Dr Marco Saponaro PhD

Dr Marco Saponaro

Institute of Cancer and Genomic Sciences
Associate Professor

Contact details

Institute of Cancer and Genomic Sciences
University of Birmingham
B15 2TT

Dr Saponaro is interested in characterising mechanisms of genome stability maintenance. In particular, he is interested in understanding how RNA Pol II transcription and DNA replication are coordinated, and how in context with defective transcription this can lead to increased genome instability. He develops his research combining whole genome analyses with functional studies. He characterises RNA Pol II progression identifying how it is affected in mutant contexts, correlating transcription problems with the sites of genome instability. All these allow identifying the mechanisms of transcription-induced genome instability.

He is also interested in the relevance for human health of transcription-associated genome instability, identifying instances where these problems arise and approaches to exploit therapeutically these situations.


  • Associate Professor, University of Birmingham (UK), 2021
  • Birmingham Fellow, University of Birmingham (UK), 2015
  • PhD in Molecular Medicine, University of Milan (Italy) 2009
  • MSc (Hons) in Medical Biotechnology, University of Bologna (Italy), 2004



Recent publications


Rojas, P, Wang, J, Guglielmi, G, Sadurnì, MM, Pavlou, L, Leung, GHD, Rajagopal, V, Spill, F & Saponaro, M 2024, 'Genome-wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression', Genome Biology, vol. 25, no. 1, 126. https://doi.org/10.1186/s13059-024-03278-8

Scaramuzza, S, Jones, RM, Sadurni, MM, Reynolds-Winczura, A, Poovathumkadavil, D, Farrell, A, Natsume, T, Rojas, P, Cuesta, CF, Kanemaki, MT, Saponaro, M & Gambus, A 2023, 'TRAIP resolves DNA replication-transcription conflicts during the S-phase of unperturbed cells', Nature Communications, vol. 14, no. 1, 5071. https://doi.org/10.1038/s41467-023-40695-y

De, S, Edwards, DM, Dwivedi, V, Wang, J, Varsally, W, Dixon, HL, Singh, AK, Owuamalam, PO, Wright, MT, Summers, RP, Hossain, MN, Price, EM, Wojewodzic, MW, Falciani, F, Hodges, NJ, Saponaro, M, Tanaka, K, Azzalin, CM, Baumann, P, Hebenstreit, D & Brogna, S 2022, 'Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe', Nucleic Acids Research, vol. 50, no. 1, pp. 350-367. https://doi.org/10.1093/nar/gkab1249

Bayley, R, Borel, V, Moss, R, Sweatman, E, Ruis, P, Ormrod, A, Goula, A, Mottram, R, Stanage, T, Hewitt, G, Saponaro, M, Stewart, G, Boulton, S & Higgs, M 2022, 'H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ', Molecular Cell, vol. 82, no. 10, pp. 1924-1939.e10. https://doi.org/10.1016/j.molcel.2022.03.030

Saponaro, M 2022, 'Transcription–replication coordination', Life, vol. 12, no. 1, 108. https://doi.org/10.3390/life12010108

Wang, J, Rojas, P, Mao, J, Muste Sadurni, M, Garnier, O, Xiao, S, Higgs, M, Garcia, P & Saponaro, M 2021, 'Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M', Cell Reports, vol. 34, no. 7, 108759. https://doi.org/10.1016/j.celrep.2021.108759

Wang, J & Saponaro, M 2021, 'Protocol for analysis of G2/M DNA synthesis in human cells', STAR Protocols, vol. 2, no. 2, 100570. https://doi.org/10.1016/j.xpro.2021.100570

Bowry, A, Piberger, AL, Rojas, P, Saponaro, M & Petermann, E 2018, 'BET inhibition induces HEXIM1- and RAD51-dependent conflicts between transcription and replication', Cell Reports, vol. 25, no. 8, pp. 2061–2069.e4. https://doi.org/10.1016/j.celrep.2018.10.079


Saponaro, M 2018, Transcription in the context of genome instability. in DNA Replication and Double Strand Break Repair: Mechanisms and Clinical Significance..


Saponaro, M 2024, 'Adding a transcription-coupled repair pathway', Nature Cell Biology, vol. 26, no. 5, pp. 670-671. https://doi.org/10.1038/s41556-024-01399-7


Scaramuzza, S, Muste Sadurni, M, Poovathumkadavil, D, Natsume, T, Rojas, P, Kanemaki, MT, Saponaro, M & Gambus, A 2022 'Ubiquitin ligase TRAIP plays an essential role during the S-phase of unperturbed cell cycle in the resolution of DNA replication – transcription conflicts' bioRxiv. https://doi.org/10.1101/2022.03.23.485338

De, S, Dwivedi, V, Wang, J, Edwards, DM, Varsally, W, Singh, AK, Dixon, HL, Wojewodzic, MW, Falciani, F, Hodges, NJ, Saponaro, M, Tanaka, K, Azzalin, CM, Baumann, P, Hebenstreit, D & Brogna, S 2021 'Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe' bioRxiv. https://doi.org/10.1101/2021.04.12.437332

Winczura, K, Ceylan, H, Sledziowska, M, Jones, M, Fagarasan, H, Wang, J, Saponaro, M, Arnold, R, Hebenstreit, D & Grzechnik, P 2021 'RPRD proteins control transcription in human cells' bioRxiv. https://doi.org/10.1101/2021.06.20.449126

Review article

Muste Sadurni, M & Saponaro, M 2023, 'Deregulations of RNA Pol II Subunits in Cancer', Applied Biosciences, vol. 2, no. 3, pp. 459-476. https://doi.org/10.3390/applbiosci2030029

Wang, J, Sadurni, MM & Saponaro, M 2022, 'RNAPII response to transcription‐blocking DNA lesions in mammalian cells', The FEBS journal. https://doi.org/10.1111/febs.16561

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