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Items: 1 to 50 of 62

1.

The interplay of chromatin and transcription factors during cell fate transitions in development and reprogramming.

Peñalosa-Ruiz G, Bright AR, Mulder KW, Veenstra GJC.

Biochim Biophys Acta Gene Regul Mech. 2019 Sep;1862(9):194407. doi: 10.1016/j.bbagrm.2019.194407. Epub 2019 Jul 26. Review.

2.

The Complexity of PRC2 Subcomplexes.

van Mierlo G, Veenstra GJC, Vermeulen M, Marks H.

Trends Cell Biol. 2019 Aug;29(8):660-671. doi: 10.1016/j.tcb.2019.05.004. Epub 2019 Jun 6. Review.

3.

WDR5, BRCA1, and BARD1 Co-regulate the DNA Damage Response and Modulate the Mesenchymal-to-Epithelial Transition during Early Reprogramming.

Peñalosa-Ruiz G, Bousgouni V, Gerlach JP, Waarlo S, van de Ven JV, Veenstra TE, Silva JCR, van Heeringen SJ, Bakal C, Mulder KW, Veenstra GJC.

Stem Cell Reports. 2019 Apr 9;12(4):743-756. doi: 10.1016/j.stemcr.2019.02.006. Epub 2019 Mar 14.

4.

Mass Spectrometry-Based Absolute Quantification of Single Xenopus Embryo Proteomes.

Lindeboom RGH, Smits AH, Perino M, Veenstra GJC, Vermeulen M.

Cold Spring Harb Protoc. 2019 Jun 3;2019(6):pdb.prot098376. doi: 10.1101/pdb.prot098376.

PMID:
30104410
5.

ChIP-Sequencing in Xenopus Embryos.

Hontelez S, van Kruijsbergen I, Veenstra GJC.

Cold Spring Harb Protoc. 2019 Jan 2;2019(1):pdb.prot097907. doi: 10.1101/pdb.prot097907.

PMID:
30042137
6.

Assay for Transposase-Accessible Chromatin-Sequencing Using Xenopus Embryos.

Bright AR, Veenstra GJC.

Cold Spring Harb Protoc. 2019 Jan 2;2019(1):pdb.prot098327. doi: 10.1101/pdb.prot098327.

PMID:
30042136
7.

MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding.

Perino M, van Mierlo G, Karemaker ID, van Genesen S, Vermeulen M, Marks H, van Heeringen SJ, Veenstra GJC.

Nat Genet. 2018 Jul;50(7):1002-1010. doi: 10.1038/s41588-018-0134-8. Epub 2018 May 28.

PMID:
29808031
8.

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus.

Gibeaux R, Acker R, Kitaoka M, Georgiou G, van Kruijsbergen I, Ford B, Marcotte EM, Nomura DK, Kwon T, Veenstra GJC, Heald R.

Nature. 2018 Jan 18;553(7688):337-341. doi: 10.1038/nature25188. Epub 2018 Jan 10.

9.

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.

Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA, van Heeringen SJ, Veenstra GJC.

Genome Biol. 2017 Oct 24;18(1):198. doi: 10.1186/s13059-017-1335-7.

10.

Loss of transcriptional activation of the potassium channel Kir5.1 by HNF1β drives autosomal dominant tubulointerstitial kidney disease.

Kompatscher A, de Baaij JHF, Aboudehen K, Hoefnagels APWM, Igarashi P, Bindels RJM, Veenstra GJC, Hoenderop JGJ.

Kidney Int. 2017 Nov;92(5):1145-1156. doi: 10.1016/j.kint.2017.03.034. Epub 2017 May 31.

11.

Genome evolution in the allotetraploid frog Xenopus laevis.

Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS.

Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.

12.

Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis.

Suzuki A, Yoshida H, van Heeringen SJ, Takebayashi-Suzuki K, Veenstra GJC, Taira M.

Dev Biol. 2017 Jun 15;426(2):336-359. doi: 10.1016/j.ydbio.2016.09.016. Epub 2016 Sep 28.

13.

Chromatin Control of Developmental Dynamics and Plasticity.

Perino M, Veenstra GJ.

Dev Cell. 2016 Sep 26;38(6):610-20. doi: 10.1016/j.devcel.2016.08.004. Review.

14.

Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos.

van Kruijsbergen I, Hontelez S, Elurbe DM, van Heeringen SJ, Huynen MA, Veenstra GJC.

Dev Biol. 2017 Jun 15;426(2):460-471. doi: 10.1016/j.ydbio.2016.08.031. Epub 2016 Sep 14.

15.

Erratum: Embryonic transcription is controlled by maternally defined chromatin state.

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ.

Nat Commun. 2016 Jul 5;7:12208. doi: 10.1038/ncomms12208. No abstract available.

