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Items: 1 to 20 of 101

1.

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

Krijger PH, Di Stefano B, de Wit E, Limone F, van Oevelen C, de Laat W, Graf T.

Cell Stem Cell. 2016 Mar 8. pii: S1934-5909(16)00008-4. doi: 10.1016/j.stem.2016.01.007. [Epub ahead of print]

2.

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

Marks H, Kerstens HH, Barakat TS, Splinter E, Dirks RA, van Mierlo G, Joshi O, Wang SY, Babak T, Albers CA, Kalkan T, Smith A, Jouneau A, de Laat W, Gribnau J, Stunnenberg HG.

Genome Biol. 2016 Feb 5;17(1):22. doi: 10.1186/s13059-016-0885-4. No abstract available.

3.

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

Wijchers PJ, Krijger PH, Geeven G, Zhu Y, Denker A, Verstegen MJ, Valdes-Quezada C, Vermeulen C, Janssen M, Teunissen H, Anink-Groenen LC, Verschure PJ, de Laat W.

Mol Cell. 2016 Feb 4;61(3):461-73. doi: 10.1016/j.molcel.2016.01.001. Epub 2016 Jan 28.

4.

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

Vermunt MW, Tan SC, Castelijns B, Geeven G, Reinink P, de Bruijn E, Kondova I, Persengiev S; Netherlands Brain Bank, Bontrop R, Cuppen E, de Laat W, Creyghton MP.

Nat Neurosci. 2016 Mar;19(3):494-503. doi: 10.1038/nn.4229. Epub 2016 Jan 25.

PMID:
26807951
5.

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

Melo CA, Léveillé N, Rooijers K, Wijchers PJ, Geeven G, Tal A, Melo SA, de Laat W, Agami R.

Oncogene. 2016 Jan 18. doi: 10.1038/onc.2015.502. [Epub ahead of print]

PMID:
26776159
6.

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

Geeven G, Zhu Y, Kim BJ, Bartholdy BA, Yang SM, Macfarlan TS, Gifford WD, Pfaff SL, Verstegen MJ, Pinto H, Vermunt MW, Creyghton MP, Wijchers PJ, Stamatoyannopoulos JA, Skoultchi AI, de Laat W.

Genome Biol. 2015 Dec 23;16:289. doi: 10.1186/s13059-015-0857-0.

7.

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

Austenaa LM, Barozzi I, Simonatto M, Masella S, Della Chiara G, Ghisletti S, Curina A, de Wit E, Bouwman BA, de Pretis S, Piccolo V, Termanini A, Prosperini E, Pelizzola M, de Laat W, Natoli G.

Mol Cell. 2015 Nov 5;60(3):460-74. doi: 10.1016/j.molcel.2015.09.018. Epub 2015 Oct 22.

PMID:
26593720
8.

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

Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL.

BMC Genomics. 2015 Nov 21;16:982. doi: 10.1186/s12864-015-2137-5.

9.

CTCF Binding Polarity Determines Chromatin Looping.

de Wit E, Vos ES, Holwerda SJ, Valdes-Quezada C, Verstegen MJ, Teunissen H, Splinter E, Wijchers PJ, Krijger PH, de Laat W.

Mol Cell. 2015 Nov 19;60(4):676-84. doi: 10.1016/j.molcel.2015.09.023. Epub 2015 Oct 29.

PMID:
26527277
10.

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

Galli GG, Carrara M, Yuan WC, Valdes-Quezada C, Gurung B, Pepe-Mooney B, Zhang T, Geeven G, Gray NS, de Laat W, Calogero RA, Camargo FD.

Mol Cell. 2015 Oct 15;60(2):328-37. doi: 10.1016/j.molcel.2015.09.001. Epub 2015 Oct 1.

PMID:
26439301
11.

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 KC, Georgiev P, Chung HR, Lajoie BR, de Wit E, Zhan Y, de Laat W, Dekker J, Manke T, Akhtar A.

Mol Cell. 2015 Oct 1;60(1):146-62. doi: 10.1016/j.molcel.2015.08.024.

12.

A Long-Distance Chromatin Affair.

Denker A, de Laat W.

Cell. 2015 Aug 27;162(5):942-3. doi: 10.1016/j.cell.2015.08.022.

PMID:
26317462
13.

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

Bouwman BA, de Laat W.

Genome Biol. 2015 Aug 10;16:154. doi: 10.1186/s13059-015-0730-1.

14.

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

Marks H, Kerstens HH, Barakat TS, Splinter E, Dirks RA, van Mierlo G, Joshi O, Wang SY, Babak T, Albers CA, Kalkan T, Smith A, Jouneau A, de Laat W, Gribnau J, Stunnenberg HG.

Genome Biol. 2015 Aug 3;16:149. doi: 10.1186/s13059-015-0698-x.

15.

Architectural hallmarks of the pluripotent genome.

Bouwman BA, de Laat W.

FEBS Lett. 2015 Oct 7;589(20 Pt A):2905-13. doi: 10.1016/j.febslet.2015.04.055. Epub 2015 May 7. Review.

16.

Characterization and dynamics of pericentromere-associated domains in mice.

Wijchers PJ, Geeven G, Eyres M, Bergsma AJ, Janssen M, Verstegen M, Zhu Y, Schell Y, Vermeulen C, de Wit E, de Laat W.

Genome Res. 2015 Jul;25(7):958-69. doi: 10.1101/gr.186643.114. Epub 2015 Apr 16.

17.

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

Léveillé N, Melo CA, Rooijers K, Díaz-Lagares A, Melo SA, Korkmaz G, Lopes R, Akbari Moqadam F, Maia AR, Wijchers PJ, Geeven G, den Boer ML, Kalluri R, de Laat W, Esteller M, Agami R.

Nat Commun. 2015 Mar 27;6:6520. doi: 10.1038/ncomms7520.

18.

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

Vermunt MW, Reinink P, Korving J, de Bruijn E, Creyghton PM, Basak O, Geeven G, Toonen PW, Lansu N, Meunier C, van Heesch S; Netherlands Brain Bank, Clevers H, de Laat W, Cuppen E, Creyghton MP.

Cell Rep. 2014 Oct 23;9(2):767-79. doi: 10.1016/j.celrep.2014.09.023. Epub 2014 Oct 16.

19.

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

de Vree PJ, de Wit E, Yilmaz M, van de Heijning M, Klous P, Verstegen MJ, Wan Y, Teunissen H, Krijger PH, Geeven G, Eijk PP, Sie D, Ylstra B, Hulsman LO, van Dooren MF, van Zutven LJ, 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 MJ, ter Brugge P, Jonkers J, Foekens JA, Martens JW, van der Luijt R, van Amstel HK, van Min M, Splinter E, de Laat W.

Nat Biotechnol. 2014 Oct;32(10):1019-25. doi: 10.1038/nbt.2959. Epub 2014 Aug 17.

PMID:
25129690
20.

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

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.

Circ Res. 2014 Aug 1;115(4):432-41. doi: 10.1161/CIRCRESAHA.115.303591. Epub 2014 Jun 24.

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