Wouter de Laat

2024

A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs

Venema, W. J., Hiddingh, S., van Loosdregt, J., Bowes, J., Balliu, B., de Boer, J. H., Ossewaarde-van Norel, J., Thompson, S. D., Langefeld, C. D., de Ligt, A., van der Veken, L. T., Krijger, P. H. L., de Laat, W. & Kuiper, J. J. W., 10 Jan 2024, In: Cell genomics. 4, 1, 100460.

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2023

CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands

Rouillon, C., Eckhardt, B. V., Kollenstart, L., Gruss, F., Verkennis, A. E. E., Rondeel, I., Krijger, P. H. L., Ricci, G., Biran, A., van Laar, T., Delvaux de Fenffe, C. M., Luppens, G., Albanese, P., Sato, K., Scheltema, R. A., de Laat, W., Knipscheer, P., Dekker, N. H., Groth, A. & Mattiroli, F., 8 May 2023, In: Nucleic acids research. 51, 8, p. 3770-3792 23 p.

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Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

Smits, W. K., Vermeulen, C., Hagelaar, R., Kimura, S., Vroegindeweij, E. M., Buijs-Gladdines, J. G. C. A. M., van de Geer, E., Verstegen, M. J. A. M., Splinter, E., van Reijmersdal, S. V., Buijs, A., Galjart, N., van Eyndhoven, W., van Min, M., Kuiper, R., Kemmeren, P., Mullighan, C. G., de Laat, W. & Meijerink, J. P. P., 25 Apr 2023, In: Cell Reports. 42, 4, 25 p., 112373.

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Formalin-Fixed, Paraffin-Embedded-Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors

Stelloo, E., Meijers, R. W. J., Swennenhuis, J. F., Allahyar, A., Hajo, K., Cangiano, M., de Leng, W. W. J., van Helvert, S., Van der Meulen, J., Creytens, D., van Kempen, L. C., Cleton-Jansen, A.-M., Bovee, J. V. M. G., de Laat, W., Splinter, E. & Feitsma, H., Oct 2023, In: Journal of Molecular Diagnostics. 25, 10, p. 758-770 13 p.

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2022

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

Rinzema, N. J., Sofiadis, K., Tjalsma, S. J. D., Verstegen, M. J. A. M., Oz, Y., Valdes-Quezada, C., Felder, A. K., Filipovska, T., van der Elst, S., de Andrade dos Ramos, Z., Han, R., Krijger, P. H. L. & de Laat, W., Jun 2022, In: Nature Structural and Molecular Biology. 29, 6, p. 563-574 12 p.

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6 Citations (Scopus)

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Current challenges in understanding the role of enhancers in disease

Zaugg, J. B., Sahlén, P., Andersson, R., Alberich-Jorda, M., de Laat, W., Deplancke, B., Ferrer, J., Mandrup, S., Natoli, G., Plewczynski, D., Rada-Iglesias, A. & Spicuglia, S., Dec 2022, In: Nature Structural and Molecular Biology. 29, 12, p. 1148-1158 11 p.

Research output: Contribution to journal › Article › Academic › peer-review

Role of the cellular factor CTCF in the regulation of bovine leukemia virus latency and three-dimensional chromatin organization

Bellefroid, M., Rodari, A., Galais, M., Krijger, P. H. L., Tjalsma, S. J. D., Nestola, L., Plant, E., Vos, E. S. M., Cristinelli, S., Van Driessche, B., Vanhulle, C., Ait-Ammar, A., Burny, A., Ciuffi, A., De Laat, W. & Van Lint, C., 8 Apr 2022, In: Nucleic acids research. 50, 6, p. 3190-3202 13 p.

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2021

A public–private partnership model for COVID-19 diagnostics

Krijger, P. H. L., Hoek, T. A., Boersma, S., Donders, L. I. P. M., Broeders, M. M. C., Pieterse, M., Toonen, P. W., Logister, I., Verhagen, B. M. P., Verstegen, M. J. A. M., van Ravesteyn, T. W., Roymans, R. J. T. M., Mattiroli, F., Vandesompele, J., Nijhuis, M., Meijer, S., van Weert, A., Dekker, E., Dom, F. J. & Ruijtenbeek, R. & 5 others, van der Velden, L. B. J., van de Bovenkamp, J. H. B., Bosch, M., de Laat, W. & Tanenbaum, M. E., Oct 2021, In: Nature Biotechnology. 39, 10, p. 1182-1184 3 p.

