms are not understood yet. Our lab is using an innovative tool developed by Dr. Fouquerel during her postdoc training that allows local induction of oxidative lesion at a specific loci of the genome. In this project we have targeted the FAP system to the centromeres. Our goals are to:

- Delineate the cellular and molecular responses to centromeric oxidative DNA lesions

- Define the impact of chronic exposure to oxidative stress on centromeric histone CENP-A deposition.

Project 3. Roles of ART enzyme PARP2 in the response to replication stress at teloemres. PARP2 is a DNA-dependent ADP-ribosyl transferase (ARTs) enzyme with Poly(ADP-ribosyl)ation activity that is triggered by DNA breaks. It is involved in the Base Excision Repair pathway alongside PARP1 with which it has overlapping functions. However, additional roles for PARP2 have emerged in the mediation of replication stress. In this study, we demonstrate that PARP2 promotes replication stress-induced telomere fragility and prevents telomere loss in cells subjected to chronic induction of oxidative DNA lesions. Telomere fragility results from the activity of the break-induced replication pathway (BIR) during which PARP2 mediates DNA end resection independently of its catalytic activity. We further show that PARP2 also promotes BIR-dependent mitotic DNA synthesis through PARylation of the Pol delta subunit POLD3. Our study reveals that PARP2 has a critical role in the response to replication stress at telomeres and can trigger telomere fragility by orchestrating the BIR pathway. This unique role for PARP2 in the response to replication stress may encourage the development of new therapeutic approaches differentially targeting DNA-dependent ART enzymes, especially in cancer cells harboring high levels of replication stress. We are now setting out to further delineate the molecular mechanisms and the targets of PARP2 in the BIR process.