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Publications

de Laat group

2014

de Vree PJP, de Wit E, Yilmaz M, van de Heijning M, Klous P, Verstegen MJAM, Wan Y, Teunissen H, Krijger PHL, Geeven G, Eijk PP, Sie D, Ylstra B, Hulsman LOM, van Dooren MF, van Zutven LJCM, van den Ouweland A, Verbeek S, van Dijk KW, Cornelissen M, Das AT, Berkhout B, Sikkema-Raddatz B, van den Berg E, van der Vlies P, Weening D, den Dunnen JT, Matusiak M, Lamkanfi M, Ligtenberg MJL, ter Brugge P, Jonkers J, Foekens JA, Martens JW, van der Luijt R, Ploos van Amstel HK, van Min M, Splinter E, de Laat W (2014). Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nature Biotechnol. 32(10):1019-25.

van Weerd JH, Badi I, van den Boogaard M, Stefanovic S, van de Werken HJ, Gomez-Velazquez M, Badia-Careaga C, Manzanares M, de Laat W, Barnett P, Christoffels VM (2014). A large permissive regulatory domain exclusively controls tbx3 expression in the cardiac conduction system. Circ Res. 115(4):432-41.

Gröschel S, Sanders MA, Hoogenboezem R, de Wit E, Bouwman BA, Erpelinck C, van der Velden VH, Havermans M, Avellino R, van Lom K, Rombouts EJ, van Duin M, Döhner K, Beverloo HB, Bradner JE, Döhner H, Löwenberg B, Valk PJ, Bindels EM, de Laat W, Delwel R (2014). A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia. Cell 157(2):369-81.

van den Boogaard M, Smemo S, Burnicka-Turek O, Arnolds DE, van de Werken HJ, Klous P, McKean D, Muehlschlegel JD, Moosmann J, Toka O, Yang XH, Koopmann TT, Adriaens ME, Bezzina CR, de Laat W, Seidman C, Seidman JG, Christoffels VM, Nobrega MA, Barnett P, Moskowitz IP (2014). A common genetic variant within SCN10A modulates cardiac SCN5A expression. J Clin Invest. 124(4):1844-52.

2013



Wijchers P, de Laat W. (2013). For Genomes to Stay in Shape, Insulators Must Be up to PAR. Cell, 155(1):15-6.

Denholtz M, Bonora G, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, Plath K. Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization. Cell Stem Cell. 2013 Sep 11.         

de Wit E, Bouwman BA, Zhu Y, Klous P, Splinter E, Verstegen MJ, Krijger PH, Festuccia N, Nora EP, Welling M, Heard E, Geijsen N, Poot RA, Chambers I, de Laat W.The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature. 2013 Jul 24

Medvedovic J, Ebert A, Tagoh H, Tamir IM, Schwickert TA, Novatchkova M, Sun Q, Huis In 't Veld PJ, Guo C, Yoon HS, Denizot Y, Holwerda SJ, de Laat W, Cogné M, Shi Y, Alt FW, Busslinger M. Flexible Long-Range Loops in the VH Gene Region of the Igh Locus Facilitate the Generation of a Diverse Antibody Repertoire. Immunity. 2013 Aug 22;39(2):229-44.

Holwerda SJ, van de Werken HJ, Ribeiro de Almeida C, Bergen IM, de Bruijn MJ, Verstegen MJ, Simonis M, Splinter E, Wijchers PJ, Hendriks RW, de Laat W. Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells. Nucleic Acids Res. 2013 Aug 1;41(14):6905-16.

Kaaij LT, van de Wetering M, Fang F, Decato B, Molaro A, van de Werken HJ, van Es JH, Schuijers J, de Wit E, de Laat W, Hannon GJ, Clevers HC, Smith AD, Ketting RF.DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus. Genome Biol. 2013 May 28;14(5):R50.

Holwerda SJ, de Laat W. CTCF: the protein, the binding partners, the binding sites and their chromatin loops. Philos Trans R Soc Lond B Biol Sci. 2013 May6; 368(1620

Krijger PH, de Laat W. Identical cells with different 3D genomes; cause and consequences? Curr Opin Genet Dev. 2013 Apr;23(2):191-6

Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Léveillé N, Kalluri R, de Laat W, Agami R. eRNAs are required for p53- dependent enhancer activity and gene transcription. Mol Cell. 2013 Feb 7;49(3):524-35.

2012
van de Werken H, Landan G, Holwerda S, Hoichman M, Klous P, Chachik R, Splinter E, Valdes Quezada C, Öz Y, Bouwman B, Verstegen M, de Wit E, Tanay A, de Laat W. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods, 9:969-72

Moindrot B, Audit B, Klous P, Baker A, Thermes C, de Laat W, Bouvet P, Mongelard F, Arneodo A. (2012). 3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res Aug 8.

de Laat W, Dekker J. 3C-based technologies to study the shape of the genome. Methods. 2012 Nov;58(3):189-91

van de Werken HJ, de Vree PJ, Splinter E, Holwerda SJ, Klous P, de Wit E, de Laat W.4C technology: protocols and data analysis. Methods Enzymol. 2012;513:89-112.

