Deconstructing gene regulation through functional dissection of the 3D genome

Project Information

FuncDis3D

Grant agreement ID: 865459

DOI

10.3030/865459

Project closed

EC signature date 25 February 2020

Start date 1 September 2020

End date 31 August 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 925,00

EU contribution

€ 1 997 425,00

Coordinated by

STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Netherlands

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (14)

Pioneer activity distinguishes activating from non‐activating <scp>SOX2</scp> binding sites

Author(s): Michela Maresca, Teun van den Brand, Hangpeng Li, Hans Teunissen, James Davies, Elzo de Wit
Published in: The EMBO Journal, Issue 42, 2025, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2022113150

Coordinated control of genome–nuclear lamina interactions by topoisomerase 2B and lamin B receptor

Author(s): Tom van Schaik, Mikhail Magnitov, Marcel de Haas, Jeremie Breda, Elzo de Wit, Anna G Manjon, René H Medema, Henrike Johanna Gothe, Vassilis Roukos, Adam J Buckle, Catherine Naughton, Nick Gilbert, Bas van Steensel, Stefano G Manzo
Published in: Nucleic Acids Research, Issue 53, 2025, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaf964

Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers

Author(s): Ning Qing Liu, Mikhail Magnitov, Marijne M G A Schijns, Tom van Schaik, Hans Teunissen, Bas van Steensel, Elzo de Wit
Published in: Nucleic Acids Research, Issue 53, 2025, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaf549

Synergy between regulatory elements can render cohesin dispensable for distal enhancer function

Author(s): Karissa L. Hansen, Annie S. Adachi, Luca Braccioli, Smit Kadvani, Ryan M. Boileau, Moreno Martinovic, Bozhena Pokorny, Rini Shah, Erika C. Anderson, Kaite Zhang, Irié Carel, Kenya Bonitto, Robert Blelloch, Geoffrey Fudenberg, Elzo de Wit, Elphège P. Nora
Published in: Science, Issue 391, 2026, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.adt4221

Interactions between the genome and the nuclear lamina are multivalent and cooperative

Author(s): Lise Dauban, Mathias Eder, Marcel de Haas, Vinícius H. Franceschini-Santos, J. Omar Yañez-Cuna, Moreno Martinovic, Tom van Schaik, Christ Leemans, Hans Teunissen, Koen Rademaker, Miguel Martinez Ara, Martijn Verkuilen, Elzo de Wit, Bas van Steensel
Published in: Nature Structural &amp; Molecular Biology, Issue 32, 2025, Page(s) 2335-2348, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-025-01655-w

WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation

Author(s): Ning Qing Liu, Michela Maresca, Teun van den Brand, Luca Braccioli, Marijne M. G. A. Schijns, Hans Teunissen, Benoit G. Bruneau, Elphѐge P. Nora & Elzo de Wit
Published in: Nature Genetics, 2021, ISSN 1546-1718
Publisher: Springer Nature
DOI: 10.1038/s41588-020-00744-4

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

Author(s): Mikhail D. Magnitov, Michela Maresca, Noemí Alonso Saiz, Hans Teunissen, Jinhong Dong, Kizhakke M. Sathyan, Luca Braccioli, Michael J. Guertin, Elzo de Wit
Published in: Molecular Cell, Issue 85, 2025, Page(s) 24-41.e11, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2024.11.031

SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors

Author(s): Ning Qing Liu, Irene Paassen, Lars Custers, Peter Zeller, Hans Teunissen, Dilara Ayyildiz, Jiayou He, Juliane Laura Buhl, Eelco Wieger Hoving, Alexander van Oudenaarden, Elzo de Wit, Jarno Drost
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-43498-3

New insights into genome folding by loop extrusion from inducible degron technologies

Author(s): Elzo de Wit, Elphège P. Nora
Published in: Nature Reviews Genetics, Issue 24, 2023, Page(s) 73-85, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-022-00530-4

Attraction and disruption: how loop extrusion and compartmentalisation shape the nuclear genome

Author(s): Mikhail Magnitov, Elzo de Wit
Published in: Current Opinion in Genetics &amp; Development, Issue 86, 2025, Page(s) 102194, ISSN 0959-437X
Publisher: Elsevier BV
DOI: 10.1016/j.gde.2024.102194

Understanding and reversing mammary tumor-driven reprogramming of myelopoiesis to reduce metastatic spread

Author(s): Hannah Garner, Moreno Martinovic, Ning Qing Liu, Noor A.M. Bakker, Irene Querol Velilla, Cheei-Sing Hau, Kim Vrijland, Daphne Kaldenbach, Marleen Kok, Elzo de Wit, Karin E. de Visser
Published in: Cancer Cell, Issue 43, 2025, Page(s) 1279-1295.e9, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2025.04.007

The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism

Author(s): Marjon S. van Ruiten, Démi van Gent, Ángela Sedeño Cacciatore, Astrid Fauster, Laureen Willems, Maarten L. Hekkelman, Liesbeth Hoekman, Maarten Altelaar, Judith H. I. Haarhuis, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
Published in: Nature Structural &amp; Molecular Biology, Issue 29, 2022, Page(s) 586-591, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-022-00773-z

A 3D genome compendium of breast cancer progression

Author(s): Teun van den Brand, Maria Donaldson Collier, Koen D. Flach, Sebastian Gregoricchio, Isabel Mayayo-Peralta, Zhanna Dauyey, Karianne Schuurman, Hans Teunissen, Wilbert Zwart, Elzo de Wit
Published in: iScience, Issue 28, 2026, Page(s) 113268, ISSN 2589-0042
Publisher: Elsevier BV
DOI: 10.1016/j.isci.2025.113268

Identifying cross-lineage dependencies of cell-type specific regulators in gastruloids

Author(s): Luca Braccioli, Teun van den Brand, Noemi Alonso Saiz, Charis Fountas, Patrick H. N. Celie, Justina Kazokaitė-Adomaitienė, Elzo de Wit
Published in: Developmental Cell, 2026, ISSN 1878-1551
Publisher: Cell Press
DOI: 10.1101/2022.11.01.514697

Other (1)

Rapid depletion of CTCF and cohesin proteins reveals dynamic features of chromosome architecture

Author(s): Ning Qing Liu, Mikhail Magnitov, Marijne Schijns, Tom van Schaik, Robin H. van der Weide, Hans Teunissen, Bas van Steensel, Elzo de Wit
Published in: 2021
Publisher: bioRxiv
DOI: 10.1101/2021.08.27.457977