Wouter de Laat

Wouter de Laat

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Wouter de Laat

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

Authors:
Malou van den Boogaard Jan Hendrik van Weerd Amira C Bawazeer Ingeborg B Hooijkaas Harmen J G van de Werken Federico Tessadori Wouter de Laat Phil Barnett Jeroen Bakkers Vincent M Christoffels

Cell Rep 2019 Sep;28(10):2704-2714.e5

Amsterdam UMC, University of Amsterdam, Department of Medical Biology, Amsterdam Cardiovascular Sciences, 1105AZ Amsterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.08.007DOI Listing
September 2019

Noncoding deletions reveal a gene that is critical for intestinal function.

Authors:
Danit Oz-Levi Tsviya Olender Ifat Bar-Joseph Yiwen Zhu Dina Marek-Yagel Iros Barozzi Marco Osterwalder Anna Alkelai Elizabeth K Ruzzo Yujun Han Erica S M Vos Haike Reznik-Wolf Corina Hartman Raanan Shamir Batia Weiss Rivka Shapiro Ben Pode-Shakked Pavlo Tatarskyy Roni Milgrom Michael Schvimer Iris Barshack Denise M Imai Devin Coleman-Derr Diane E Dickel Alex S Nord Veena Afzal Kelly Lammerts van Bueren Ralston M Barnes Brian L Black Christopher N Mayhew Matthew F Kuhar Amy Pitstick Mehmet Tekman Horia C Stanescu James M Wells Robert Kleta Wouter de Laat David B Goldstein Elon Pras Axel Visel Doron Lancet Yair Anikster Len A Pennacchio

Nature 2019 07 19;571(7763):107-111. Epub 2019 Jun 19.

Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/s41586-019-1312-2DOI Listing
July 2019

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

Authors:
Peter H L Krijger Geert Geeven Valerio Bianchi Catharina R E Hilvering Wouter de Laat

Methods 2019 Jul 26. Epub 2019 Jul 26.

Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.07.014DOI Listing
July 2019

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

Authors:
Josef Redolfi Yinxiu Zhan Christian Valdes-Quezada Mariya Kryzhanovska Isabel Guerreiro Vytautas Iesmantavicius Tim Pollex Ralph S Grand Eskeatnaf Mulugeta Jop Kind Guido Tiana Sebastien A Smallwood Wouter de Laat Luca Giorgetti

Nat Struct Mol Biol 2019 Jun 27;26(6):471-480. Epub 2019 May 27.

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

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http://www.nature.com/articles/s41594-019-0231-0
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http://dx.doi.org/10.1038/s41594-019-0231-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6561777PMC
June 2019

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

Authors:
Melanie D Laarman Geert Geeven Phil Barnett Gabriël J E Rinkel Wouter de Laat Ynte M Ruigrok Jeroen Bakkers

J Am Heart Assoc 2019 May;8(9):e011201

2 Hubrecht Institute (Royal Netherlands Academy of Arts and Sciences (KNAW)) University Medical Center, Utrecht the Netherlands.

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http://dx.doi.org/10.1161/JAHA.118.011201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6512097PMC
May 2019

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

Authors:
Tanner O Monroe Matthew C Hill Yuka Morikawa John P Leach Todd Heallen Shuyi Cao Peter H L Krijger Wouter de Laat Xander H T Wehrens George G Rodney James F Martin

Dev Cell 2019 03 14;48(6):765-779.e7. Epub 2019 Feb 14.

Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Cardiomyocyte Renewal Laboratory, Texas Heart Institute, 6770 Bertner Avenue, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15345807193004
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http://dx.doi.org/10.1016/j.devcel.2019.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6435425PMC
March 2019

peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data.

Authors:
Geert Geeven Hans Teunissen Wouter de Laat Elzo de Wit

Nucleic Acids Res 2018 09;46(15):e91

Oncode Institute and Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.

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http://dx.doi.org/10.1093/nar/gky443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125690PMC
September 2018

Enhancer hubs and loop collisions identified from single-allele topologies.

Authors:
Amin Allahyar Carlo Vermeulen Britta A M Bouwman Peter H L Krijger Marjon J A M Verstegen Geert Geeven Melissa van Kranenburg Mark Pieterse Roy Straver Judith H I Haarhuis Kees Jalink Hans Teunissen Ivo J Renkens Wigard P Kloosterman Benjamin D Rowland Elzo de Wit Jeroen de Ridder Wouter de Laat

Nat Genet 2018 08 9;50(8):1151-1160. Epub 2018 Jul 9.

Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1038/s41588-018-0161-5DOI Listing
August 2018

Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm.

Authors:
Xinan H Yang Rangarajan D Nadadur Catharina Re Hilvering Valerio Bianchi Michael Werner Stefan R Mazurek Margaret Gadek Kaitlyn M Shen Joseph Aaron Goldman Leonid Tyan Jenna Bekeny Johnathon M Hall Nutishia Lee Carlos Perez-Cervantes Ozanna Burnicka-Turek Kenneth D Poss Christopher R Weber Wouter de Laat Alexander J Ruthenburg Ivan P Moskowitz

Elife 2017 12 27;6. Epub 2017 Dec 27.

Department of Pediatrics, The University of Chicago, Chicago, United States.

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http://dx.doi.org/10.7554/eLife.31683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745077PMC
December 2017

Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping.