16.

The positive transcriptional elongation factor (P-TEFb) is required for neural crest specification.

Hatch VL, Marin-Barba M, Moxon S, Ford CT, Ward NJ, Tomlinson ML, Desanlis I, Hendry AE, Hontelez S, van Kruijsbergen I, Veenstra GJ, Münsterberg AE, Wheeler GN.

Dev Biol. 2016 Aug 15;416(2):361-72. doi: 10.1016/j.ydbio.2016.06.012. Epub 2016 Jun 23.

17.

Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β-catenin recruitment to cis-regulatory modules.

Nakamura Y, de Paiva Alves E, Veenstra GJ, Hoppler S.

Development. 2016 Jun 1;143(11):1914-25. doi: 10.1242/dev.131664. Epub 2016 Apr 11.

18.

Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors.

Gazdag E, Jacobi UG, van Kruijsbergen I, Weeks DL, Veenstra GJ.

Development. 2016 Apr 15;143(8):1340-50. doi: 10.1242/dev.127936. Epub 2016 Mar 7.

19.

Active DNA demethylation at enhancers during the vertebrate phylotypic period.

Bogdanović O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra GJ, Manzanares M, Sauka-Spengler T, Ecker JR, Vermeulen M, Gómez-Skarmeta JL, Lister R.

Nat Genet. 2016 Apr;48(4):417-26. doi: 10.1038/ng.3522. Epub 2016 Feb 29.

20.

Embryonic transcription is controlled by maternally defined chromatin state.

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJC.

Nat Commun. 2015 Dec 18;6:10148. doi: 10.1038/ncomms10148. Erratum in: Nat Commun. 2016 Jul 05;7:12208.

21.

Recruiting polycomb to chromatin.

van Kruijsbergen I, Hontelez S, Veenstra GJ.

Int J Biochem Cell Biol. 2015 Oct;67:177-87. doi: 10.1016/j.biocel.2015.05.006. Epub 2015 May 14. Review.

22.

Establishing pluripotency in early development.

Paranjpe SS, Veenstra GJ.

Biochim Biophys Acta. 2015 Jun;1849(6):626-36. doi: 10.1016/j.bbagrm.2015.03.006. Epub 2015 Apr 7. Review.

23.

Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.

Smits AH, Lindeboom RG, Perino M, van Heeringen SJ, Veenstra GJ, Vermeulen M.

Nucleic Acids Res. 2014 Sep;42(15):9880-91. doi: 10.1093/nar/gku661. Epub 2014 Jul 23.

24.

Principles of nucleation of H3K27 methylation during embryonic development.

van Heeringen SJ, Akkers RC, van Kruijsbergen I, Arif MA, Hanssen LL, Sharifi N, Veenstra GJ.

Genome Res. 2014 Mar;24(3):401-10. doi: 10.1101/gr.159608.113. Epub 2013 Dec 11.

25.

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development.

Paranjpe SS, Jacobi UG, van Heeringen SJ, Veenstra GJ.

BMC Genomics. 2013 Nov 6;14:762. doi: 10.1186/1471-2164-14-762.

26.

The Wnt signaling mediator tcf1 is required for expression of foxd3 during Xenopus gastrulation.

Janssens S, Van Den Broek O, Davenport IR, Akkers RC, Liu F, Veenstra GJ, Hoppler S, Vleminckx K, Destrée O.

Int J Dev Biol. 2013;57(1):49-54. doi: 10.1387/ijdb.120191kv.

27.

Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development.

Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG.

Cell. 2012 Dec 7;151(6):1200-13. doi: 10.1016/j.cell.2012.11.014.

28.

Chromatin immunoprecipitation analysis of Xenopus embryos.

Akkers RC, Jacobi UG, Veenstra GJ.

Methods Mol Biol. 2012;917:279-92. doi: 10.1007/978-1-61779-992-1_17.

PMID:
22956095
29.

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

Bogdanovic O, Fernandez-Miñán A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I, van Heeringen SJ, Veenstra GJ, Gómez-Skarmeta JL.

Genome Res. 2012 Oct;22(10):2043-53. doi: 10.1101/gr.134833.111. Epub 2012 May 16.

30.

The epigenome in early vertebrate development.

Bogdanović O, van Heeringen SJ, Veenstra GJ.

Genesis. 2012 Mar;50(3):192-206. doi: 10.1002/dvg.20831. Epub 2011 Dec 27. Review.

31.

Affinity-based enrichment strategies to assay methyl-CpG binding activity and DNA methylation in early Xenopus embryos.

Bogdanović O, Veenstra GJ.

BMC Res Notes. 2011 Aug 18;4:300. doi: 10.1186/1756-0500-4-300.

