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4. Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway

Author

Longman, Dasa, Plasterk, Ronald H. A., Johnstone, Iain L., and Caceres, Javier P.

Subjects
Caenorhabditis elegans -- Genetic aspects, RNA processing -- Research, Genetic research, Biological sciences
Abstract

The analysis of the cis-acting sequences and trans-acting factors required in for nonsense-mediated mRNA decay (NMD) in Caenorhabditis elegans is used to investigate the mechanistic insights and identify two new novel factors in the substance. The spotted two genes are used for the purpose of proper embryonic development, as the proteins required in the complex are conserved throughout evolution and are also required in the human cells.

Published
2007

6. The zebrafish reference genome sequence and its relationship to the human genome

Author

Howe, Kerstin, Clark, Matthew D., Torroja, Carlos F., Torrance, James, Berthelot, Camille, Muffato, Matthieu, Collins, John E., Humphray, Sean, McLaren, Karen, Matthews, Lucy, McLaren, Stuart, Sealy, Ian, Caccamo, Mario, Churcher, Carol, Scott, Carol, Barrett, Jeffrey C., Koch, Romke, Rauch, Gerd-Jörg, White, Simon, Chow, William, Kilian, Britt, Quintais, Leonor T., Guerra-Assunção, José A., Zhou, Yi, Gu, Yong, Yen, Jennifer, Vogel, Jan-Hinnerk, Eyre, Tina, Redmond, Seth, Banerjee, Ruby, Chi, Jianxiang, Fu, Beiyuan, Langley, Elizabeth, Maguire, Sean F., Laird, Gavin K., Lloyd, David, Kenyon, Emma, Donaldson, Sarah, Sehra, Harminder, Almeida-King, Jeff, Loveland, Jane, Trevanion, Stephen, Jones, Matt, Quail, Mike, Willey, Dave, Hunt, Adrienne, Burton, John, Sims, Sarah, McLay, Kirsten, Plumb, Bob, Davis, Joy, Clee, Chris, Oliver, Karen, Clark, Richard, Riddle, Clare, Eliott, David, Threadgold, Glen, Harden, Glenn, Ware, Darren, Mortimer, Beverly, Kerry, Giselle, Heath, Paul, Phillimore, Benjamin, Tracey, Alan, Corby, Nicole, Dunn, Matthew, Johnson, Christopher, Wood, Jonathan, Clark, Susan, Pelan, Sarah, Griffiths, Guy, Smith, Michelle, Glithero, Rebecca, Howden, Philip, Barker, Nicholas, Stevens, Christopher, Harley, Joanna, Holt, Karen, Panagiotidis, Georgios, Lovell, Jamieson, Beasley, Helen, Henderson, Carl, Gordon, Daria, Auger, Katherine, Wright, Deborah, Collins, Joanna, Raisen, Claire, Dyer, Lauren, Leung, Kenric, Robertson, Lauren, Ambridge, Kirsty, Leongamornlert, Daniel, McGuire, Sarah, Gilderthorp, Ruth, Griffiths, Coline, Manthravadi, Deepa, Nichol, Sarah, Barker, Gary, Whitehead, Siobhan, Kay, Michael, Brown, Jacqueline, Murnane, Clare, Gray, Emma, Humphries, Matthew, Sycamore, Neil, Barker, Darren, Saunders, David, Wallis, Justene, Babbage, Anne, Hammond, Sian, Mashreghi-Mohammadi, Maryam, Barr, Lucy, Martin, Sancha, Wray, Paul, Ellington, Andrew, Matthews, Nicholas, Ellwood, Matthew, Woodmansey, Rebecca, Clark, Graham, Cooper, James, Tromans, Anthony, Grafham, Darren, Skuce, Carl, Pandian, Richard, Andrews, Robert, Harrison, Elliot, Kimberley, Andrew, Garnett, Jane, Fosker, Nigel, Hall, Rebekah, Garner, Patrick, Kelly, Daniel, Bird, Christine, Palmer, Sophie, Gehring, Ines, Berger, Andrea, Dooley, Christopher M., Ersan-Ürün, Zübeyde, Eser, Cigdem, Geiger, Horst, Geisler, Maria, Karotki, Lena, Kirn, Anette, Konantz, Judith, Konantz, Martina, Oberländer, Martina, Rudolph-Geiger, Silke, Teucke, Mathias, Osoegawa, Kazutoyo, Zhu, Baoli, Rapp, Amanda, Widaa, Sara, Langford, Cordelia, Yang, Fengtang, Carter, Nigel P., Harrow, Jennifer, Ning, Zemin, Herrero, Javier, Searle, Steve M. J., Enright, Anton, Geisler, Robert, Plasterk, Ronald H. A., Lee, Charles, Westerfield, Monte, de Jong, Pieter J., Zon, Leonard I., Postlethwait, John H., Nüsslein-Volhard, Christiane, Hubbard, Tim J. P., Crollius, Hugues Roest, Rogers, Jane, and Stemple, Derek L.

Published
2013
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7. Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi

Author

Sijen, Titia and Plasterk, Ronald H. A.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Titia Sijen; Ronald H. A. Plasterk (corresponding author) Transposable elements are stretches of DNA that can move and multiply within the genome of an organism. The Caenorhabditis elegans genome [...]