Authors:
Carlo Vermeulen Geert Geeven Elzo de Wit Marjon J A M Verstegen Rumo P M Jansen Melissa van Kranenburg Ewart de Bruijn Sara L Pulit Evelien Kruisselbrink Zahra Shahsavari Davood Omrani Fatemeh Zeinali Hossein Najmabadi Theodora Katsila Christina Vrettou George P Patrinos Joanne Traeger-Synodinos Erik Splinter Jeffrey M Beekman Sima Kheradmand Kia Gerard J Te Meerman Hans Kristian Ploos van Amstel Wouter de Laat

Am J Hum Genet 2017 Sep 24;101(3):326-339. Epub 2017 Aug 24.

Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297173029
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http://dx.doi.org/10.1016/j.ajhg.2017.07.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590845PMC
September 2017

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

Authors:
Rajat M Gupta Joseph Hadaya Aditi Trehan Seyedeh M Zekavat Carolina Roselli Derek Klarin Connor A Emdin Catharina R E Hilvering Valerio Bianchi Christian Mueller Amit V Khera Russell J H Ryan Jesse M Engreitz Robbyn Issner Noam Shoresh Charles B Epstein Wouter de Laat Jonathan D Brown Renate B Schnabel Bradley E Bernstein Sekar Kathiresan

Cell 2017 Jul;170(3):522-533.e15

Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.06.049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5785707PMC
July 2017

Small chromosomal regions position themselves autonomously according to their chromatin class.

Authors:
Harmen J G van de Werken Josien C Haan Yana Feodorova Dominika Bijos An Weuts Koen Theunis Sjoerd J B Holwerda Wouter Meuleman Ludo Pagie Katharina Thanisch Parveen Kumar Heinrich Leonhardt Peter Marynen Bas van Steensel Thierry Voet Wouter de Laat Irina Solovei Boris Joffe

Genome Res 2017 06 24;27(6):922-933. Epub 2017 Mar 24.

Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany.

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http://dx.doi.org/10.1101/gr.213751.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453326PMC
June 2017

Can We Just Say: Transcription Second?

Authors:
Peter Hugo Lodewijk Krijger Wouter de Laat

Cell 2017 04;169(2):184-185

Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.03.026DOI Listing
April 2017

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

Authors:
Koen M A Dreijerink Anna C Groner Erica S M Vos Alba Font-Tello Lei Gu David Chi Jaime Reyes Jennifer Cook Elgene Lim Charles Y Lin Wouter de Laat Prakash K Rao Henry W Long Myles Brown

Cell Rep 2017 03;18(10):2359-2372

Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston 02215, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston 02215, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.02.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609449PMC
March 2017

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

Authors:
Peter Hugo Lodewijk Krijger Wouter de Laat

Nat Rev Mol Cell Biol 2016 12 9;17(12):771-782. Epub 2016 Nov 9.

Hubrecht Institute of The Royal Netherlands Academy of Arts and Sciences (KNAW) and the University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nrm.2016.138DOI Listing
December 2016

Polarized regulatory landscape and Wnt responsiveness underlie Hox activation in embryos.

Authors:
Roel Neijts Shilu Amin Carina van Rooijen Sander Tan Menno P Creyghton Wouter de Laat Jacqueline Deschamps

Genes Dev 2016 Sep 15;30(17):1937-42. Epub 2016 Sep 15.

Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1101/gad.285767.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066237PMC
September 2016

Enhancers reside in a unique epigenetic environment during early zebrafish development.

Authors:
Lucas J T Kaaij Michal Mokry Meng Zhou Michael Musheev Geert Geeven Adrien S J Melquiond António M de Jesus Domingues Wouter de Laat Christof Niehrs Andrew D Smith René F Ketting

Genome Biol 2016 07 5;17(1):146. Epub 2016 Jul 5.

Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.

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http://dx.doi.org/10.1186/s13059-016-1013-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934011PMC
July 2016

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

Authors:
Annette Denker Wouter de Laat

Genes Dev 2016 06;30(12):1357-82

Hubrecht Institute-Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) and University Medical Center Utrecht, 3584CT Utrecht, the Netherlands.

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http://dx.doi.org/10.1101/gad.281964.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926860PMC
June 2016

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming.

Authors:
Peter Hugo Lodewijk Krijger Bruno Di Stefano Elzo de Wit Francesco Limone Chris van Oevelen Wouter de Laat Thomas Graf

Cell Stem Cell 2016 05 10;18(5):597-610. Epub 2016 Mar 10.

Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG) and Pompeu Fabra University, Dr Aiguader 88, 08003 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.01.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858530PMC
May 2016

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

Authors:
Xinchen Wang Nathan R Tucker Gizem Rizki Robert Mills Peter Hl Krijger Elzo de Wit Vidya Subramanian Eric Bartell Xinh-Xinh Nguyen Jiangchuan Ye Jordan Leyton-Mange Elena V Dolmatova Pim van der Harst Wouter de Laat Patrick T Ellinor Christopher Newton-Cheh David J Milan Manolis Kellis Laurie A Boyer

Elife 2016 05 10;5. Epub 2016 May 10.

Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.

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http://dx.doi.org/10.7554/eLife.10557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862755PMC
May 2016

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

Authors:
Marit W Vermunt Sander C Tan Bas Castelijns Geert Geeven Peter Reinink Ewart de Bruijn Ivanela Kondova Stephan Persengiev Ronald Bontrop Edwin Cuppen Wouter de Laat Menno P Creyghton

Nat Neurosci 2016 Mar 25;19(3):494-503. Epub 2016 Jan 25.

Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1038/nn.4229DOI Listing
March 2016

Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments.