Research output: Contribution to journal › Letter › Academic › peer-review

Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart

Man, J. C., van Duijvenboden, K., Krijger, P. H., Hooijkaas, I. B., van der Made, I., de Gier-de Vries, C., Wakker, V., Creemers, E. E., de Laat, W., Boukens, B. J. & Christoffels, V. M., 8 Jan 2021, In: Circulation research. 128, 1, p. 115-129 15 p.

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Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression

Vos, E. S. M., Valdes-Quezada, C., Huang, Y., Allahyar, A., Verstegen, M. J. A. M., Felder, A. K., van der Vegt, F., Uijttewaal, E. C. H., Krijger, P. H. L. & de Laat, W., 5 Aug 2021, In: Molecular Cell. 81, 15, p. 3082-3095.e6

Research output: Contribution to journal › Article › Academic › peer-review

Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture

Tjalsma, S. J. & de Laat, W., Apr 2021, In: Current Opinion in Genetics & Development. 67, p. 10-17 8 p.

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Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing

Allahyar, A., Pieterse, M., Swennenhuis, J., Los-de Vries, G. T., Yilmaz, M., Leguit, R., Meijers, R. W. J., van der Geize, R., Vermaat, J., Cleven, A., van Wezel, T., Diepstra, A., van Kempen, L. C., Hijmering, N. J., Stathi, P., Sharma, M., Melquiond, A. S. J., de Vree, P. J. P., Verstegen, M. J. A. M. & Krijger, P. H. L. & 9 others, Hajo, K., Simonis, M., Rakszewska, A., van Min, M., de Jong, D., Ylstra, B., Feitsma, H., Splinter, E. & de Laat, W., 7 Jun 2021, In: Nature Communications. 12, 1, p. 1-15 3361.

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2020

4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis

Krijger, P. H. L., Geeven, G., Bianchi, V., Hilvering, C. R. E. & de Laat, W., 1 Jan 2020, In: Methods. 170, p. 17-32 16 p.

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Epigenetic Analyses of Human Left Atrial Tissue Identifies Gene Networks Underlying Atrial Fibrillation

Hall, A. W., Chaffin, M., Roselli, C., Lin, H., Lubitz, S. A., Bianchi, V., Geeven, G., Bedi, K., Margulies, K. B., de Laat, W., Tucker, N. R. & Ellinor, P. T., Dec 2020, In: Circulation. Genomic and precision medicine. 13, 6, p. 588-598 11 p.

Research output: Contribution to journal › Article › Academic › peer-review

Epigenetic and Transcriptional Networks Underlying Atrial Fibrillation

van Ouwerkerk, A. F., Hall, A. W., Kadow, Z. A., Lazarevic, S., Reyat, J. S., Tucker, N. R., Nadadur, R. D., Bosada, F. M., Bianchi, V., Ellinor, P. T., Fabritz, L., Martin, J. F., de Laat, W., Kirchhof, P., Moskowitz, I. P. & Christoffels, V. M., 19 Jun 2020, In: Circulation research. 127, 1, p. 34-50 17 p.

Research output: Contribution to journal › Article › Academic › peer-review

Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients

Castelijns, B., Baak, M. L., Timpanaro, I. S., Wiggers, C. R. M., Vermunt, M. W., Shang, P., Kondova, I., Geeven, G., Bianchi, V., de Laat, W., Geijsen, N. & Creyghton, M. P., 16 Jan 2020, In: Nature Communications. 11, 1, 12 p., 301.

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How chromosome topologies get their shape: views from proximity ligation and microscopy methods

Huang, Y., Neijts, R. & de Laat, W., Nov 2020, In: FEBS letters. 594, 21, p. 3439-3449 11 p.

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Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies

Vermeulen, C., Allahyar, A., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., Valdes-Quezada, C., Renkens, I., Straver, R., Kloosterman, W. P., de Ridder, J. & de Laat, W., 1 Feb 2020, In: Nature Protocols. 15, 2, p. 364-397 34 p.

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Recently Evolved Enhancers Emerge with High Interindividual Variability and Less Frequently Associate with Disease

Castelijns, B., Baak, M. L., Geeven, G., Vermunt, M. W., Wiggers, C. R. M., Timpanaro, I. S., Kondova, I., de Laat, W. & Creyghton, M. P., 23 Jun 2020, In: Cell Reports. 31, 12, p. 1-18 107799.