Published
2003
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8. The Wnt/β-catenin pathway regulates cardiac valve formation

Author

Hurlstone, Adam F. L., Haramis, Anna-Pavlina G., Wienholds, Erno, Begthel, Harry, Korving, Jeroen, van Eeden, Fredericus, Cuppen, Edwin, Zivkovic, Danica, Plasterk, Ronald H. A., and Clevers, Hans

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Adam F. L. Hurlstone [1, 2]; Anna-Pavlina G. Haramis [1, 2]; Erno Wienholds [1]; Harry Begthel [1]; Jeroen Korving [1]; Fredericus van Eeden [1]; Edwin Cuppen [1]; Danica Zivkovic [...]

Published
2003
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9. A micrococcal nuclease homologue in RNAi effector complexes

Author

Caudy, Amy A., Ketting, Rene F., Hammond, Scott M., Denli, Ahmet M., Bathoorn, Anja M. P., Tops, Bastiaan B. J., Silva, Jose M., Myers, Mike M., Hannon, Gregory J., and Plasterk, Ronald H. A.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Amy A. Caudy [1, 3]; René F. Ketting [2, 3]; Scott M. Hammond [1, 4]; Ahmet M. Denli [1]; Anja M. P. Bathoorn [1, 2]; Bastiaan B. J. Tops [...]

Published
2003
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10. On the role of RNA amplification in dsRNA-triggered gene silencing

Author

Sijen, Titia, Fleenor, Jamie, Simmer, Femke, Thijssen, Karen L., Parrish, Susan, Timmons, Lisa, Plasterk, Ronald H. A., and Fire, Andrew

Subjects
Cell research -- Analysis, Messenger RNA -- Genetic aspects, Caenorhabditis elegans -- Physiological aspects, Genetic translation -- Physiological aspects, Brain research -- Analysis, Carrier proteins -- Physiological aspects, Biological sciences
Abstract

Research has been conducted on the trigger RNA amplification. The effect of this amplification on the RNA interference in Caenorhabditis elegans has been investigated and the results indicate that the amplification mechanism augments the RNA interference-based surveillance potency.

Published
2001

11. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans

Author

Ketting, Rene F., Fischer, Sylvia E. J., Bernstein, Emily, Sijen, Titia, Hannon, Gregory J., and Plasterk, Ronald H. A.

Subjects
Genetic research -- Analysis, RNA -- Genetic aspects, Caenorhabditis elegans -- Genetic aspects, Gene expression -- Physiological aspects, Genetic transcription -- Regulation, Molecules -- Analysis, Biological sciences
Abstract

Research has been conducted on the double-stranded RNAs suppressing homologous gene expression via RNA interference or post-transcriptional silencing. The characterization of Caenorhabditis elegans ortholog of Dicer has been carried out in vivo and in vitro and the results indicate that Dicer is involved in the maturation of the small RNA molecule regulating developmental silencing.

Published
2001

12. Retraction

Author

Sijen, Titia, primary, Steiner, Florian A., additional, Thijssen, Karen L., additional, and Plasterk, Ronald H. A., additional

Published
2020
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13. Mouse microRNA profiles determined with a new and sensitive cloning method

Author

Takada, Shuji, Berezikov, Eugene, Yamashita, Yoshihiro, Lagos-Quintana, Mariana, Kloosterman, Wigard P., Enomoto, Munehiro, Hatanaka, Hisashi, Fujiwara, Shin-ichiro, Watanabe, Hideki, Soda, Manabu, Choi, Young Lim, Plasterk, Ronald H. A., Cuppen, Edwin, and Mano, Hiroyuki

Published
2006

15. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells

Author

Ivics, Zoltan, Hackett, Perry B., Plasterk, Ronald H., and Izsvak, Zsuzsanna

Subjects
Mutagenesis -- Research, Gene mutations -- Research, Biological sciences
Abstract

A novel strategy of the first reconstruction of an open reading frame for a salmonoid transposase and systematic introduction of amino acid replacements were illustrated. The transposon system was named Sleeping Beauty (SB) can be developed as an instrument for germline transformation and insertional mutagenesis in vertebrates. The effectiveness of phylogenetic approach for constructing the active transposon was demonstrated by the activities of SB.

Published
1997

30. Chromatin and RNAi factors protect the C. elegans germline against repetitive sequence

Author

Robert, Valerie J. P., Sijen, Titia, Wolfswinkel, Josien van, and Plasterk, Ronald H. A.

Subjects
Chromatin -- Research, Gene silencing -- Research, Caenorhabditis elegans -- Genetic aspects, Biological sciences
Abstract

The RNA interference (RNAi) screens that were performed to catalog genes required for cosuppression in the Caenorhabditis elegans germline is reported. Results suggest that in Caenorhabditis elegans repetitive sequences trigger transcriptional gene silencing using RNAi and chromatin factors.

