Publications

Journal Article

Stumberger, G.; Hörl, D.; Tsouraki, D.; Steinek, C.; Oudelaar, A. M.; Leonhardt, H.; Harz, H.: Nanoscale dynamics of enhancer–promoter interactions during exit from pluripotency. Nucleic Acids Research 53 (22), gkaf1255 (2025)

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Journal Article

Oncins, A.; Zaurin, R.; Toukabri, H.; Quililan, K.; Mora, J. R. H.; Karpinska, M. A.; Wernersson, E.; Smith, A.; Bianchi, A.; Albinati, L. et al.; Cozzuto , L.; Rivero, A.; Gulliver, C.; Velten, J.; Denkena, J.; Serra, F.; Gómez, R.; López, C.; Beà, S.; Paulsen, J.; Halidi, N.; Valencia, A.; Bienko, M.; Oudelaar, A. M.; Beekman, R.: Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms. Nucleic Acids Research 53 (15), gkaf677 (2025)

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Journal Article

Karpinska, M. A.; Zhu, Y.; Fakhraei Ghazvini, Z.; Ramasamy, S.; Barbieri, M.; Cao, N. T. B.; Varahram, N.; Aljahani, A.; Lidschreiber, M.; Papantonis, A. et al.; Oudelaar, A. M.: CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation. Nature Structural & Molecular Biology 32, pp. 1268 - 1281 (2025)

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Journal Article

Georgiades, E.; Harrold, C.; Roberts, N.; Kassouf, M.; Riva, S. G.; Sanders, E.; Downes, D.; Francis, H. S.; Blayney, J.; Oudelaar, A. M. et al.; Milne, T. A.; Higgs, D.; Hughes, J. R.: Active regulatory elements recruit cohesin to establish cell specific chromatin domains. Scientific Reports 15, 11780 (2025)

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Journal Article

Papantonis, A.; Oudelaar, A. M.: Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome. Annual Review of Genomics and Human Genetics 26, pp. 4.1 - 4.26 (2025)

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Journal Article

Kassouf, M. T.; Francis, H. S.; Gosden, M.; Suciu, M. C.; Downes, D. J.; Harrold, C.; Larke, M.; Oudelaar, M.; Cornell, L.; Blayney, J. et al.; Telenius, J.; Xella, B.; Shen, Y.; Sousos, N.; Sharpe, J. A.; Sloane-Stanley, J.; Smith, A. J. H.; Babbs, C.; Hughes, J. R.; Higgs, D. R.: The α-globin super-enhancer acts in an orientation-dependent manner. Nature Communications 16, 1033 (2025)

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supplementary-material

Journal Article

Tsouraki, D.; Oudelaar, A. M.: Bridging the gap: How enhancers cooperate to regulate gene expression over large genomic distances. Molecular Cell 85 (2), pp. 199 - 201 (2025)

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Journal Article

de Luca, K. L.; Rullens, P. M. J.; Karpinska, M. A.; de Vries, S. S.; Gacek-Matthews, A.; Pongor, L. S.; Legube, G.; Jachowicz, J. W.; Oudelaar, A. M.; Kind, J.: Genome-wide profiling of DNA repair proteins in single cells. Nature Communications 15, 9918 (2024)

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10.

Journal Article

Aljahani, A.; Mauksch, C.; Oudelaar, A. M.: The relationship between nucleosome positioning and higher-order genome folding. Current Opinion in Cell Biology 89, 102398 (2024)

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11.

Journal Article

Palikyras, S.; Varamogiani-Mamatsi, V.; Zhu, Y.; Ramasamy, S.; Mizi, A.; Liebermann, I.; Stavropoulou, A.; Papadionysiou, I.; Bartsch, D.; Kargapolova, Y. et al.; Sofiadis, K.; Nikolaou, C.; Kurian, L.; Oudelaar, A. M.; Barbieri, M.; Papantonis, A.: Senescent cells cluster CTCF on nuclear speckles to sustain their splicing program. bioRxiv (2024)

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12.

Journal Article

Žumer, K.; Ochmann, M.; Aljahani, A.; Zheenbekova, A.; Devadas, A.; Maier, K. C.; Rus, P.; Neef, U.; Oudelaar, A. M.; Cramer, P.: FACT maintains chromatin architecture and thereby stimulates RNA polymerase II pausing during transcription in vivo. Molecular Cell 84 (11), pp. 2053 - 2069.e9 (2024)

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13.