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2019

An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo

Man, J. C. K., Mohan, R. A., Boogaard, M. V. D., Hilvering, C. R. E., Jenkins, C., Wakker, V., Bianchi, V., Laat, W. D., Barnett, P., Boukens, B. J. & Christoffels, V. M., 1 Dec 2019, In: Nature Communications. 10, 1, 15 p., 4943.

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Chromatin Conformation Links Putative Enhancers in Intracranial Aneurysm–Associated Regions to Potential Candidate Genes

7 May 2019, In: Journal of the American Heart Association. 8, 9, e011201.

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DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Redolfi, J., Zhan, Y., Valdes-Quezada, C., Kryzhanovska, M., Guerreiro, I., Iesmantavicius, V., Pollex, T., Grand, R. S., Mulugeta, E., Kind, J., Tiana, G., Smallwood, S. A., de Laat, W. & Giorgetti, L., Jun 2019, In: Nature Structural and Molecular Biology. 26, 6, p. 471-480 10 p.

Research output: Contribution to journal › Article › Academic › peer-review

Identification and Characterization of a Transcribed Distal Enhancer Involved in Cardiac Kcnh2 Regulation

van den Boogaard, M., van Weerd, J. H., Bawazeer, A. C., Hooijkaas, I. B., van de Werken, H. J. G., Tessadori, F., de Laat, W., Barnett, P., Bakkers, J. & Christoffels, V. M., 3 Sept 2019, In: Cell Reports. 28, 10, p. 2704-2714.e5

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Noncoding deletions reveal a gene that is critical for intestinal function

Oz-Levi, D., Olender, T., Bar-Joseph, I., Zhu, Y., Marek-Yagel, D., Barozzi, I., Osterwalder, M., Alkelai, A., Ruzzo, E. K., Han, Y., Vos, E. S. M., Reznik-Wolf, H., Hartman, C., Shamir, R., Weiss, B., Shapiro, R., Pode-Shakked, B., Tatarskyy, P., Milgrom, R. & Schvimer, M. & 23 others, Barshack, I., Imai, D. M., Coleman-Derr, D., Dickel, D. E., Nord, A. S., Afzal, V., van Bueren, K. L., Barnes, R. M., Black, B. L., Mayhew, C. N., Kuhar, M. F., Pitstick, A., Tekman, M., Stanescu, H. C., Wells, J. M., Kleta, R., de Laat, W., Goldstein, D. B., Pras, E., Visel, A., Lancet, D., Anikster, Y. & Pennacchio, L. A., Jul 2019, In: Nature. 571, 7763, p. 107-111 5 p.

Research output: Contribution to journal › Article › Academic › peer-review

YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis In Vivo

Monroe, T. O., Hill, M. C., Morikawa, Y., Leach, J. P., Heallen, T., Cao, S., Krijger, P. H. L., de Laat, W., Wehrens, X. H. T., Rodney, G. G. & Martin, J. F., 25 Mar 2019, In: Developmental Cell. 48, 6, p. 765-779.e7

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12 Citations (Scopus)

2018

Enhancer hubs and loop collisions identified from single-allele topologies

Allahyar, A., Vermeulen, C., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., van Kranenburg, M., Pieterse, M., Straver, R., Haarhuis, J. H. I., Jalink, K., Teunissen, H., Renkens, I. J., Kloosterman, W. P., Rowland, B. D., de Wit, E., de Ridder, J. & de Laat, W., 1 Aug 2018, In: Nature Genetics. 50, 8, p. 1151-1160 10 p.

Research output: Contribution to journal › Article › Academic › peer-review

7 Citations (Scopus)

2017

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression

Gupta, R. M., Hadaya, J., Trehan, A., Zekavat, S. M., Roselli, C., Klarin, D., Emdin, C. A., Hilvering, C. R. E., Bianchi, V., Mueller, C., Khera, A. V., Ryan, R. J. H., Engreitz, J. M., Issner, R., Shoresh, N., Epstein, C. B., de Laat, W., Brown, J. D., Schnabel, R. B. & Bernstein, B. E. & 1 others, Kathiresan, S., 27 Jul 2017, In: Cell. 170, 3, p. 522-533.e15

Research output: Contribution to journal › Article › Academic › peer-review

Can We Just Say: Transcription Second?