Authors:
Patrick J Wijchers Peter H L Krijger Geert Geeven Yun Zhu Annette Denker Marjon J A M Verstegen Christian Valdes-Quezada Carlo Vermeulen Mark Janssen Hans Teunissen Lisette C M Anink-Groenen Pernette J Verschure Wouter de Laat

Mol Cell 2016 Feb 28;61(3):461-473. Epub 2016 Jan 28.

Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747903PMC
February 2016

Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.

Authors:
Hendrik Marks Hindrik H D Kerstens Tahsin Stefan Barakat Erik Splinter René A M Dirks Guido van Mierlo Onkar Joshi Shuang-Yin Wang Tomas Babak Cornelis A Albers Tüzer Kalkan Austin Smith Alice Jouneau Wouter de Laat Joost Gribnau Hendrik G Stunnenberg

Genome Biol 2016 Feb 5;17:22. Epub 2016 Feb 5.

Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, 6500HB, The Netherlands.

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http://link.springer.com/content/pdf/10.1186%2Fs13059-016-08
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http://genomebiology.com/2016/17/1/22
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http://dx.doi.org/10.1186/s13059-016-0885-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743200PMC
February 2016

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

Authors:
Geert Geeven Yun Zhu Byung Ju Kim Boris A Bartholdy Seung-Min Yang Todd S Macfarlan Wesley D Gifford Samuel L Pfaff Marjon J A M Verstegen Hugo Pinto Marit W Vermunt Menno P Creyghton Patrick J Wijchers John A Stamatoyannopoulos Arthur I Skoultchi Wouter de Laat

Genome Biol 2015 Dec 23;16:289. Epub 2015 Dec 23.

Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.

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http://dx.doi.org/10.1186/s13059-015-0857-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4699363PMC
December 2015

CTCF Binding Polarity Determines Chromatin Looping.

Authors:
Elzo de Wit Erica S M Vos Sjoerd J B Holwerda Christian Valdes-Quezada Marjon J A M Verstegen Hans Teunissen Erik Splinter Patrick J Wijchers Peter H L Krijger Wouter de Laat

Mol Cell 2015 Nov 29;60(4):676-84. Epub 2015 Oct 29.

Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.09.023DOI Listing
November 2015

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.

Authors:
Cinthya J Zepeda-Mendoza Swagatam Mukhopadhyay Emily S Wong Nathalie Harder Erik Splinter Elzo de Wit Melanie A Eckersley-Maslin Thomas Ried Roland Eils Karl Rohr Alea Mills Wouter de Laat Paul Flicek Anirvan M Sengupta David L Spector

BMC Genomics 2015 Nov 21;16:982. Epub 2015 Nov 21.

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.

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http://dx.doi.org/10.1186/s12864-015-2137-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654810PMC
November 2015

Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination.

Authors:
Liv M I Austenaa Iros Barozzi Marta Simonatto Silvia Masella Giulia Della Chiara Serena Ghisletti Alessia Curina Elzo de Wit Britta A M Bouwman Stefano de Pretis Viviana Piccolo Alberto Termanini Elena Prosperini Mattia Pelizzola Wouter de Laat Gioacchino Natoli

Mol Cell 2015 Nov 22;60(3):460-74. Epub 2015 Oct 22.

Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.09.018DOI Listing
November 2015

Architectural hallmarks of the pluripotent genome.

Authors:
Britta A M Bouwman Wouter de Laat

FEBS Lett 2015 Oct 7;589(20 Pt A):2905-13. Epub 2015 May 7.

Hubrecht Institute - KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.febslet.2015.04.055DOI Listing
October 2015

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

Authors:
Fidel Ramírez Thomas Lingg Sarah Toscano Kin Chung Lam Plamen Georgiev Ho-Ryun Chung Bryan R Lajoie Elzo de Wit Ye Zhan Wouter de Laat Job Dekker Thomas Manke Asifa Akhtar

Mol Cell 2015 Oct;60(1):146-62

Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.08.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806858PMC
October 2015

YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers.

Authors:
Giorgio G Galli Matteo Carrara Wei-Chien Yuan Christian Valdes-Quezada Basanta Gurung Brian Pepe-Mooney Tinghu Zhang Geert Geeven Nathanael S Gray Wouter de Laat Raffaele A Calogero Fernando D Camargo

Mol Cell 2015 Oct 1;60(2):328-37. Epub 2015 Oct 1.

Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765150069
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http://dx.doi.org/10.1016/j.molcel.2015.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624327PMC
October 2015

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

Authors:
Hendrik Marks Hindrik H D Kerstens Tahsin Stefan Barakat Erik Splinter René A M Dirks Guido van Mierlo Onkar Joshi Shuang-Yin Wang Tomas Babak Cornelis A Albers Tüzer Kalkan Austin Smith Alice Jouneau Wouter de Laat Joost Gribnau Hendrik G Stunnenberg

Genome Biol 2015 Aug 3;16:149. Epub 2015 Aug 3.

Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/s13059-015-0698-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546214PMC
August 2015

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

Authors:
Britta A M Bouwman Wouter de Laat

Genome Biol 2015 Aug 10;16:154. Epub 2015 Aug 10.

Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.

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http://dx.doi.org/10.1186/s13059-015-0730-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536798PMC
August 2015

A Long-Distance Chromatin Affair.

Authors:
Annette Denker Wouter de Laat

Cell 2015 Aug;162(5):942-3

Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.08.022DOI Listing
August 2015

Characterization and dynamics of pericentromere-associated domains in mice.