Splinter E, de Wit E, van de Werken HJ, Klous P, de Laat W. Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods. 2012 Nov;58(3):221-30.

de Wit E, de Laat W. (2012). A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26:11-24.

2011
Montavon T, Soshnikova N, Mascrez B, Joye E, Thévenet L, Splinter E, de Laat W, Spitz F, Duboule D. (2011).  A regulatory archipelo controls the transcription of Hox genes in digits. Cell 147:1132-45.

Splinter E, de Laat W. (2011). The complex transcription regulatory landscape of our genome: control in three dimensions. EMBO J 30:4345-55.

Noordermeer D, Leleu M, Splinter E, Rougemont J, de Laat W, Duboule D. (2011) The dynamic architecture of Hox gene clusters. Science 334:222-5.

Noordermeer D, de Wit E, Klous P, van de Werken H, Simonis M, Lopez-Jones M, Eussen B, de Klein A, Singer RH, de Laat W. (2011). Variegated gene expression caused by cell-specific long-range DNA interactions. Nat Cell Biol 13:944-51.

Splinter E, de Wit E, Nora EP, Klous P, van de Werken HJG, Zhu Y, Kaaij LJT, van Ijcken W, Gribnau J, Heard E, de Laat W. (2011). The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev 25: 1371-83.

Wijchers PJ, de Laat W. (2011). Genome organization influences partner selection for chromosomal rearrangements. Trends Genet. 27(2):63-71.

Homminga I, Pieters R, Langerak AW, de Rooi JJ, Stubbs A, Verstegen M, Vuerhard M, Buijs-Gladdines J, Kooi C, Klous P, van Vlierberghe P, Ferrando AA, Cayuela JM, Verhaaf B, Beverloo HB, Horstmann M, de Haas V, Wiekmeijer AS, Pike-Overzet K, Staal FJ, de Laat W, Soulier J, Sigaux F, Meijerink JP. (2011). Integrated Transcript and Genome Analyses Reveal NKX2-1 and MEF2C as Potential Oncogenes in T Cell Acute Lymphoblastic Leukemia. Cancer Cell 19(4):484-97.

Tena JJ, Alonso ME, de la Calle-Mustienes E, Splinter E, de Laat W, Manzanares M, Gómez-Skarmeta JL. An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation (2011). Nat Commun. 2: 310.

Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL (2011). Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 21(5):697-706.

Tolhuis B, Blom M, Kerkhoven RM, Pagie L, Teunissen H, Nieuwland M, Simonis M, de Laat W, van Lohuizen M, van Steensel B. (2011). Interactions among Polycomb domains are guided by chromosome architecture. PLoS Genet. 7(3):e1001343.

2009
Simonis, M., Klous, P., Homminga, I., Galjaard, RJ., Grosveld, F., Meijerink, JP., de Laat, W. (2009). High-resolution identification of balanced and chromosomal rearrangements by 4C technology. Nat. Methods 6: 837-42.

Louwers, M., Splinter, E., van Driel, R., de Laat, W., Stam, M. (2009) Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C). Nat. Protoc. 4:1216-19.

2008
Louwers, M., Bader, R., Haring, M., van Driel, R., de Laat, W., Stam, M. Tissue- and expression level-specific chromatin looping at maize b1 epialleles (2008). Plant Cell. 21: 832-42.

Simonis, M., de Laat, W. (2008) FISH-eyed and genome-wide views on the spatial organisation of gene expression. Biochim Biophys Acta. 1783:2052-60.
 
Noordermeer D, de Laat W. (2008) Joining the loops: beta-Globin gene regulation. IUBMB Life. 60:824-33.
 
Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M.B., Talhout, W., Eussen, BH, de Klein, A., Wessels, L., de Laat, W., van Steensel, B. (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453:948-51.
 
Noordermeer, D., Branco, M.R., Splinter, E., Klous P., van IJcken W., Swagemakers, S., Koutsourakis, M., van der Spek P., Pombo A., and de Laat, W (2008). Transcription and chromatin organization of a housekeeping gene cluster containing an integrated b-globin Locus Control Region. PLOS Genetics 4:e1000016.
 
Palstra, R.J., Simonis, M., Klous, P., Brasset, E., Eijkelkamp, B. and de Laat, W. (2008). Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription. PLOS One3(2):e1661
 
de Laat, W., Klous, P., Kooren, J., Noordermeer,. D, Palstra, R-J., Simonis, M., Splinter, E.,  Grosveld, F. (2008) Three-dimensional organisation of gene expression in erythroid cells. Chapter 5, Curr Top Dev Biol.82:117-39.
 
Palstra, R-J., de Laat, W., Grosveld F. (2008) Beta Globin Regulation and Long Range Interactions. Chapter 4, Adv Genet. 61:107-42.
 
2007
Simonis M, Kooren J, de Laat W. (2007). An evaluation of 3C-based methods to capture DNA interactions. Nature Methods 4:895-901.
 
De Laat, W., Grosveld F. (2007). Interchromosomal gene regulation in the mammalian cell nucleus. Current Opinion in Genetics and Development, 17(5):456-64.
 
