Máté Pálfy, Gunnar Schulze, Eivind Valen, Nadine L Vastenhouw
Chromatin accessibility established by Pou5f3, Sox19b, and Nanog primes genes for activity during zebrafish genome activation
Posted on the bioRxiv in May 2019, and submitted

Yuko Sato, Lennart Hilbert, Haruka Oda, Yinan Wan, John M. Heddleston, Teng-Leong Chew, Vasily Zaburdaev, Philipp Keller, Timothee Lionnet, Nadine Vastenhouw, Hiroshi Kimura
Quantitative measurements of chromatin modification dynamics during zygotic genome activation
Posted on the bioRxiv April 8 2019, and in revision

Nadine L Vastenhouw, Wen Xi Cao, Howard D Lipshitz
The maternal-to-zygotic transition revisited
Development. 2019
Free copies available here.


Máté Pálfy
The role of transcription factors in shaping the chromatin landscape and regulating the timing of zygotic genome activation in zebrafish
PhD Thesis, Technische Universität Dresden, defense date: 2018.04.26

Pavel Vopalensky, Sabrina Pralow and Nadine L Vastenhouw
Reduced expression of the Nodal coreceptor Oep causes loss of mesendodermal competence in zebrafish
Development. 2018 Mar 6;145(5)
Article page

Stapel LC, Broaddus C, Vastenhouw NL
Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos
Methods Mol Biol 1649:143-162 (2018)
Article page


Lennart Hilbert, Yuko Sato, Hiroshi Kimura, Frank Jülicher, Alf Honigmann, Vasily Zaburdaev, and Nadine Vastenhouw
Transcription establishes microenvironments that organize euchromatin
Posted on the bioRxiv on Dec 15 2017, in revision

Kumar M, Joseph SR, Augsburg M, Bogdanova A, Drechsel D, Vastenhouw NL, Buchholz F, Gentzel M, Shevchenko A.
MS Western, a Method of Multiplexed Absolute Protein Quantification is a Practical Alternative to Western Blotting.
Mol Cell Proteomics (2017 Nov 30) [Epub ahead of print]
Article page

Stapel, L Carine; Zechner, Christoph; Vastenhouw, Nadine L
Uniform gene expression in embryos is achieved by temporal averaging of transcription noise.
Genes Dev 31: 1635-1640 (2017)
Article pageRecommended in F1000Prime

Shai Joseph
Competition for DNA binding between histones and transcription factors regulates the timing of zygotic genome activation in zebrafish embryos
PhD Thesis, Technische Universität Dresden, defense date: 2017.10.30

Boothe, Tobias; Hilbert, Lennart; Heide, Michael; Berninger, Lea; Hüttner, Wieland B ; Zaburdaev, Vasily; Vastenhouw, Nadine; Myers, Eugene W; Drechsel, David N; Rink, Jochen C
A tunable refractive index matching medium for live imaging cells, tissues and model organisms.
eLife, 27240 2017
Article PageAlso see Tobias' post on the Node

Joseph, Shai R; Pálfy, Máté; Hilbert, Lennart; Kumar, Mukesh; Karschau, Jens; Zaburdaev, Vasily; Shevchenko, Andrej; Vastenhouw, Nadine L
Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos.
eLife, 23326 (2017)
Article Page

Max Krause
The role of Histone H3 Lysine 4 trimethylation in zebrafish embryonic development
PhD Thesis, Technische Universität Dresden, defense date: 2017.03.09

Palfy, Máté; Joseph, Shai R; Vastenhouw, Nadine L
The timing of zygotic genome activation.
Current Opinion in Genetics and Development, 43, pp. 53-60 (2017)
Article Page


Stapel, L Carine; Lombardot, Benoit; Broaddus, Coleman; Kainmueller, Dagmar; Jug, Florian; Myers, Eugene W.; Vastenhouw, Nadine
Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.
Development, 143, no. 3, pp. 540-546 (2016)
Pubmed EntryAlso see our post on the Node

Carine Stapel
The road to uniform gene expression – How zebrafish embryos overcome a game of chance
PhD Thesis, Technische Universität Dresden, defense date: 2016.09.23


Stapel, L Carine; Vastenhouw, Nadine
Message control in developmental transitions; deciphering chromatin's role using zebrafish genomics.
Brief Funct Genomics, 13, no. 2, pp. 106-120 (2014)
Pubmed Entry

Zhang, Yang; Vastenhouw, Nadine; Feng, Jianxing; Fu, Kai; Wang, Chenfei; Ge, Ying; Hummelen, Paul van; Schier, Alexander F; Liu, Xiaole Shirley
Canonical nucleosome organization at promoters forms during genome activation.
Genome Res, 24, no. 2, pp. 260-266 (2014)
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Vastenhouw, Nadine; Schier, Alexander F
Bivalent histone modifications in early embryogenesis.
Curr Opin Cell Biol, 24, no. 3, pp. 374-386 (2012)
Pubmed Entry, Download PDF

Pauli, Andrea; Valen, Eivind; Lin, Michael F; Garber, Manuel; Vastenhouw, Nadine; Levin, Joshua Z; Fan, Lin; Sandelin, Albin; Rinn, John L; Regev, Aviv; Schier, Alexander F
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
Genome Res, 22, no. 3, pp. 577-591 (2012)
Pubmed Entry


Vastenhouw, Nadine; Zhang, Yang; Woods, Ian G; Imam, Farhad; Regev, Aviv; Liu, X Shirley; Rinn, John L; Schier, Alexander F
Chromatin signature of embryonic pluripotency is established during genome activation.
Nature, 464, no. 7290, pp. 922-926 (2010)
Pubmed Entry


Vastenhouw, Nadine; Brunschwig, Karin; Okihara, Kristy L; Müller, Fritz; Tijsterman, Marcel; Plasterk, Ronald H A
Gene expression: long-term gene silencing by RNAi.
Nature, 442, no. 7105, pp. 882-882 (2006)
Pubmed Entry


Haaften, Gijs van; Vastenhouw, Nadine; Nollen, Ellen A A; Plasterk, Ronald H A; Tijsterman, Marcel
Gene interactions in the DNA damage-response pathway identified by genome-wide RNA-interference analysis of synthetic lethality.
Proc Natl Acad Sci U.S.A., 101, no. 35, pp. 12992-12996 (2004)
Pubmed Entry

Vastenhouw, Nadine; Plasterk, Ronald H A
RNAi protects the Caenorhabditis elegans germline against transposition.
Trends Genet., 20, no. 7, pp. 314-319 (2004)
Pubmed Entry

Robert, V J P; Vastenhouw, Nadine; Plasterk, Ronald H A
RNA interference, transposon silencing, and cosuppression in the Caenorhabditis elegans germ line: similarities and differences.
Cold Spring Harb Symp Quant Biol, 69, pp. 397-402 (2004)
Pubmed Entry


Vastenhouw, Nadine; Fischer, Steffi; Robert, V J P; Thijssen, Karen L; Fraser, Andrew G; Kamath, Ravi S; Ahringer, Julie; Plasterk, Ronald H A
A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans.
Curr Biol, 13, no. 15, pp. 1311-1316 (2003)
Pubmed Entry


Masselink, H; Vastenhouw, Nadine; Bernards, René
B-myb rescues ras-induced premature senescence, which requires its transactivation domain.
Cancer Lett, 171, no. 1, pp. 87-101 (2001)
Pubmed Entry

Berkhout, B; Vastenhouw, Nadine; Klasens, B I; Huthoff, H
Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription.
RNA, 7, no. 8, pp. 1097-1114 (2001)
Pubmed Entry