Authors:
Patrick J Wijchers Geert Geeven Michael Eyres Atze J Bergsma Mark Janssen Marjon Verstegen Yun Zhu Yori Schell Carlo Vermeulen Elzo de Wit Wouter de Laat

Genome Res 2015 Jul 16;25(7):958-69. Epub 2015 Apr 16.

Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1101/gr.186643.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484393PMC
July 2015

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

Authors:
Nicolas Léveillé Carlos A Melo Koos Rooijers Angel Díaz-Lagares Sonia A Melo Gozde Korkmaz Rui Lopes Farhad Akbari Moqadam Ana R Maia Patrick J Wijchers Geert Geeven Monique L den Boer Raghu Kalluri Wouter de Laat Manel Esteller Reuven Agami

Nat Commun 2015 Mar 27;6:6520. Epub 2015 Mar 27.

Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://search.proquest.com/openview/72f1f0dc5f5c1ab65b42368a
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http://dspace.library.uu.nl/bitstream/handle/1874/333244/p53
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http://www.nature.com/doifinder/10.1038/ncomms7520
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http://dx.doi.org/10.1038/ncomms7520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4389233PMC
March 2015

Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping.

Authors:
Paula J P de Vree Elzo de Wit Mehmet Yilmaz Monique van de Heijning Petra Klous Marjon J A M Verstegen Yi Wan Hans Teunissen Peter H L Krijger Geert Geeven Paul P Eijk Daoud Sie Bauke Ylstra Lorette O M Hulsman Marieke F van Dooren Laura J C M van Zutven Ans van den Ouweland Sjef Verbeek Ko Willems van Dijk Marion Cornelissen Atze T Das Ben Berkhout Birgit Sikkema-Raddatz Eva van den Berg Pieter van der Vlies Desiree Weening Johan T den Dunnen Magdalena Matusiak Mohamed Lamkanfi Marjolijn J L Ligtenberg Petra ter Brugge Jos Jonkers John A Foekens John W Martens Rob van der Luijt Hans Kristian Ploos van Amstel Max van Min Erik Splinter Wouter de Laat

Nat Biotechnol 2014 Oct 17;32(10):1019-25. Epub 2014 Aug 17.

1] Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands. [2] Cergentis B.V., Utrecht, the Netherlands.

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http://dx.doi.org/10.1038/nbt.2959DOI Listing
October 2014

Large-scale identification of coregulated enhancer networks in the adult human brain.

Authors:
Marit W Vermunt Peter Reinink Jeroen Korving Ewart de Bruijn Paul M Creyghton Onur Basak Geert Geeven Pim W Toonen Nico Lansu Charles Meunier Sebastiaan van Heesch Hans Clevers Wouter de Laat Edwin Cuppen Menno P Creyghton

Cell Rep 2014 Oct 16;9(2):767-79. Epub 2014 Oct 16.

Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.09.023DOI Listing
October 2014

A large permissive regulatory domain exclusively controls Tbx3 expression in the cardiac conduction system.

Authors:
Jan Hendrik van Weerd Ileana Badi Malou van den Boogaard Sonia Stefanovic Harmen J G van de Werken Melisa Gomez-Velazquez Claudio Badia-Careaga Miguel Manzanares Wouter de Laat Phil Barnett Vincent M Christoffels

Circ Res 2014 Aug 24;115(4):432-41. Epub 2014 Jun 24.

From the Department of Anatomy, Embryology, and Physiology, Academic Medical Center, Amsterdam, The Netherlands (J.H.v.W., I.B., M.v.d.B., S.S., P.B., V.M.C.); Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands (H.J.G.v.d.W., W.d.L.); Department of Cell Biology, Erasmus MC Rotterdam, Rotterdam, The Netherlands (H.J.G.v.d.W.); and Cardiovascular Development and Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (M.G.-V., C.B.-C., M.M.).

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http://dx.doi.org/10.1161/CIRCRESAHA.115.303591DOI Listing
August 2014

A common genetic variant within SCN10A modulates cardiac SCN5A expression.

Authors:
Malou van den Boogaard Scott Smemo Ozanna Burnicka-Turek David E Arnolds Harmen J G van de Werken Petra Klous David McKean Jochen D Muehlschlegel Julia Moosmann Okan Toka Xinan H Yang Tamara T Koopmann Michiel E Adriaens Connie R Bezzina Wouter de Laat Christine Seidman J G Seidman Vincent M Christoffels Marcelo A Nobrega Phil Barnett Ivan P Moskowitz

J Clin Invest 2014 Apr 18;124(4):1844-52. Epub 2014 Mar 18.

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http://dx.doi.org/10.1172/JCI73140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973109PMC
April 2014

A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia.

Authors:
Stefan Gröschel Mathijs A Sanders Remco Hoogenboezem Elzo de Wit Britta A M Bouwman Claudia Erpelinck Vincent H J van der Velden Marije Havermans Roberto Avellino Kirsten van Lom Elwin J Rombouts Mark van Duin Konstanze Döhner H Berna Beverloo James E Bradner Hartmut Döhner Bob Löwenberg Peter J M Valk Eric M J Bindels Wouter de Laat Ruud Delwel

Cell 2014 Apr 3;157(2):369-381. Epub 2014 Apr 3.

Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.02.019DOI Listing
April 2014

CTCF: the protein, the binding partners, the binding sites and their chromatin loops.