Journal Article

Oberbeckmann, E.; Quililan, K.; Cramer, P.; Oudelaar, A. M.: In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization. Nature Genetics 56, pp. 483 - 492 (2024)

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14.

Journal Article

Oberbeckmann, E.; Oudelaar, A. M.: Genome organization across scales: mechanistic insights from in vitro reconstitution studies. Biochemical Society Transactions 52 (2), pp. 793 - 802 (2024)

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15.

Journal Article

Oudelaar, A. M.: The Mediator complex regulates long-range communication in the genome. Nature Structural & Molecular Biology 30 (7), pp. 876 - 877 (2023)

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16.

Journal Article

Ramasamy, S.; Aljahani, A.; Karpinska, M. A.; Cao, N. T. B.; Velychko, T.; Cruz, J. N.; Lidschreiber, M.; Oudelaar, A. M.: The Mediator complex regulates enhancer-promoter interactions. Nature Structural and Molecular Biology 30, pp. 991 - 1000 (2023)

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17.

Journal Article

Karpinska, M. A.; Oudelaar, A. M.: The role of loop extrusion in enhancer-mediated gene activation. Current Opinion in Genetics & Development 79, 102022 (2023)

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18.

Journal Article

Oudelaar, A. M.: Deciphering the regulatory logic of a chromatin domain boundary. Nature Genetics 54 (7), pp. 914 - 915 (2022)

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19.

Journal Article

Aljahani, A.; Hua, P.; Karpinska, M. A.; Quililan, K.; Davies, J. O. J.; Oudelaar, A. M.: Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nature Communications 13, 2139 (2022)

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20.

Journal Article

Downes, D. J.; Smith, A. L.; Karpinska, M. A.; Velychko, T.; Rue-Albrecht, K.; Sims, D.; Milne, T. A.; Davies, J. O. J.; Oudelaar, A. M.; Hughes, J. R.: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature Protocols 17 (2), pp. 445 - 475 (2022)

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21.

Journal Article

Owens, D. D. G.; Anselmi, G.; Oudelaar, A. M.; Downes, D. J.; Cavallo, A.; Harman, J. R.; Schwessinger, R.; Bucakci, A.; Greder, L.; de Ornellas, S. et al.; Jeziorska, D.; Telenius, J.; Hughes, J. R.; de Bruijn, M. F. T. R.: Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. Nature Communications 13, 773 (2022)

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22.

Journal Article

King, A. J.; Songdej, D.; Downes, D. J.; Beagrie, R. A.; Liu, S.; Buckley, M.; Hua, P.; Suciu, M. C.; Oudelaar, A. M.; Hanssen, L. L. P. et al.; Jeziorska, D.; Roberts, N.; Carpenter, S. J.; Francis, H.; Telenius, J.; Olijnik, A.-A.; Sharpe, J. A.; Sloane-Stanley, J.; Eglinton, J.; Kassouf, M. T.; Orkin, S. H.; Pennacchio, L. A.; Davies, J. O. J.; Hughes, J. R.; Higgs, D. R.; Babbs, C.: Reactivation of a developmentally silenced embryonic globin gene. Nature Communications 12, 4439 (2021)

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23.

Journal Article

Hua, P.; Badat, M.; Hanssen, L. L. P.; Hentges, L. D.; Crump, N.; Downes, D. J.; Jeziorska, D. M.; Oudelaar, A. M.; Schwessinger, R.; Taylor, S. et al.; Milne, T. A.; Hughes, J. R.; Higgs, D. R.; Davies, J. O. J.: Defining genome architecture at base-pair resolution. Nature 595 (7865), pp. 125 - 129 (2021)

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24.

Journal Article

Bozhilov, Y. K.; Downes, D. J.; Telenius, J.; Oudelaar, A. M.; Olivier, E. N.; Mountford, J. C.; Hughes, J. R.; Gibbons, R. J.; Higgs, D. R.: A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker. Nature Communications 12, 3806 (2021)

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25.