Kooren, J., Palstra, RJ., Klous, P., Splinter, E., von Lindern, M., Grosveld, F., de Laat, W. (2007). Beta-globin active chromatin Hub formation in differentiating erythroid cells and in p45 NF-E2 knock-out mice. Journal of Biological Chemistry. 282:16544-52.
 
De Laat, W. (2007). Long-range DNA contacts: romance in the nucleus? Current Opinion in Cell Biology, 19:317-320.                                                                                                             
Hagège, H., Klous, P., Braem C., Splinter, E., Dekker, J., Cathala, G., de Laat, W., Forné, T. (2007) Quantitative analysis of Chromosome Conformation Capture assays (qPCR-3C). Nature Protocols, 2:1722-1733.
 
Skok, JA., Gisler, R., Novatchkova, M., Farmer, D., de Laat W., Busslinger M. (2007). Reversible contraction by looping of the Tcrb and Tcra loci in rearranging thymocytes. Nature Immunology, 8:378-387.
 
2006
Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., de Laat, W. (2006). Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genetics 38:1348-1354.
 
Splinter, E., Heath, H., Kooren, J., Palstra, R.J., Klous, P., Grosveld, F., Galjart, N., de Laat, W. (2006). CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes & Development 20: 2349-2354.
 
2004
Drissen, R., Palstra, R.J., Gillemans, N., Splinter, E., Grosveld, F., Philipsen, S., de Laat, W. (2004). The active spatial organisation of the b-globin locus requires the transcription factor EKLF. Genes & Development 18: 2485-2490.
 
Patrinos, G.P., de Krom, M., de Boer, E., Langeveld, A., Imam, A.M.A, Strouboulis, J., de Laat, W., and Grosveld, F.G. (2004). Multiple interactions between regulatory regions are required to stabilize an active chromatin hub. Genes & Development. 18: 1495-1509.
 
Splinter E., Grosveld F., de Laat W. (2004). 3C technology: analyzing the spatial organisation of genomic loci in vivo. Methods in Enzymology 375: 493-507.
 
2003
Palstra R-J., Tolhuis B., Splinter E., Nijmeijer R., Grosveld F., de Laat W. (2003). The beta-globin nuclear compartment in development and erythroid differentiation. Nature Genetics 35, 190-194.
 
de Laat W., Grosveld F. (2003). Spatial organization of gene expression: the Active Chromatin Hub. Chromosome Research. 5: 447-459.
 
2002
Tolhuis B., Palstra R-J, Splinter E., Grosveld F., de Laat W. (2002). Looping and interaction between hypersensitive sites in the active beta-globin locus. Molecular Cell 10: 1453-1465.
 

Winkler, G.S., Sugasawa, K., Eker, A.P., de Laat, W.L., Hoeijmakers, J.H. (2001). Novel functional interactions between nucleotide excision DNA repair proteins influencing the enzymatic activities of TFIIH, XPG, and ERCC1-XPF. Biochemistry 40: 160-165.
 
de Laat, W.L., Jaspers, N.G.J., and Hoeijmakers, J.H.J. (1999). Molecular mechanism of nucleotide excision repair. Genes & Development 13: 768-785.
 
de Laat, W.L., Appeldoorn, E., Sugasawa, K., Jaspers, N.G.J., and Hoeijmakers, J.H.J. (1998). DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes & Development 12: 2598-2609.
 
de Laat, W.L., Sijbers, A.M., Odijk, H., Japers, N.G.J., and Hoeijmakers, J.H.J. (1998). Mapping of interaction domains between human repair proteins ERCC1 and XPF. Nucl. Acids Res. 26: 4146-4152.
 
de Laat, W.L., Appeldoorn, E., Jaspers, and N.G.J., Hoeijmakers, J.H.J. (1998). DNA structural elements required for ERCC1-XPF endonuclease activity. J. Biol. Chem. 273: 7835-7842.
 
van Leeuwen, H.C., Strating, M., Rensen, M., de Laat, W.L., and van der Vliet, P.C. (1997). Linker length and composition influence the flexibility of Oct-1 DNA binding. EMBO J. 16(8): 2043-2053.
 
Sijbers, A.M.#, de Laat W.L.#, Ariza, R.R.#, Biggerstaff, M.#, Wei, Y.-F., Moggs, J.G., Carter, K.C., Shell,B.K., Evans, E., de Jong, M.C., Rademakers, S., de Rooij J., Jaspers, N.G.J., Hoeijmakers, J.H.J., and Wood, R.D. (1996). (#equal contr.). Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease. Cell 86: 811-82.
 
Cox, M., van Tilborg, P.J., de Laat W.L., Boelens, R., van Leeuwen, H.C., van der Vliet, P.C., and Kaptein, R. (1995). Solution structure of the Oct-1 POU homeodomain determined by NMR and restrained molecular dynamics. J. Biomol. NMR. 6: 23-32.
 
Medema R.H., de Laat, W.L., Martin, G.A., McCormick, F., and Bos, J.L. (1992). GTPase-activating protein SH2-SH3 domains induce gene expression in a Ras-dependent fashion. Mol. Cell. Biol. 12: 3425-3430.

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