32.

TBP-related factors: a paradigm of diversity in transcription initiation.

Akhtar W, Veenstra GJ.

Cell Biosci. 2011 Jun 27;1(1):23. doi: 10.1186/2045-3701-1-23.

33.

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis.

Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra GJ.

Genome Res. 2011 Aug;21(8):1313-27. doi: 10.1101/gr.114843.110. Epub 2011 Jun 2.

34.

Nucleotide composition-linked divergence of vertebrate core promoter architecture.

van Heeringen SJ, Akhtar W, Jacobi UG, Akkers RC, Suzuki Y, Veenstra GJ.

Genome Res. 2011 Mar;21(3):410-21. doi: 10.1101/gr.111724.110. Epub 2011 Jan 10.

35.

HNF-1B specifically regulates the transcription of the γa-subunit of the Na+/K+-ATPase.

Ferrè S, Veenstra GJ, Bouwmeester R, Hoenderop JG, Bindels RJ.

Biochem Biophys Res Commun. 2011 Jan 7;404(1):284-90. doi: 10.1016/j.bbrc.2010.11.108. Epub 2010 Dec 2.

PMID:
21130072
36.

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.

van Heeringen SJ, Veenstra GJ.

Bioinformatics. 2011 Jan 15;27(2):270-1. doi: 10.1093/bioinformatics/btq636. Epub 2010 Nov 15.

37.

Insightful tales from single embryonic cells.

Marks H, Veenstra GJ, Stunnenberg HG.

Cell Stem Cell. 2010 May 7;6(5):397-8. doi: 10.1016/j.stem.2010.04.008.

38.

ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation.

Akkers RC, van Heeringen SJ, Manak JR, Green RD, Stunnenberg HG, Veenstra GJ.

PLoS One. 2010 Jan 21;5(1):e8820. doi: 10.1371/journal.pone.0008820.

39.

Examining the cardiac NK-2 genes in early heart development.

Bartlett H, Veenstra GJ, Weeks DL.

Pediatr Cardiol. 2010 Apr;31(3):335-41. doi: 10.1007/s00246-009-9605-0. Epub 2009 Dec 5. Review.

40.

A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.

Akkers RC, van Heeringen SJ, Jacobi UG, Janssen-Megens EM, Françoijs KJ, Stunnenberg HG, Veenstra GJ.

Dev Cell. 2009 Sep;17(3):425-34. doi: 10.1016/j.devcel.2009.08.005.

41.

TBP2 is a substitute for TBP in Xenopus oocyte transcription.

Akhtar W, Veenstra GJ.

BMC Biol. 2009 Aug 3;7:45. doi: 10.1186/1741-7007-7-45.

42.

DNA methylation and methyl-CpG binding proteins: developmental requirements and function.

Bogdanović O, Veenstra GJ.

Chromosoma. 2009 Oct;118(5):549-65. doi: 10.1007/s00412-009-0221-9. Epub 2009 Jun 9. Review.

43.

TBP paralogs accommodate metazoan- and vertebrate-specific developmental gene regulation.

Jacobi UG, Akkers RC, Pierson ES, Weeks DL, Dagle JM, Veenstra GJ.

EMBO J. 2007 Sep 5;26(17):3900-9. Epub 2007 Aug 16.

44.

Uncleaved TFIIA is a substrate for taspase 1 and active in transcription.

Zhou H, Spicuglia S, Hsieh JJ, Mitsiou DJ, Høiby T, Veenstra GJ, Korsmeyer SJ, Stunnenberg HG.

Mol Cell Biol. 2006 Apr;26(7):2728-35.

45.

Specialized and redundant roles of TBP and a vertebrate-specific TBP paralog in embryonic gene regulation in Xenopus.

Jallow Z, Jacobi UG, Weeks DL, Dawid IB, Veenstra GJ.

Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13525-30. Epub 2004 Sep 2.

46.

When the embryonic genome flexes its muscles.

Rupp RA, Singhal N, Veenstra GJ.

Eur J Biochem. 2002 May;269(9):2294-9.

47.

Gene-selective developmental roles of general transcription factors.

Veenstra GJ, Wolffe AP.

Trends Biochem Sci. 2001 Nov;26(11):665-71. Review.

PMID:
11701325
48.

Constitutive genomic methylation during embryonic development of Xenopus.

Veenstra GJ, Wolffe AP.

Biochim Biophys Acta. 2001 Oct 31;1521(1-3):39-44.

PMID:
11690634
49.

Distinct roles for TBP and TBP-like factor in early embryonic gene transcription in Xenopus.

Veenstra GJ, Weeks DL, Wolffe AP.

Science. 2000 Dec 22;290(5500):2312-5.

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