Publications of A. Marieke Oudelaar

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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

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)

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

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

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)

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)

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)

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)

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)

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)