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Items: 24

1.

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

Krijger PHL, Geeven G, Bianchi V, Hilvering CRE, de Laat W.

Methods. 2019 Jul 26. pii: S1046-2023(18)30474-2. doi: 10.1016/j.ymeth.2019.07.014. [Epub ahead of print]

2.

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

Monroe TO, Hill MC, Morikawa Y, Leach JP, Heallen T, Cao S, Krijger PHL, de Laat W, Wehrens XHT, Rodney GG, Martin JF.

Dev Cell. 2019 Mar 25;48(6):765-779.e7. doi: 10.1016/j.devcel.2019.01.017. Epub 2019 Feb 14.

PMID:
30773489
3.

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

Allahyar A, Vermeulen C, Bouwman BAM, Krijger PHL, Verstegen MJAM, Geeven G, van Kranenburg M, Pieterse M, Straver R, Haarhuis JHI, Jalink K, Teunissen H, Renkens IJ, Kloosterman WP, Rowland BD, de Wit E, de Ridder J, de Laat W.

Nat Genet. 2018 Aug;50(8):1151-1160. doi: 10.1038/s41588-018-0161-5. Epub 2018 Jul 9.

PMID:
29988121
4.

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.

Haarhuis JHI, van der Weide RH, Blomen VA, Yáñez-Cuna JO, Amendola M, van Ruiten MS, Krijger PHL, Teunissen H, Medema RH, van Steensel B, Brummelkamp TR, de Wit E, Rowland BD.

Cell. 2017 May 4;169(4):693-707.e14. doi: 10.1016/j.cell.2017.04.013.

5.

Can We Just Say: Transcription Second?

Krijger PHL, de Laat W.

Cell. 2017 Apr 6;169(2):184-185. doi: 10.1016/j.cell.2017.03.026.

6.

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

Krijger PH, de Laat W.

Nat Rev Mol Cell Biol. 2016 Dec;17(12):771-782. doi: 10.1038/nrm.2016.138. Epub 2016 Nov 9. Review.

PMID:
27826147
7.

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

Wang X, Tucker NR, Rizki G, Mills R, Krijger PH, de Wit E, Subramanian V, Bartell E, Nguyen XX, Ye J, Leyton-Mange J, Dolmatova EV, van der Harst P, de Laat W, Ellinor PT, Newton-Cheh C, Milan DJ, Kellis M, Boyer LA.

Elife. 2016 May 10;5. pii: e10557. doi: 10.7554/eLife.10557.

8.

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 May 5;18(5):597-610. doi: 10.1016/j.stem.2016.01.007. Epub 2016 Mar 10.

9.

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

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

Mol Cell. 2016 Feb 4;61(3):461-473. doi: 10.1016/j.molcel.2016.01.001. Epub 2016 Jan 28.

10.

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.

11.

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
12.

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

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.

Nature. 2013 Sep 12;501(7466):227-31. doi: 10.1038/nature12420. Epub 2013 Jul 24.

PMID:
23883933
13.

Rev1 is essential in generating G to C transversions downstream of the Ung2 pathway but not the Msh2+Ung2 hybrid pathway.

Krijger PH, Tsaalbi-Shtylik A, Wit N, van den Berk PC, de Wind N, Jacobs H.

Eur J Immunol. 2013 Oct;43(10):2765-70. doi: 10.1002/eji.201243191. Epub 2013 Aug 5.

14.

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

Krijger PH, de Laat W.

Curr Opin Genet Dev. 2013 Apr;23(2):191-6. doi: 10.1016/j.gde.2012.12.010. Epub 2013 Feb 14. Review.

PMID:
23415810
15.

PCNA ubiquitination is important, but not essential for translesion DNA synthesis in mammalian cells.

Hendel A, Krijger PH, Diamant N, Goren Z, Langerak P, Kim J, Reissner T, Lee KY, Geacintov NE, Carell T, Myung K, Tateishi S, D'Andrea A, Jacobs H, Livneh Z.

PLoS Genet. 2011 Sep;7(9):e1002262. doi: 10.1371/journal.pgen.1002262. Epub 2011 Sep 8.

16.

PCNA ubiquitination-independent activation of polymerase η during somatic hypermutation and DNA damage tolerance.

Krijger PH, van den Berk PC, Wit N, Langerak P, Jansen JG, Reynaud CA, de Wind N, Jacobs H.

DNA Repair (Amst). 2011 Oct 10;10(10):1051-9. doi: 10.1016/j.dnarep.2011.08.005. Epub 2011 Sep 1.

PMID:
21889916
17.

Lysine residue 185 of Rad1 is a topological but not a functional counterpart of lysine residue 164 of PCNA.

Wit N, Krijger PH, van den Berk PC, Jacobs H.

PLoS One. 2011 Jan 31;6(1):e16669. doi: 10.1371/journal.pone.0016669.

18.

HLTF and SHPRH are not essential for PCNA polyubiquitination, survival and somatic hypermutation: existence of an alternative E3 ligase.

Krijger PH, Lee KY, Wit N, van den Berk PC, Wu X, Roest HP, Maas A, Ding H, Hoeijmakers JH, Myung K, Jacobs H.

DNA Repair (Amst). 2011 Apr 3;10(4):438-44. doi: 10.1016/j.dnarep.2010.12.008. Epub 2011 Jan 26.

19.

The Fanconi anemia core complex is dispensable during somatic hypermutation and class switch recombination.

Krijger PH, Wit N, van den Berk PC, Jacobs H.

PLoS One. 2010 Dec 29;5(12):e15236. doi: 10.1371/journal.pone.0015236.

20.

Dependence of nucleotide substitutions on Ung2, Msh2, and PCNA-Ub during somatic hypermutation.

Krijger PH, Langerak P, van den Berk PC, Jacobs H.

J Exp Med. 2009 Nov 23;206(12):2603-11. doi: 10.1084/jem.20091707. Epub 2009 Nov 9.

21.

Mice deficient for CD137 ligand are predisposed to develop germinal center-derived B-cell lymphoma.

Middendorp S, Xiao Y, Song JY, Peperzak V, Krijger PH, Jacobs H, Borst J.

Blood. 2009 Sep 10;114(11):2280-9. doi: 10.1182/blood-2009-03-208215. Epub 2009 Jul 16.

PMID:
19608748
22.

Analysis of somatic hypermutation in X-linked hyper-IgM syndrome shows specific deficiencies in mutational targeting.

Longo NS, Lugar PL, Yavuz S, Zhang W, Krijger PH, Russ DE, Jima DD, Dave SS, Grammer AC, Lipsky PE.

Blood. 2009 Apr 16;113(16):3706-15. doi: 10.1182/blood-2008-10-183632. Epub 2008 Nov 20.

23.

Somatic hypermutation of immunoglobulin genes: lessons from proliferating cell nuclear antigenK164R mutant mice.

Langerak P, Krijger PH, Heideman MR, van den Berk PC, Jacobs H.

Philos Trans R Soc Lond B Biol Sci. 2009 Mar 12;364(1517):621-9. doi: 10.1098/rstb.2008.0223.

24.

A/T mutagenesis in hypermutated immunoglobulin genes strongly depends on PCNAK164 modification.

Langerak P, Nygren AO, Krijger PH, van den Berk PC, Jacobs H.

J Exp Med. 2007 Aug 6;204(8):1989-98. Epub 2007 Jul 30.

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