Authors:
Sjoerd Johannes Bastiaan Holwerda Wouter de Laat

Philos Trans R Soc Lond B Biol Sci 2013 6;368(1620):20120369. Epub 2013 May 6.

Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1098/rstb.2012.0369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682731PMC
December 2013

Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization.

Authors:
Matthew Denholtz Giancarlo Bonora Constantinos Chronis Erik Splinter Wouter de Laat Jason Ernst Matteo Pellegrini Kathrin Plath

Cell Stem Cell 2013 Nov 12;13(5):602-16. Epub 2013 Sep 12.

Department of Biological Chemistry at the David Geffen School of Medicine, Los Angeles, CA, 90095, USA.

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http://dx.doi.org/10.1016/j.stem.2013.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825755PMC
November 2013

Topology of mammalian developmental enhancers and their regulatory landscapes.

Authors:
Wouter de Laat Denis Duboule

Nature 2013 Oct;502(7472):499-506

Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.

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http://dx.doi.org/10.1038/nature12753DOI Listing
October 2013

Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II profiling.

Authors:
Astrid Eijkelenboom Michal Mokry Elzo de Wit Lydia M Smits Paulien E Polderman Miranda H van Triest Ruben van Boxtel Almut Schulze Wouter de Laat Edwin Cuppen Boudewijn M T Burgering

Mol Syst Biol 2013 ;9:638

Department of Molecular Cancer Research, University Medical Centre, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/msb.2012.74DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564262PMC
September 2013

The pluripotent genome in three dimensions is shaped around pluripotency factors.

Authors:
Elzo de Wit Britta A M Bouwman Yun Zhu Petra Klous Erik Splinter Marjon J A M Verstegen Peter H L Krijger Nicola Festuccia Elphège P Nora Maaike Welling Edith Heard Niels Geijsen Raymond A Poot Ian Chambers Wouter de Laat

Nature 2013 Sep 24;501(7466):227-31. Epub 2013 Jul 24.

Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nature12420DOI Listing
September 2013

For genomes to stay in shape, insulators must be up to PAR.

Authors:
Patrick J Wijchers Wouter de Laat

Cell 2013 Sep;155(1):15-6

Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.

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http://dx.doi.org/10.1016/j.cell.2013.09.012DOI Listing
September 2013

Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells.

Authors:
Sjoerd J B Holwerda Harmen J G van de Werken Claudia Ribeiro de Almeida Ingrid M Bergen Marjolein J W de Bruijn Marjon J A M Verstegen Marieke Simonis Erik Splinter Patrick J Wijchers Rudi W Hendriks Wouter de Laat

Nucleic Acids Res 2013 Aug 7;41(14):6905-16. Epub 2013 Jun 7.

Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkt491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737562PMC
August 2013

Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.

Authors:
Jasna Medvedovic Anja Ebert Hiromi Tagoh Ido M Tamir Tanja A Schwickert Maria Novatchkova Qiong Sun Pim J Huis In 't Veld Chunguang Guo Hye Suk Yoon Yves Denizot Sjoerd J B Holwerda Wouter de Laat Michel Cogné Yang Shi Frederick W Alt Meinrad Busslinger

Immunity 2013 Aug;39(2):229-44

Research Institute of Molecular Pathology, Vienna Biocenter, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.

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http://dx.doi.org/10.1016/j.immuni.2013.08.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810778PMC
August 2013

DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus.

Authors:
Lucas T J Kaaij Marc van de Wetering Fang Fang Benjamin Decato Antoine Molaro Harmen J G van de Werken Johan H van Es Jurian Schuijers Elzo de Wit Wouter de Laat Gregory J Hannon Hans C Clevers Andrew D Smith René F Ketting

Genome Biol 2013 May 28;14(5):R50. Epub 2013 May 28.

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http://dx.doi.org/10.1186/gb-2013-14-5-r50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053812PMC
May 2013

Identical cells with different 3D genomes; cause and consequences?

Authors:
Peter H L Krijger Wouter de Laat

Curr Opin Genet Dev 2013 Apr 14;23(2):191-6. Epub 2013 Feb 14.

Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Urecht, The Netherlands.

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http://dx.doi.org/10.1016/j.gde.2012.12.010DOI Listing
April 2013

eRNAs are required for p53-dependent enhancer activity and gene transcription.

Authors:
Carlos A Melo Jarno Drost Patrick J Wijchers Harmen van de Werken Elzo de Wit Joachim A F Oude Vrielink Ran Elkon Sónia A Melo Nicolas Léveillé Raghu Kalluri Wouter de Laat Reuven Agami

Mol Cell 2013 Feb 27;49(3):524-35. Epub 2012 Dec 27.

Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands; Doctoral Programme in Biomedicine and Experimental Biology, Centre for Neuroscience and Cell Biology, 3004-517 Coimbra, Portugal.

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http://dx.doi.org/10.1016/j.molcel.2012.11.021DOI Listing
February 2013

4C technology: protocols and data analysis.

Authors:
Harmen J G van de Werken Paula J P de Vree Erik Splinter Sjoerd J B Holwerda Petra Klous Elzo de Wit Wouter de Laat

Methods Enzymol 2012 ;513:89-112

Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1016/B978-0-12-391938-0.00004-5DOI Listing
December 2012

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation.

Authors:
Erik Splinter Elzo de Wit Harmen J G van de Werken Petra Klous Wouter de Laat

Methods 2012 Nov 17;58(3):221-30. Epub 2012 May 17.

Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht 3584 CT, The Netherlands.

