The INO80 chromatin remodeler in oncogenic transcription and replication stress: mechanism and functional implications in acute myeloid leukemia.


This project focuses on the emerging field of transcription-replication conflicts in cancer.

Cancer is driven by unrestricted cell proliferation. Activation of oncogenes induces aberrant gene expression, enabling cells to evade growth suppressors and escape cell cycle controls and resulting in unrestricted cell duplication and oncogenesis. Oncogene-dependent transcription is also a major source of genomic instability. Extensive hybrids between newly synthesized RNA and template DNA, known as R-loops, are formed during oncogenic transcription. R-loops can interfere with the replication fork and trigger replication stress, leading to defective DNA replication and DNA damage. How cancers cells counteract these inherently genotoxic conditions to proliferate is largely unclear. This knowledge gap will be addressed in this project.

Here, we will characterize the molecular mechanisms resolving R-loops to prevent transcription-replication conflicts and investigate their role and functional implications in a cancer of great unmet need, acute myeloid leukemia (AML).

AML is an aggressive blood and bone marrow cancer characterized by abnormal proliferation and differentiation of myeloid cells. Despite extensive research, poor understanding of AML pathology has impeded the development of effective treatments, resulting in dismal survival rates.

Development of AML is oncogene dependent and associated with R-loop-induced replication stress. We recently demonstrated that the ATP-dependent chromatin remodelling enzyme INO80 promotes R-loop resolution to enable DNA replication and cancer cell proliferation (Prendergast et al., Nature Communications 2020). INO80 is overexpressed in AML, correlating with poor prognosis. Notably, we discovered that depletion of INO80 has a severe detrimental effect in AML cell growth suggesting a critical role for INO80 in AML progression.


The goal of this project is to characterize novel regulatory pathways that promote cancer cell proliferation. We will test the exciting hypothesis that the resolution of R-loops by the chromatin remodeler INO80 enables continuous oncogene-driven transcription to coordinate with replication, thereby preventing DNA damage and promoting AML growth.

Specifically, this project will:

  1. Characterize how R-loop resolution by INO80 controls oncogenic transcription.
  2. Elucidate the R-loop-associated mechanisms of INO80 suppressing DNA replication stress.
  3. Characterize the dependence of AML patient cells on INO80.

Experimental Approach

This is a cross-cutting collaboration between a Chromatin (Dr Papamichos-Chronakis), an AML Biology (Prof David MacEwan), and a Computational Biology (Dr Aditi Kanhere) team. We will utilize lentiviral shRNA and CRISPR technologies to deplete INO80 and relevant factors. Employing a powerful combination of state-of-the-art and innovative genomics, transcriptomics and super-resolution microscopy technologies together with reporter-assays and advanced bioinformatics analysis in well-characterised AML cell lines and primary patient cells, this study will provide insight into the role of INO80 in genome function and stability and AML.

Novelty and Impact

This project will reveal mechanisms of oncogene-dependent transcription and response to replication stress, providing a deeper understanding of AML pathogenesis and cancer cell proliferation. Dissecting transcription-replication conflicts and R-loop resolution pathways forms a rational, innovative and promising approach for identifying targets for new therapeutic intervention. Elucidating the mechanism and function of INO80 in AML will pave the way for urgently-needed more effective treatments for the disease.

Benefits of being in the DiMeN DTP:

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: 

Further information on the programme and how to apply can be found on our website: 


Open to students worldwide

Funding information

Funded studentship

Studentships are fully funded by the Medical Research Council (MRC) for 4yrs. Funding will cover tuition fees, stipend (£18,622 p.a. for 2023/24) and project costs. We also aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of full studentships to international applicants. Please read additional guidance here: View Website
Studentships commence: 1st October 2024
Good luck!



  1. Prendergast L, McClurg UL, Hristova R, Berlinguer-Palmini R, Greener S, Veitch K, Hernandez I, Pasero P, Rico D, Higgins JMG, Gospodinov A, and Papamichos-Chronakis M. (2020). Resolution of R-loops by INO80 promotes DNA replication and maintains cancer cell proliferation and viability. Nature Communications, 2020 Sep 10;11(1):4534. Selected as Editors Highlight. DOI: 10.1038/s41467-020-18306-x
  2. Poli J, Gasser SM, & Papamichos-Chronakis M. (2017). The INO80 remodeller in transcription, replication and repair. Philos Trans R Soc Lond B Biol Sci. 2017 Oct 5;372(1731). DOI: 10.1098/rstb.2016.0290
  3. Luzzi S, Szachnowski U, Greener S, Schumacher K, Fulton S, Han KH, Darke J, Piccinno R, Lafon A, Pugh BF, Devys D, Tora L, Morillon A and Papamichos-Chronakis M (2021). Chromatin remodelling by INO80 at promoter proximal pause sites promotes premature termination of mRNA synthesis. bioRxiv
  4. Lafon A*., Taranum S*., Pietrocola F., Dingli F., Damarys., Brahma S., Bartholomew B., and Papamichos-Chronakis M. (2015). INO80 Chromatin Remodeler Facilitates Release of RNA Polymerase II from Chromatin for Ubiquitin-Mediated Proteasomal Degradation. Molecular Cell, 60: 784–796. DOI: 10.1016/j.molcel.2015.10.028