Journal Article

Oudelaar, A. M.; Beagrie, R. A.; Kassouf, M. T.; Higgs, D. R.: The mouse alpha-globin cluster: A paradigm for studying genome regulation and organization. Current Opinion in Genetics & Development 67, pp. 18 - 24 (2021)

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26.

Journal Article

Larke, M. S. C.; Schwessinger, R.; Nojima, T.; Telenius, J.; Beagrie, R. A.; Downes, D. J.; Oudelaar, A. M.; Truch, J.; Graham, B.; Bender, M. A. et al.; Proudfoot, N. J.; Higgs, D. R.; Hughes, J. R.: Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Molecular Cell 81 (5), pp. 983 - 997.e7 (2021)

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27.

Journal Article

Oudelaar, A. M.; Higgs, D. R.: The relationship between genome structure and function. Nature Reviews Genetics 22, pp. 154 - 168 (2021)

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28.

Journal Article

Downes, D. J.; Beagrie, R. A.; Gosden, M. E.; Telenius, J.; Carpenter, S. J.; Nussbaum, L.; Ornellas, S. D.; Sergeant, M.; Eijsbouts, C. Q.; Schwessinger, R. et al.; Kerry, J.; Roberts, N.; Shivalingam, A.; El-Sagheer, A.; Oudelaar, A. M.; Brown, T.; Buckle, V. J.; Davies, J. O. J.; Hughes, J. R.: High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nature Communications 12, 531 (2021)

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29.

Journal Article

Schwessinger, R.; Gosden, M.; Downes, D.; Brown, R. C.; Oudelaar, A. M.; Telenius, J.; Teh, Y. W.; Lunter, G.; Hughes, J. R.: DeepC: predicting 3D genome folding using megabase-scale transfer learning. Nature Methods 17 (11), pp. 1118 - 1124 (2020)

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30.

Journal Article

Oudelaar, A. M.; Beagrie, R. A.; Gosden, M.; de Ornellas, S.; Georgiades, E.; Kerry, J.; Hidalgo, D.; Carrelha, J.; Shivalingam, A.; El-Sagheer, A. H. et al.; Telenius, J. M.; Brown, T.; Buckle, V. J.; Socolovsky, M.; Higgs, D. R.; Hughes, J. R.: Dynamics of the 4D genome during in vivo lineage specification and differentiation. Nature Communications 11, 2722 (2020)

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31.

Journal Article

Chiariello, A. M.; Bianco, S.; Oudelaar, A. M.; Esposito, A.; Annunziatella, C.; Fiorillo, L.; Conte, M.; Corrado, A.; Prisco, A.; Larke, M. S. C. et al.; Telenius, J. M.; Sciarretta, R.; Musella, F.; Buckle, V. J.; Higgs, D. R.; Hughes, J. R.; Nicodemi, M.: A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells. Cell Reports 30 (7), pp. 2125 - 2135.e1-e5 (2020)

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32.

Journal Article

Oudelaar, A. M.; Harrold, C. L.; Hanssen, L. L. P.; Telenius, J. M.; Higgs, D. R.; Hughes, J. R.: A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus. Nature Communications 10, 5412 (2019)

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33.

Journal Article

Godfrey, L.; Crump, N. T.; Thorne, R.; Lau, I.-J.; Repapi, E.; Dimou, D.; Smith, A. L.; Harman, J. R.; Telenius, J. M.; Oudelaar, A. M. et al.; Downes, D. J.; Vyas, P.; Hughes, J. R.; Milne, T. A.: DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation. Nature Communications 10, 2803 (2019)

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34.

Journal Article

Oudelaar, A. M.; Davies, J. O. J.; Hanssen, L. L. P.; Telenius, J. M.; Schwessinger, R.; Liu, Y.; Brown, J. M.; Downes, D. J.; Chiariello, A. M.; Bianco, S. et al.; Nicodemi, M.; Buckle, V. J.; Dekker, J.; Higgs, D. R.; Hughes, J. R.: Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nature Genetics 50 (12), pp. 1744 - 1751 (2018)

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35.

Journal Article

Brown, J. M.; Roberts, N. A.; Graham, B.; Waithe, D.; Lagerholm, C.; Telenius, J. M.; Ornellas, S. D.; Oudelaar, A. M.; Scott, C.; Szczerbal, I. et al.; Babbs, C.; Kassouf, M. T.; Hughes, J. R.; Higgs, D. R.; Buckle, V. J.: A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. Nature Communications 9, 3849 (2018)

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36.