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http://dx.doi.org/10.1016/j.ymeth.2012.04.009DOI Listing
November 2012

3C-based technologies to study the shape of the genome.

Authors:
Wouter de Laat Job Dekker

Methods 2012 Nov;58(3):189-91

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http://dx.doi.org/10.1016/j.ymeth.2012.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874834PMC
November 2012

3D chromatin conformation correlates with replication timing and is conserved in resting cells.

Authors:
Benoit Moindrot Benjamin Audit Petra Klous Antoine Baker Claude Thermes Wouter de Laat Philippe Bouvet Fabien Mongelard Alain Arneodo

Nucleic Acids Res 2012 Oct 8;40(19):9470-81. Epub 2012 Aug 8.

Laboratoire Joliot-Curie, Ecole Normale Supérieure de Lyon, CNRS, F-69007 Lyon, France.

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http://dx.doi.org/10.1093/nar/gks736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479194PMC
October 2012

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

Authors:
Harmen J G van de Werken Gilad Landan Sjoerd J B Holwerda Michael Hoichman Petra Klous Ran Chachik Erik Splinter Christian Valdes-Quezada Yuva Oz Britta A M Bouwman Marjon J A M Verstegen Elzo de Wit Amos Tanay Wouter de Laat

Nat Methods 2012 Oct 9;9(10):969-72. Epub 2012 Sep 9.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nmeth.2173DOI Listing
October 2012

Chromatin loops, gene positioning, and gene expression.

Authors:
Sjoerd Holwerda Wouter de Laat

Front Genet 2012 17;3:217. Epub 2012 Oct 17.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht Utrecht, Netherlands.

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http://dx.doi.org/10.3389/fgene.2012.00217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473233PMC
October 2012

A decade of 3C technologies: insights into nuclear organization.

Authors:
Elzo de Wit Wouter de Laat

Genes Dev 2012 Jan;26(1):11-24

Hubrecht Institute-KNAW, University Medical Center Utrecht, CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1101/gad.179804.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258961PMC
January 2012

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation.

Authors:
Juan J Tena M Eva Alonso Elisa de la Calle-Mustienes Erik Splinter Wouter de Laat Miguel Manzanares José Luis Gómez-Skarmeta

Nat Commun 2011 ;2:310

Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013 Sevilla, Spain.

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http://dx.doi.org/10.1038/ncomms1301DOI Listing
November 2011

A regulatory archipelago controls Hox genes transcription in digits.

Authors:
Thomas Montavon Natalia Soshnikova Bénédicte Mascrez Elisabeth Joye Laurie Thevenet Erik Splinter Wouter de Laat François Spitz Denis Duboule

Cell 2011 Nov;147(5):1132-45

National Research Centre, Frontiers in Genetics, School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, Switzerland.

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http://dx.doi.org/10.1016/j.cell.2011.10.023DOI Listing
November 2011

The dynamic architecture of Hox gene clusters.

Authors:
Daan Noordermeer Marion Leleu Erik Splinter Jacques Rougemont Wouter De Laat Denis Duboule

Science 2011 Oct;334(6053):222-5

National Research Centre Frontiers in Genetics, School of Life Sciences, Ecole Polytechnique Fédérale (EPFL), Lausanne, Switzerland.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1207194
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http://dx.doi.org/10.1126/science.1207194DOI Listing
October 2011

The complex transcription regulatory landscape of our genome: control in three dimensions.

Authors:
Erik Splinter Wouter de Laat

EMBO J 2011 Sep 27;30(21):4345-55. Epub 2011 Sep 27.

Hubrecht Insitute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/emboj.2011.344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230377PMC
September 2011

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

Authors:
Erik Splinter Elzo de Wit Elphège P Nora Petra Klous Harmen J G van de Werken Yun Zhu Lucas J T Kaaij Wilfred van Ijcken Joost Gribnau Edith Heard Wouter de Laat

Genes Dev 2011 Jul 20;25(13):1371-83. Epub 2011 Jun 20.

Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands.

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http://dx.doi.org/10.1101/gad.633311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134081PMC
July 2011

Variegated gene expression caused by cell-specific long-range DNA interactions.

Authors:
Daan Noordermeer Elzo de Wit Petra Klous Harmen van de Werken Marieke Simonis Melissa Lopez-Jones Bert Eussen Annelies de Klein Robert H Singer Wouter de Laat

Nat Cell Biol 2011 Jun 26;13(8):944-51. Epub 2011 Jun 26.

Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/ncb2278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151580PMC
June 2011

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements.

Authors:
Ofir Hakim Myong-Hee Sung Ty C Voss Erik Splinter Sam John Peter J Sabo Robert E Thurman John A Stamatoyannopoulos Wouter de Laat Gordon L Hager

Genome Res 2011 May 6;21(5):697-706. Epub 2011 Apr 6.

Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.111153.110
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http://dx.doi.org/10.1101/gr.111153.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083086PMC
May 2011

Integrated transcript and genome analyses reveal NKX2-1 and MEF2C as potential oncogenes in T cell acute lymphoblastic leukemia.

Authors:
Irene Homminga Rob Pieters Anton W Langerak Johan J de Rooi Andrew Stubbs Monique Verstegen Maartje Vuerhard Jessica Buijs-Gladdines Clarissa Kooi Petra Klous Pieter van Vlierberghe Adolfo A Ferrando Jean Michel Cayuela Brenda Verhaaf H Berna Beverloo Martin Horstmann Valerie de Haas Anna-Sophia Wiekmeijer Karin Pike-Overzet Frank J T Staal Wouter de Laat Jean Soulier Francois Sigaux Jules P P Meijerink

Cancer Cell 2011 Apr;19(4):484-97

Department of Pediatric Oncology/Hematology, Erasmus MC/Sophia Children's Hospital, Rotterdam, The Netherlands.

