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Martino Ugolini, Maciej A. Kerlin, Ksenia Kuznetsova, Haruka Oda, Hiroshi Kimura, Nadine L. Vastenhouw

Transcription bodies regulate gene expression by sequestering CDK9

Nature Cell Biology (2024).

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Edlyn Wu and Nadine L. Vastenhouw

Sleeping embryonic genomes are awoken by OBOX proteins

Nature (2023).

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Martino Ugolini, Ksenia Kuznetsova, Haruka Oda, Hiroshi Kimura, Nadine L. Vastenhouw

Transcription bodies regulate gene expression by sequestering CDK9

biorxiv (2022), biorxiv (2023).

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Haruka Oda, Yuko Sato, Shigehiro A. Kawashima, Yusuke Fujiwara, Máté Pálfy, Edlyn Wu, Nadine L. Vastenhouw, Motomu Kanai, Hiroshi Kimura

Actin filaments accumulate in the nucleus during interphase and remain in the vicinity of condensing chromosomes during prophase to metaphase in zebrafish early embryos

biorxiv (2022). now published in Biology Open (2023). 

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Ksenia Kuznetsova, Noémie M. Chabot, Martino Ugolini, Edlyn Wu, Manan Lalit, Haruka Oda, Yuko Sato, Hiroshi Kimura, Florian Jug, Nadine Vastenhouw

Nanog organizes transcription bodies

biorxiv (2022). now published in Current Biology (2023). 

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Martino Ugolini and Nadine L. Vastenhouw

Maternally loaded RNAs: no time to die

Cell Research (2022).

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Lennart Hilbert, Yuko Sato, Ksenia Kuznetsova, Tommaso Bianucci, Hiroshi Kimura, Frank Jülicher, Alf Honigmann, Vasily Zaburdaev, and Nadine Vastenhouw

Transcription organizes euchromatin via microphase separation

Nature Communications, 12:1360 (2021).

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Edlyn Wu, Nadine L Vastenhouw
From mother to embryo: A molecular perspective on zygotic genome activation
Current Topics in Developmental Biology, 140: 209-254 (2020).
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Amanda Amodeo, Johanna Gassler, Ksenia Kuznetsova, Philip Zegerman
Meeting report: 2nd EMBO workshop "Awakening of the genome: the maternal-to-zygotic transition"
The Node. 2020.
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Elliott W. Abrams, Ricardo Fuentes, Florence L. Marlow, Manami Kobayashi, Hong Zhang, Sumei Lu, Lee Kapp, Shai R. Joseph, Amy Kugath, Tripti Gupta, Virginia Lemon, Greg Runke, Amanda A. Amodeo, Nadine L Vastenhouw, Mary C. Mullins
Molecular genetics of maternally-controlled cell divisions
PLoS Genetics. 16(4):e1008652 (2020)
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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
PLoS Genetics. 16(1):e1008546 (2020)
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Yuko Sato, Lennart Hilbert, Haruka Oda, Yinan Wan, John M. Heddleston, Teng-Leong Chew, Vasily Zaburdaev, Philipp Keller, Timothee Lionnet, Nadine Vastenhouw, Hiroshi Kimura
Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis
Development. 146(19):dev179127 (2019)
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Nadine L Vastenhouw, Wen Xi Cao, Howard D Lipshitz
The maternal-to-zygotic transition revisited
Development. 146(11):dev161471 (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. 145(5):dev158832 (2018)
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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)
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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 17(2):384-396 (2017)
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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)
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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)
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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 Entry, Also 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

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