Krijger, P. H. L. & de Laat, W., 6 Apr 2017, In: Cell. 169, 2, p. 184-185 2 p.

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Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer

Dreijerink, K. M. A., Groner, A. C., Vos, E. S. M., Font-Tello, A., Gu, L., Chi, D., Reyes, J., Cook, J., Lim, E., Lin, C. Y., de Laat, W., Rao, P. K., Long, H. W. & Brown, M., 7 Mar 2017, In: Cell Reports [E]. 18, 10, p. 2359-2372 14 p.

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Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping

Vermeulen, C., Geeven, G., de Wit, E., Verstegen, M. J. A. M., Jansen, R. P. M., van Kranenburg, M., de Bruijn, E., Pulit, S. L., Kruisselbrink, E., Shahsavari, Z., Omrani, D., Zeinali, F., Najmabadi, H., Katsila, T., Vrettou, C., Patrinos, G. P., Traeger-Synodinos, J., Splinter, E., Beekman, J. M. & Kheradmand Kia, S. & 3 others, Te Meerman, G. J., Ploos van Amstel, H. K. & de Laat, W., 7 Sept 2017, In: American Journal of Human Genetics. 101, 3, p. 326-339 14 p.

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Small chromosomal regions position themselves autonomously according to their chromatin class

Van De Werken, H. J. G., Haan, J. C., Feodorova, Y., Bijos, D., Weuts, A., Theunis, K., Holwerda, S. J. B., Meuleman, W., Pagie, L., Thanisch, K., Kumar, P., Leonhardt, H., Marynen, P., van Steensel, B., Voet, T., De Laat, W., Solovei, I. & Joffe, B., 1 Jun 2017, In: Genome Research. 27, 6, p. 922-933 12 p.

Research output: Contribution to journal › Article › Academic › peer-review

2016

A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response

Melo, C. A., Léveillé, N., Rooijers, K., Wijchers, P. J., Geeven, G., Tal, A., Melo, S. A., de Laat, W. & Agami, R., 18 Jan 2016, In: Oncogene. 35, p. 4399–4406

Research output: Contribution to journal › Article › Academic › peer-review

Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments

Wijchers, P. J., Krijger, P. H. L., Geeven, G., Zhu, Y., Denker, A., Verstegen, M. J. A. M., Valdes-Quezada, C., Vermeulen, C., Janssen, M., Teunissen, H., Anink-Groenen, L. C. M., Verschure, P. J. & de Laat, W., 4 Feb 2016, In: Molecular Cell. 61, 3, p. 461-473 13 p.

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9 Citations (Scopus)

Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming

Krijger, P. H. L., Di Stefano, B., de Wit, E., Limone, F., Van Oevelen, C., De Laat, W. & Graf, T., 5 May 2016, In: Cell Stem Cell. 18, 5, p. 597-610 14 p.

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15 Citations (Scopus)

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

Wang, X., Tucker, N. R., Rizki, G., Mills, R., Krijger, P. H. L., de Wit, E., Subramanian, V., Bartell, E., Nguyen, X. X., Ye, J., Leyton-Mange, J., Dolmatova, E. V., Harst, P. V. D., Laat, W. D., Ellinor, P. T., Newton-Cheh, C., Milan, D. J., Kellis, M. & Boyer, L. A., 10 May 2016, In: eLife. 2016, 5, e10557.

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1 Citation (Scopus)

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Enhancers reside in a unique epigenetic environment during early zebrafish development

Kaaij, L. J. T., Mokry, M., Zhou, M., Musheev, M., Geeven, G., Melquiond, A. S. J., de Jesus Domingues, A. M., de Laat, W., Niehrs, C., Smith, A. D. & Ketting, R. F., 5 Jul 2016, In: Genome Biology. 17, 1, 17:146.

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Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

Vermunt, M. W., Tan, S. C., Castelijns, B., Geeven, G., Reinink, P., de Bruijn, E., Kondova, I., Persengiev, S., Bontrop, R., Cuppen, E., de laat, W., Creyghton, M. P., Mar 2016, In: Nature Neuroscience. 19, 3, p. 494-503 13 p.

Research output: Contribution to journal › Article › Academic › peer-review

Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq [Genome Biol. 2015;16:149]

Marks, H., Kerstens, H. H. D., Barakat, T. S., Splinter, E., Dirks, R. A. M., van Mierlo, G., Joshi, O., Wang, S. Y., Babak, T., Albers, C. A., Kalkan, T., Smith, A., Jouneau, A., de Laat, W., Gribnau, J. & Stunnenberg, H. G., 5 Feb 2016, In: Genome Biology. 17, 17:22.