Journal Article

Oudelaar, A. M.; Davies, J. O. J.; Downes, D. J.; Higgs, D. R.; Hughes, J. R.: Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C. Nucleic Acids Research 45 (22), e184 (2017)

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37.

Journal Article

Oudelaar, A. M.; Downes, D. J.; Davies, J. O. J.; Hughes, J. R.: Low-input Capture-C: A chromosome conformation capture assay to analyze chromatin architecture in small numbers of cells. Bio-protocol 7 (23), e2645 (2017)

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38.

Journal Article

Oudelaar, A. M.; Hanssen, L. L. P.; Hardison, R. C.; Kassouf, M. T.; Hughes, J. R.; Higgs, D. R.: Between form and function: the complexity of genome folding. Human Molecular Genetics 26 (R2), pp. R208 - R215 (2017)

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39.

Journal Article

Hanssen, L. L. P.; Kassouf, M. T.; Oudelaar, A. M.; Biggs, D.; Preece, C.; Downes, D. J.; Gosden, M.; Sharpe, J. A.; Sloane-Stanley, J. A.; Hughes, J. R. et al.; Davies, B.; Higgs, D. R.: Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nature Cell Biology 19 (8), pp. 952 - 961 (2017)

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40.

Journal Article

Davies, J. O. J.; Oudelaar, A. M.; Higgs, D. R.; Hughes, J. R.: How best to identify chromosomal interactions: A comparison of approaches. Nature Methods 14 (2), pp. 125 - 134 (2017)

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41.

Journal Article

Hay, D.; Hughes, J. R.; Babbs, C.; Davies, J. O. J.; Graham, B. J.; Hanssen, L. L. P.; Kassouf, M. T.; Oudelaar, A. M.; Sharpe, J. A.; Suciu, M. C. et al.; Telenius, J.; Williams, R.; Rode, C.; Li, P.-S.; Pennacchio, L. A.; Sloane-Stanley, J. A.; Ayyub, H.; Butler, S.; Sauka-Spengler, T.; Gibbons, R. J.; Smith, A. J. H.; Wood, W. G.; Higgs, D. R.: Genetic dissection of the α-globin super-enhancer in vivo. Nature Genetics 48 (8), pp. 895 - 903 (2016)

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Book Chapter (1)

42.

Book Chapter

Oudelaar, A. M.; Downes, D. J.; Hughes, J. R.: Assessment of multiway interactions with Tri-C. In: Spatial Genome Organization, pp. 95 - 112 (Ed. Sexton, T.). Humana Pr., Springer, New York, NY (2022)

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Preprint (4)

43.

Preprint

Haro, E.; Iliadou, M.; Ramasamy, S.; Ealo, T.; Campa, V. M.; Pachano, T.; Oudelaar, A. M.; Rada-Iglesias, A.: Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts. bioRxiv (2025)

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44.

Preprint

Karpinska, M. A.; Zhu, Y.; Fakhraei Ghazvini, Z.; Ramasamy, S.; Barbieri, M.; Cao, N. T. B.; Lidschreiber, M.; Papantonis, A.; Oudelaar, A. M.: CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation during cellular differentiation. bioRxiv (2025)

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45.

Preprint

Oncins, A.; Zaurin, R.; Toukabri, H.; Quililan, K.; Mora, J. R. H.; Karpinska, M. A.; Wernersson, E.; Smith, A.; Bianchi, A.; Albinati, L. et al.; Rivero, A.; Serra, F.; Gómez, R.; López, C.; Beà, S.; Halidi, N.; Valencia, A.; Bienko, M.; Oudelaar, A. M.; Beekman, R.: Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms. bioRxiv (2024)

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46.

Preprint

Georgiades, E.; Harrold, C. L.; Roberts, N.; Kassouf, M.; Riva, S. G.; Sanders, E.; Francis, H. S.; Blayney, J.; Oudelaar, A. M.; Milne, T. A. et al.; Higgs, D. R.; Hughes, J.: Active regulatory elements recruit cohesin to establish cell-specific chromatin domains. bioRxiv (2023)

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