Publications

Publications since the start of EpiC. See previous relevant publications under the individual group leaders

EpiC Publications

Graphical abstract showing cells turning from one cell type (A) to another (B). Below these cells is a graphic showing that transcription factors that are bound in cell type B, start binding on replicating DNA during identity transition — EpiC researchers from the Groth and Stewart- Morgan labs used technology to study freshly- replicated chromatin in cells undergoing identity change. They found that newly- replicated chromatin’s increased accessibility permits transcription factor-driven cell identity change. Figure reproduced from Knudsen et al. (2026), Stem Cell Reports, 21(3), 102821. Licensed under CC BY-NC-ND 4.0

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A Micro-C interaction heatmap comparing 3D chromatin structure in normal (Ctrl) vs. FACT-depleted (dSPT16) cells. Highlighted are heatmap patterns that indicate regions of chromatin coalescence in FACT-depleted cells. How these align to regions of gene expression is also shown (bottom right) — EpiC researchers from the Krietenstein and Groth labs studied the critical, chromatin-organising roles of the histone chaperone, FACT, in DNA replication and transcription. They further found that nucleosome arrangement can protect against gene aggregation. Figure adapted from Figure 5, Frater et al. (2025), bioRxiv, 2026.02.25.707725. Reproduced with permission from the copyright holder

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Top: Molecular models of transcription factors, including Cramp1, that regulate histone H1 gene expression. Bottom: An illustration of how reduced histone H1 increases Top2 demand and inhibitor sensitivity — Researchers from the Mailand lab discovered a transcription factor, Cramp1, that regulates histone H1 biogenesis and influences TOP2 demand. This revealed a new cancer vulnerability that can be exploited with current clinical therapies. Figure reproduced from Ingham et al. (2025), Molecular Cell, 85(13) 2487– 2502.e12. Licensed under CC BY-NC-ND 4.0

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On the left is an experimental schematic of a CRISPR screen and on the right, a graph of the results showing the genes that are synthetic lethal with Okadaic acid treatment — EpiC researchers from the Nilsson lab used CRISPR screening to identify genetic vulnerabilities upon drug treatment with a PP2A-like phosphatase inhibitor. Figure adapted from Figure 1, Meeusen et al. (2025), bioRxiv, 2025.02.12.637884. Reproduced with permission from the copyright holder

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Li, J., Petersen, K. V., Ummethum, H., Bagge, J., Hinsby, E. W., Lisby, M., Nilsson, J., & Oestergaard, V. H. (2026). TOPBP1-PLK1 interaction preserves genome integrity during mitosis. Nucleic acids research, 54(9), gkag462. https://doi.org/10.1093/nar/gkag462

Ambjørn, S. M., Meeusen, B., Kliche, J., Wang, J., Garvanska, D. H., Kruse, T., Lopez Mendez, B., Mann, M., Mailand, N., Hertz, E. P. T., Davey, N. E., & Nilsson, J. (2026). A proteome-wide dependency map of protein interaction motifs. Nature structural & molecular biology, 33(3), 537–546. https://doi.org/10.1038/s41594-026-01762-2

Knudsen, T. E., Reverón-Gómez, N., Biran, A., Alcaraz, N., Cheloufi, S., Hochedlinger, K., Brickman, J. M., Groth, A., & Stewart-Morgan, K. R. (2026). Post-replicative chromatin accessibility predicts cell fate change. Stem cell reports, 21(3), 102821. https://doi.org/10.1016/j.stemcr.2026.102821

In this paper, EpiC researchers exposed a previously unrecognised mechanism that allows cells to rapidly change their identity.

Kollenstart, L., Charlton, S. J., & Groth, A. (2026). The Dynamics of Chromatin Replication. Annual review of biochemistry, 10.1146/annurev-biochem-082525-050024. Advance online publication. https://doi.org/10.1146/annurev-biochem-082525-050024

Myers, N. E. M., Whittaker, J., Cadot, M. E. H., Varga, J. K., Diallo, M., Nilsson, J., Bach, A., Sandström, A., Schueler-Furman, O., & Danielson, U. H. (2026). Identification of ZFTA as a Novel KLHL20 Substrate and Mechanistic Insights Into Fuzzy Binding of Disordered Peptides via Biosensor Analysis and Computational Modelling. Chembiochem : a European journal of chemical biology, 27(5), e70237. https://doi.org/10.1002/cbic.70237

Alvarado, R. E., Lokugamage, K. G., Garvanska, D., Estes, L. K., Ahearn, Y., McLeland, A. M., Moayyed, A., Chen, J., Mendez, B. L., Plante, J. A., Plante, K. S., Johnson, B. A., Nilsson, J., & Menachery, V. D. ( 2026). Key residues in SARS-CoV-2 NSP3 hypervariable region are necessary to modulate early stress granule activity. Journal of virology, 100(2), e0200625. https://doi.org/10.1128/jvi.02006-25

Pielies Avellí, M., Sigurdsson, A. I., Ollé López, J., Narita, T., Krietenstein, N., Choudhary, C., & Rasmussen, S. (2026). Modeling nascent transcription from chromatin landscape and structure with CLASTER. Genome biology, 27(1), 98. https://doi.org/10.1186/s13059-026-03992-5

Arroyo-Gomez, J., Murray, M. J., Guérillon, C., Wang, J., Isaakova, E., Reverón-Gómez, N., Koutrouli, M., Suryo Rahmanto, A., Mitrofanov, K., Ingham, A., Schovsbo, S., Weischenfeldt, K., Coscia, F., Typas, D., Völker-Albert, M., Solis, V., Jensen, L. J., Groth, A., Mund, A., Beli, P., … Mailand, N. (2025). Functional landscape of ubiquitin linkages couples K29-linked ubiquitylation to epigenome integrity. The EMBO journal, 44(23), 6944–6978. https://doi.org/10.1038/s44318-025-00599-7

This interdisciplinary collaborative research lead by Professor Niels Mailand uncovers a hidden mechanism that helps cells maintain the health and organization of their DNA. 

Bantele, S., Mordini, I., Biran, A., Alcaraz, N., Zonderland, G., Wenger, A., Krietenstein, N., Groth, A., & Lukas, J. (2025). Repair of DNA double-strand breaks leaves heritable impairment to genome function. Science (New York, N.Y.), 390(6773), eadk6662. https://doi.org/10.1126/science.adk6662

This collaborative study published in Science shows that following DNA repair, certain regions including those near some critical genes undergo lasting changes in DNA folding and gene activity. 

Moura, M., Barbosa, J., Pinto, I., Leça, N., Cunha-Silva, S., Verza, A. E., Pedroso, P. D., Lemaire, S., Duro, J., Simoes-da-Silva, M., Oliveira, A., Reis, R., Nilsson, J., Sunkel, C., Musacchio, A., Bollen, M., & Conde, C. (2025). Polo kinase inhibits protein phosphatase 1 to promote the spindle assembly checkpoint and prevent aneuploidy. Current biology : CB, 35(21), 5289–5307.e8. https://doi.org/10.1016/j.cub.2025.09.049

Metelova, M., Vigh, M. L., & Krietenstein, N. (2025). Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP. Nature communications, 16(1), 9331. https://doi.org/10.1038/s41467-025-64350-w

The Krietenstein group have developed Micro-C-ChIP, a technique that reveals how our DNA folds in three dimensions - a crucial layer of gene regulation with significant implications for understanding development and disease, including cancer.