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Polarized regulatory landscape and Wnt responsiveness underlie Hox activation in embryos

Neijts, R., Amin, S., Van Rooijen, E. M. H. C., Tan, S., Creyghton, M. P., De Laat, W. & Deschamps, J., 1 Sept 2016, In: Genes and Development. 30, 17, p. 1937-1942 6 p.

Research output: Contribution to journal › Article › Academic › peer-review

3 Citations (Scopus)

Regulation of disease-associated gene expression in the 3D genome

Krijger, P. H. L. & De Laat, W., 21 Nov 2016, In: Nature reviews molecular cell biology. 17, 12, p. 771-782 12 p.

Research output: Contribution to journal › Article › Academic › peer-review

2 Citations (Scopus)

The second decade of 3C technologies: Detailed insights into nuclear organization

Denker, A. & De Laat, W., 15 Jun 2016, In: Genes and Development. 30, 12, p. 1357-1382 26 p.

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18 Citations (Scopus)

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2015

A Long-Distance Chromatin Affair

Denker, A. & de Laat, W., 27 Aug 2015, In: Cell. 162, 5, p. 942-3 2 p.

Research output: Contribution to journal › Article › Academic › peer-review

Architectural hallmarks of the pluripotent genome

Bouwman, B. A. M. & de Laat, W., 2015, In: FEBS letters. 589, 20 Pt A, p. 2905-13 9 p.

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Characterization and dynamics of pericentromere-associated domains in mice

Wijchers, P. J., Geeven, G., Eyres, M., Bergsma, A. J., Janssen, M., Verstegen, M., Zhu, Y., Schell, Y., Vermeulen, C., de Wit, E. & de Laat, W., Jul 2015, In: Genome Research. 25, 7, p. 958-69 12 p.

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CTCF Binding Polarity Determines Chromatin Looping

de Wit, E., Vos, E. S. M., Holwerda, S. J. B., Valdes-Quezada, C., Verstegen, M. J. A. M., Teunissen, H., Splinter, E., Wijchers, P. J., Krijger, P. H. L. & de Laat, W., 19 Nov 2015, In: Molecular Cell. 60, 4, p. 676-84 9 p.

Research output: Contribution to journal › Article › Academic › peer-review

Dynamics of gene silencing during X inactivation using allele-specific RNA-seq

Marks, H., Kerstens, H. H. D., Barakat, T. S., Splinter, E., Dirks, R. A. M., van Mierlo, G., Joshi, O., Wang, S.-Y., Babak, T., Albers, C. A., Kalkan, T., Smith, A., Jouneau, A., de Laat, W., Gribnau, J. & Stunnenberg, H. G., 2015, In: Genome Biology. 16, 20 p., 149.

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Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

Léveillé, N., Melo, C. A., Rooijers, K., Díaz-Lagares, A., Melo, S. A., Korkmaz, G., Lopes, R., Akbari Moqadam, F., Maia, A. R., Wijchers, P. J., Geeven, G., den Boer, M. L., Kalluri, R., de Laat, W., Esteller, M. & Agami, R., 2015, In: Nature Communications [E]. 6

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Getting the genome in shape: the formation of loops, domains and compartments

Bouwman, B. A. M. & de Laat, W., 2015, In: Genome Biology. 16, 154

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High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila

Ramírez, F., Lingg, T., Toscano, S., Lam, K. C., Georgiev, P., Chung, H.-R., Lajoie, B. R., de Wit, E., Zhan, Y., de Laat, W., Dekker, J., Manke, T. & Akhtar, A., 2015, In: Molecular Cell. 60, 1, p. 146-62 17 p.

Research output: Contribution to journal › Article › Academic › peer-review

Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

Geeven, G., Zhu, Y., Kim, B. J., Bartholdy, B. A., Yang, S.-M., Macfarlan, T. S., Gifford, W. D., Pfaff, S. L., Verstegen, M. J. A. M., Pinto, H., Vermunt, M. W., Creyghton, M. P., Wijchers, P. J., Stamatoyannopoulos, J. A., Skoultchi, A. I. & de Laat, W., 2015, In: Genome Biology. 16, 289

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Wouter de Laat

Research output

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