Results 1 - 45 of 45 results
Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates. , Bright AR, van Genesen S, Li Q , Grasso A, Frölich S, van der Sande M, van Heeringen SJ, Veenstra GJC ., EMBO J. February 8, 2021; e104913.
Transcriptomics and Proteomics Methods for Xenopus Embryos and Tissues. , Gilchrist MJ , Veenstra GJC , Cho KWY., Cold Spring Harb Protoc. January 1, 2020; 2020 (2): 098350.
Genomics Methods for Xenopus Embryos and Tissues. , Gilchrist MJ , Cho KWY , Veenstra GJC ., Cold Spring Harb Protoc. January 1, 2020; 2020 (5): 097915.
ChIP-Sequencing in Xenopus Embryos. , Hontelez S , van Kruijsbergen I, Veenstra GJC ., Cold Spring Harb Protoc. January 1, 2019; 2019 (1):
Assay for Transposase-Accessible Chromatin-Sequencing Using Xenopus Embryos. , Bright AR, Veenstra GJC ., Cold Spring Harb Protoc. January 1, 2019; 2019 (1):
Mass Spectrometry-Based Absolute Quantification of Single Xenopus Embryo Proteomes. , Lindeboom RGH, Smits AH, Perino M, Veenstra GJC , Vermeulen M., Cold Spring Harb Protoc. January 1, 2019; 2019 (6):
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. January 1, 2018; 553 (7688): 337-341.
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. June 15, 2017; 426 (2): 336-359.
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. January 1, 2017; 426 (2): 460-471.
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. January 1, 2017; 18 (1): 198.
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. August 15, 2016; 416 (2): 361-72.
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. April 15, 2016; 143 (8): 1340-50.
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. April 1, 2016; 48 (4): 417-26.
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. January 1, 2016; 143 (11): 1914-25.
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. January 1, 2016; 538 (7625): 336-343.
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. December 18, 2015; 6 10148.
Establishing pluripotency in early development. , Paranjpe SS, Veenstra GJ ., Biochim Biophys Acta. June 1, 2015; 1849 (6): 626-36.
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. September 1, 2014; 42 (15): 9880-91.
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. March 1, 2014; 24 (3): 401-10.
A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. , Paranjpe SS, Jacobi UG, van Heeringen SJ, Veenstra GJ ., BMC Genomics. May 28, 2013; 14 762.
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. January 1, 2013; 57 (1): 49-54.
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. December 7, 2012; 151 (6): 1200-13.
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. October 1, 2012; 22 (10): 2043-53.
The epigenome in early vertebrate development. , Bogdanović O, van Heeringen SJ, Veenstra GJ ., Genesis. March 1, 2012; 50 (3): 192-206.
Chromatin immunoprecipitation analysis of Xenopus embryos. , Akkers RC, Jacobi UG, Veenstra GJ ., Methods Mol Biol. January 1, 2012; 917 279-92.
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. August 1, 2011; 21 (8): 1313-27.
Affinity-based enrichment strategies to assay methyl-CpG binding activity and DNA methylation in early Xenopus embryos. , Bogdanović O, Veenstra GJ ., BMC Res Notes. May 6, 2011; 4 300.
Nucleotide composition-linked divergence of vertebrate core promoter architecture. , van Heeringen SJ, Akhtar W, Jacobi UG, Akkers RC, Suzuki Y, Veenstra GJ ., Genome Res. March 1, 2011; 21 (3): 410-21.
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments. , van Heeringen SJ, Veenstra GJ ., Bioinformatics. January 15, 2011; 27 (2): 270-1.
Examining the cardiac NK-2 genes in early heart development. , Bartlett H, Veenstra GJ , Weeks DL ., Pediatr Cardiol. April 1, 2010; 31 (3): 335-41.
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. January 13, 2010; 5 (1): e8820.
DNA methylation and methyl-CpG binding proteins: developmental requirements and function. , Bogdanović O, Veenstra GJ ., Chromosoma. October 1, 2009; 118 (5): 549-65.
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. September 1, 2009; 17 (3): 425-34.
TBP2 is a substitute for TBP in Xenopus oocyte transcription. , Akhtar W, Veenstra GJ ., BMC Biol. August 3, 2009; 7 45.
TBP paralogs accommodate metazoan- and vertebrate-specific developmental gene regulation. , Jacobi UG, Akkers RC, Pierson ES, Weeks DL , Dagle JM, Veenstra GJ ., EMBO J. September 5, 2007; 26 (17): 3900-9.
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. April 1, 2006; 26 (7): 2728-35.
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. September 14, 2004; 101 (37): 13525-30.
Constitutive genomic methylation during embryonic development of Xenopus. , Veenstra GJ , Wolffe AP ., Biochim Biophys Acta. October 31, 2001; 1521 (1-3): 39-44.
Distinct roles for TBP and TBP-like factor in early embryonic gene transcription in Xenopus. , Veenstra GJ , Weeks DL , Wolffe AP ., Science. December 22, 2000; 290 (5500): 2312-5.
Translation of maternal TATA-binding protein mRNA potentiates basal but not activated transcription in Xenopus embryos at the midblastula transition. , Veenstra GJ , Destrée OH, Wolffe AP ., Mol Cell Biol. December 1, 1999; 19 (12): 7972-82.
The Oct-1 POU domain directs developmentally regulated nuclear translocation in Xenopus embryos. , Veenstra GJ , Mathu MT, Destrée OH., Biol Chem. February 1, 1999; 380 (2): 253-7.
Non-cell autonomous induction of apoptosis and loss of posterior structures by activation domain-specific interactions of Oct-1 in the Xenopus embryo. , Veenstra GJ , Peterson-Maduro J , Mathu MT, van der Vliet PC, Destrée OH., Cell Death Differ. September 1, 1998; 5 (9): 774-84.
Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. , Jones PL , Veenstra GJ , Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP ., Nat Genet. June 1, 1998; 19 (2): 187-91.
Whole-mount immunohistochemistry on Xenopus embryos using far-red fluorescent dyes. , Beumer TL, Veenstra GJ , Hage WJ, Destrée OH., Trends Genet. January 1, 1995; 11 (1): 9.
The promoter of the Xwnt-5C gene contains octamer and AP-2 motifs functional in Xenopus embryos. , Kuiken GA, Bertens PJ, Peterson-Maduro J , Veenstra GJ , Koster JG, Destrée OH., Nucleic Acids Res. May 11, 1994; 22 (9): 1675-80.