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http://linkinghub.elsevier.com/retrieve/pii/S153561081100084
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http://dx.doi.org/10.1016/j.ccr.2011.02.008DOI Listing
April 2011

Interactions among Polycomb domains are guided by chromosome architecture.

Authors:
Bas Tolhuis Marleen Blom Ron M Kerkhoven Ludo Pagie Hans Teunissen Marja Nieuwland Marieke Simonis Wouter de Laat Maarten van Lohuizen Bas van Steensel

PLoS Genet 2011 Mar 24;7(3):e1001343. Epub 2011 Mar 24.

Division of Molecular Genetics and Centre for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1371/journal.pgen.1001343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3063757PMC
March 2011

Genome organization influences partner selection for chromosomal rearrangements.

Authors:
Patrick J Wijchers Wouter de Laat

Trends Genet 2011 Feb 7;27(2):63-71. Epub 2010 Dec 7.

Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1016/j.tig.2010.11.001DOI Listing
February 2011

High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology.

Authors:
Marieke Simonis Petra Klous Irene Homminga Robert-Jan Galjaard Erik-Jan Rijkers Frank Grosveld Jules P P Meijerink Wouter de Laat

Nat Methods 2009 Nov 11;6(11):837-42. Epub 2009 Oct 11.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nmeth.1391DOI Listing
November 2009

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C).

Authors:
Marieke Louwers Erik Splinter Roel van Driel Wouter de Laat Maike Stam

Nat Protoc 2009 30;4(8):1216-29. Epub 2009 Jul 30.

Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/nprot.2009.113DOI Listing
October 2009

Tissue- and expression level-specific chromatin looping at maize b1 epialleles.

Authors:
Marieke Louwers Rechien Bader Max Haring Roel van Driel Wouter de Laat Maike Stam

Plant Cell 2009 Mar 31;21(3):832-42. Epub 2009 Mar 31.

Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands.

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http://dx.doi.org/10.1105/tpc.108.064329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671708PMC
March 2009

Joining the loops: beta-globin gene regulation.

Authors:
Daan Noordermeer Wouter de Laat

IUBMB Life 2008 Dec;60(12):824-33

Department of Cell Biology and Genetics, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands.

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http://dx.doi.org/10.1002/iub.129DOI Listing
December 2008

Beta-globin regulation and long-range interactions.

Authors:
Robert-Jan Palstra Wouter de Laat Frank Grosveld

Adv Genet 2008 ;61:107-42

Department of Cell Biology and Genetics, Erasmus MC, 3000 CA Rotterdam, The Netherlands.

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http://dx.doi.org/10.1016/S0065-2660(07)00004-1DOI Listing
November 2008

FISH-eyed and genome-wide views on the spatial organisation of gene expression.

Authors:
Marieke Simonis Wouter de Laat

Biochim Biophys Acta 2008 Nov 5;1783(11):2052-60. Epub 2008 Aug 5.

Department of Cell Biology, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.bbamcr.2008.07.020DOI Listing
November 2008

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.

Authors:
Lars Guelen Ludo Pagie Emilie Brasset Wouter Meuleman Marius B Faza Wendy Talhout Bert H Eussen Annelies de Klein Lodewyk Wessels Wouter de Laat Bas van Steensel

Nature 2008 Jun 7;453(7197):948-51. Epub 2008 May 7.

Division of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/nature06947DOI Listing
June 2008

Three-dimensional organization of gene expression in erythroid cells.

Authors:
Wouter de Laat Petra Klous Jurgen Kooren Daan Noordermeer Robert-Jan Palstra Marieke Simonis Erik Splinter Frank Grosveld

Curr Top Dev Biol 2008 ;82:117-39

Department of Cell Biology and Genetics, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands.

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http://dx.doi.org/10.1016/S0070-2153(07)00005-1DOI Listing
April 2008

Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region.

Authors:
Daan Noordermeer Miguel R Branco Erik Splinter Petra Klous Wilfred van Ijcken Sigrid Swagemakers Manousos Koutsourakis Peter van der Spek Ana Pombo Wouter de Laat

PLoS Genet 2008 Mar 7;4(3):e1000016. Epub 2008 Mar 7.

Department of Cell Biology and Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1371/journal.pgen.1000016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265466PMC
March 2008

Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription.

Authors:
Robert-Jan Palstra Marieke Simonis Petra Klous Emilie Brasset Bart Eijkelkamp Wouter de Laat

PLoS One 2008 Feb 20;3(2):e1661. Epub 2008 Feb 20.

Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001661PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2243019PMC
February 2008

An evaluation of 3C-based methods to capture DNA interactions.

Authors:
Marieke Simonis Jurgen Kooren Wouter de Laat

Nat Methods 2007 Nov;4(11):895-901

Department of Cell Biology and Genetics, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam.

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http://dx.doi.org/10.1038/nmeth1114DOI Listing
November 2007

Inter-chromosomal gene regulation in the mammalian cell nucleus.

Authors:
Wouter de Laat Frank Grosveld

Curr Opin Genet Dev 2007 Oct 20;17(5):456-64. Epub 2007 Sep 20.

Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.gde.2007.07.009DOI Listing
October 2007

Quantitative analysis of chromosome conformation capture assays (3C-qPCR).

Authors:
Hélène Hagège Petra Klous Caroline Braem Erik Splinter Job Dekker Guy Cathala Wouter de Laat Thierry Forné

Nat Protoc 2007 ;2(7):1722-33

UMR5535 CNRS-UMII, IFR122, Institut de Génétique Moléculaire de Montpellier, IGMM, 1919, Route de Mende, 34293 Montpellier Cedex 5, France.

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http://dx.doi.org/10.1038/nprot.2007.243DOI Listing
September 2007

Beta-globin active chromatin Hub formation in differentiating erythroid cells and in p45 NF-E2 knock-out mice.

Authors:
Jurgen Kooren Robert-Jan Palstra Petra Klous Erik Splinter Marieke von Lindern Frank Grosveld Wouter de Laat

J Biol Chem 2007 Jun 11;282(22):16544-52. Epub 2007 Apr 11.

Department of Cell Biology, Erasmus Medical Center, P. O. Box 2040, 3000 CA Rotterdam, The Netherlands.

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http://dx.doi.org/10.1074/jbc.M701159200DOI Listing
June 2007

Long-range DNA contacts: romance in the nucleus?

Authors:
Wouter de Laat

Curr Opin Cell Biol 2007 Jun 27;19(3):317-20. Epub 2007 Apr 27.

Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.ceb.2007.04.004DOI Listing
June 2007

Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes.

Authors:
Jane A Skok Ramiro Gisler Maria Novatchkova Deborah Farmer Wouter de Laat Meinrad Busslinger

Nat Immunol 2007 Apr 4;8(4):378-87. Epub 2007 Mar 4.

Department of Immunology and Molecular Pathology, Division of Infection and Immunity, University College London, London W1T 4JF, UK.

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http://dx.doi.org/10.1038/ni1448DOI Listing
April 2007

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

Authors:
Marieke Simonis Petra Klous Erik Splinter Yuri Moshkin Rob Willemsen Elzo de Wit Bas van Steensel Wouter de Laat

Nat Genet 2006 Nov 8;38(11):1348-54. Epub 2006 Oct 8.

Department of Cell Biology and Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands.

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http://dx.doi.org/10.1038/ng1896DOI Listing
November 2006

CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus.

Authors:
Erik Splinter Helen Heath Jurgen Kooren Robert-Jan Palstra Petra Klous Frank Grosveld Niels Galjart Wouter de Laat

Genes Dev 2006 Sep;20(17):2349-54

Department of Cell Biology and Genetics, Erasmus Medical Center, 3000 DR Rotterdam, The Netherlands.

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http://dx.doi.org/10.1101/gad.399506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560409PMC
September 2006

The active spatial organization of the beta-globin locus requires the transcription factor EKLF.

Authors:
Roy Drissen Robert-Jan Palstra Nynke Gillemans Erik Splinter Frank Grosveld Sjaak Philipsen Wouter de Laat

Genes Dev 2004 Oct;18(20):2485-90

Erasmus University Medical Center, Department of Cell Biology, The Netherlands.

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http://dx.doi.org/10.1101/gad.317004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC529536PMC
October 2004

Multiple interactions between regulatory regions are required to stabilize an active chromatin hub.

Authors:
George P Patrinos Mariken de Krom Ernie de Boer An Langeveld A M Ali Imam John Strouboulis Wouter de Laat Frank G Grosveld

Genes Dev 2004 Jun;18(12):1495-509

Erasmus University Medical Center, Faculty of Medicine and Health Sciences, MGC Department of Cell Biology and Genetics, Rotterdam, 3000 DR, The Netherlands.

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http://dx.doi.org/10.1101/gad.289704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC423198PMC
June 2004

Spatial organization of gene expression: the active chromatin hub.

Authors:
Wouter de Laat Frank Grosveld

Chromosome Res 2003 ;11(5):447-59

Department of Cell Biology and Genetics, Faculty of Medicine, Erasmus University, Rotterdam, PO Box 1738, 3000DR Rotterdam, The Netherlands.

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April 2004

3C technology: analyzing the spatial organization of genomic loci in vivo.

Authors:
Erik Splinter Frank Grosveld Wouter de Laat

Methods Enzymol 2004 ;375:493-507

Department of Cell Biology, ErasmusMC, 3015 GE Rotterdam, The Netherlands.

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http://dx.doi.org/10.1016/s0076-6879(03)75030-7DOI Listing
March 2004

The beta-globin nuclear compartment in development and erythroid differentiation.

Authors:
Robert-Jan Palstra Bas Tolhuis Erik Splinter Rian Nijmeijer Frank Grosveld Wouter de Laat

Nat Genet 2003 Oct 21;35(2):190-4. Epub 2003 Sep 21.

Department of Cell Biology and Genetics, ErasmusMC, PO Box 1738, 3000 DR Rotterdam, The Netherlands.

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http://dx.doi.org/10.1038/ng1244DOI Listing
October 2003

Looping and interaction between hypersensitive sites in the active beta-globin locus.

Authors:
Bas Tolhuis Robert Jan Palstra Erik Splinter Frank Grosveld Wouter de Laat

Mol Cell 2002 Dec;10(6):1453-65

Department of Cell Biology and Genetics, Faculty of Medicine, Erasmus University, Rotterdam, P.O. Box 1738, 3000DR, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1016/s1097-2765(02)00781-5DOI Listing
December 2002