2024
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).
2023
Edlyn Wu and Nadine L. Vastenhouw
Sleeping embryonic genomes are awoken by OBOX proteins
Nature (2023).
2022
Martino Ugolini, Ksenia Kuznetsova, Haruka Oda, Hiroshi Kimura, Nadine L. Vastenhouw
Transcription bodies regulate gene expression by sequestering CDK9
biorxiv (2022), biorxiv (2023).
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).
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).
Martino Ugolini and Nadine L. Vastenhouw
Maternally loaded RNAs: no time to die
Cell Research (2022).
2021
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).
2020
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).
Article page
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.
Article page
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)
Article page
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)
Article page
2019
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)
Article page
Nadine L Vastenhouw, Wen Xi Cao, Howard D Lipshitz
The maternal-to-zygotic transition revisited
Development. 146(11):dev161471 (2019)
Free copies available here.
2018
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)
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
2017
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)
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 page, Recommended 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 Page, Also 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
2016
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
2014
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)
Pubmed Entry, Download PDF
2012
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
2010
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
2006
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
2004
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
2003
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
2001
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