Sources and consequences of intrinsic genomic instability across human cell types

Joint project between Roukos and Beli groups

1 PhD project offered in the IPP winter call 2023/2024

Scientific Background

The formation of genome rearrangements by DNA double-strand breaks (DSBs) is a double-edged sword: it can provide genetic diversity beneficial for evolution, but can also cause various diseases including cancer. Disease-causing genome rearrangements frequently are joined at specific genomic locations, implying the existence of distinct molecular mechanisms that promote DNA fragility at these regions. While much is known about exogenously induced DNA fragile sites, what determines which genomic sites have higher probability to spontaneously break across the genome, and how this occurs mechanistically, are still open questions.

Using powerful genomics approaches to profile DNA breaks at nucleotide resolution across the genome and chromosome conformation capture techniques to unravel chromatin interactions, we have recently shown that transcription and 3D genome folding dictate the frequency of chemotherapy-induced oncogenic rearrangements by promoting DNA fragility and favouring fusions of proximal genes (Gothe et al., Mol Cell, 2019). Moving towards intrinsic DNA lesions, we were able to identify and characterise a class of endogenous DNA fragile hotspots displaying limited overlap with drug-induced common fragile sites.

PhD Project:

As part of the SFB1361 consortium, this PhD project aims to characterise the sources of intrinsic DNA fragility and uncover how it may lead to recurrent rearrangements and tissue-specific oncogenesis. To this end, we will combine sophisticated genomics approaches from the Roukos and Beli labs (Bowman et al, Nat. Protoc, 2020; Longo, Puig et al, submitted; Mosler et al., Nat Commun, 2021) to generate a compendium of intrinsic DNA fragility maps across human cell types, and characterise how they relate to gene expression, chromatin environment and 3D chromosome organisation. We will then link the molecular and cellular sources of intrinsic DNA fragility, focusing on the roles of non-canonical DNA structures, such as R-loops and G-quadruplexes, and of incomplete topoisomerase actions, and their interference with replication and transcription. This project will be performed in close collaboration with Kathi Zarnack, an expert in bioinformatics approaches to study cellular surveillance mechanisms based on next-generation sequencing data. Based on produced data, the Zarnack groupwill build predictive models for the occurrence of intrinsic DNA fragility in the human genome using machine learning models and extract the most relevant features and their interdependencies. By integrating results from multiple human cell types, we will identify tissue-specific intrinsic genomic instability hotspots and cross-correlate with publicly available tissue-specific structural variants (SVs) identified in cancer patient samples. Our findings will unravel why certain regions across the genome are highly susceptible to breakage and will offer novel insights into the emergence of recurrent genome rearrangements and their prevalence in oncogenesis.


Publications relevant to this project

Gothe HJ, Bouwman BAM, Gusmao EG, Piccinno R, Petrosino G, Sayols S, Drechsel O, Minneker V, Josipovic N, Mizi A, Nielsen CF, Wagner EM, Takeda S, Sasanuma H, Hudson DF, Kindler T, Baranello L, Papantonis A, Crosetto N and Roukos V (2019) Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations. Mol Cell, 75:267-283.e12 Link

Bouwman BAM, Agostini F, Garnerone S, Petrosino G, Gothe HJ, Sayols S, Moor AE, Itzkovitz S, Bienko M, Roukos V and Crosetto N (2020) Genome-wide detection of DNA double-strand breaks by in-suspension BLISS.Nat Protoc, 15:3894–3941 Link

Mosler T, Conte F, Longo GMC, Mikicic I, Kreim N, Möckel MM, Petrosino G, Flach J, Barau J, Luke B, Roukos V and Beli P (2021) R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability.Nat Commun, 12:7314 Link

Longo G.M.C, Sayols S, Mockel M., Beli P and Roukos V. (2023) Determinants of CRISPR/Cas9 Scissile Profile for Precise and Predictable Genome Editing, submitted


Contact Details

Vassilis Roukos

Institute of Molecular Biology gGmbH (IMB)

Ackermannweg 4, 55128 Mainz, Germany

& Assistant Professor

Medical School, University of Patras,Greece




Petra Beli

Professor for Quantitative Proteomics

Institute for Developmental Biology and Neurobiology (iDN)

University of Mainz

Group Leader and Adjunct Director

Institute of Molecular Biology gGmbH (IMB)

Ackermannweg 4

55128 Mainz, Germany