Published
2005

31. Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi

Author

Pothof, Joris, Haaften, Gijs van, Thijssen, Karen, Kamath, Ravi S., Fraser, Andrew G., Ahringer, Julie, Plasterk, Ronald H. A., and Tijsterman, Marcel

Subjects
Genetic research -- Analysis, Genomes -- Physiological aspects, Caenorhabditis elegans -- Genetic aspects, Gene mutations -- Physiological aspects, RNA -- Genetic aspects, Heredity -- Physiological aspects, Biological sciences
Abstract

Research has been conducted on genome stability in Caenorhabditis elegans somatic cells. The authors report the use of RNA interference-based ganome-wide screen in order to detect genes contributing to genome stability in C. elegans.

Published
2003

32. Regulated transposition of a fish transposon in the mouse germ line

Author

Fischer, Sylvia E. J., Wienholds, Erno, and Plasterk, Ronald H. A.

Subjects
Mutagenesis -- Research, Mice -- Physiological aspects, Antibody diversity -- Research, Science and technology
Abstract

Tc1/mariner elements are able to transpose in species other than the host from which they were isolated. As potential vectors for insertional mutagenesis and transgenesis of the mouse, these cut-and-paste transposons were tested for their ability to transpose in the mouse germ line. First, the levels of activity of several Tc1/mariner elements in mammalian cells were compared; the reconstructed fish transposon Sleeping Beauty (SB) was found to be an order of magnitude more efficient than the other tested transposons. SB then was introduced into the mouse germ line as a two-component system: one transgene for the expression of the transposase in the male germ line and a second transgene carrying a modified transposon. In 20% of the progeny of double transgenic male mice the transposon had jumped from the original chromosomal position into another locus. Analysis of the integration sites shows that these jumps indeed occurred through the action of SB transposase, and that SB has a strong preference for intrachromosomal transposition. Analysis of the excision sites suggests that double-strand breaks in haploid spermatids are repaired via non-homologous end joining. The SB system may be a powerful tool for transposon mutagenesis of the mouse germ line.

Published
2001

33. The G-Protein [Beta]-Subunit GPB-2 in Caenorhabditis elegans Regulates the [G.sub.o][Alpha]-[G.sub.q][Alpha] Signaling Network Through Interactions With the Regulator of G-Protein Signaling Proteins EGL-10 and EAT-16

Author

van der Linden, Alexander M., Simmer, Femke, Cuppen, Edwin, and Plasterk, Ronald H. A.

Subjects
Caenorhabditis elegans -- Genetic aspects, G proteins -- Analysis, Cellular signal transduction -- Genetic aspects, Neural circuitry -- Analysis, Biological sciences
Abstract

The genome of Caenorhabditis elegans harbors two genes for G-protein [Beta]-subunits. Here, we describe the characterization of the second G-protein [Beta]-subunit gene gpb-2. In contrast to gpb-1, gpb-2 is not an essential gene even though, like gpb-1, gpb-2 is expressed during development, in the nervous system, and in muscle cells. A loss-of-function mutation in gpb-2 produces a variety of behavioral defects, including delayed egg laying and reduced pharyngeal pumping. Genetic analysis shows that GPB-2 interacts with the GOA-1 (homologue of mammalian [G.sub.o][Alpha]) and EGL-30 (homologue of mammalian [G.sub.q][Alpha]) signaling pathways. GPB-2 is most similar to the divergent mammalian G[Beta]5 subunit, which has been shown to mediate a specific interaction with a G[Gamma]-subunit-like (GGL) domain of RGS proteins. We show here that GPB-2 physically and genetically interacts with the GGL-containing RGS proteins EGL-10 and EAT-16. Taken together, our results suggest that GPB-2 works in concert with the RGS proteins EGL-10 and EAT-16 to regulate GOA-1 ([G.sub.o][Alpha]) and EGL-30 ([G.sub.q][Alpha]) signaling.

Published
2001

34. CHE-3, a Cytosolic Dynein Heavy Chain, Is Required for Sensory Cilia Structure and Function in Caenorhabditis elegans

Author

Wicks, Stephen R., de Vries, Corry J., van Luenen, Henri G. A. M., and Plasterk, Ronald H. A.

Subjects
Developmental biology -- Research, Caenorhabditis elegans -- Research, Cilia and ciliary motion -- Research, Biological sciences
Abstract

Forward genetic screens using novel assays of nematode chemotaxis to soluble compounds identified three independent transposon-insertion mutations in the gene encoding the Caenorhabditis elegans dynein heavy chain (DHC) 1b isoform. These disruptions were mapped and cloned using a newly developed PCR-based transposon display. The mutations were demonstrated to be allelic to the che-3 genetic locus. This isoform of dynein shows temporally and spatially restricted expression in ciliated sensory neurons, and mutants show progressive developmental defects of the chemosensory cilia. These results are consistent with a role for this motor protein in the process of intraflagellar transport; DHC 1b acts in concert with a number of other proteins to establish and maintain the structural integrity of the ciliated sensory endings in C. elegans. Key Words: chemotaxis; cilium; flagella; nonmotile; dynein; IFT; DHC1b; taste.

Published
2000

35. Efficient targeted-selected mutagenesis in Caenorhabditis elegans: Toward a knockout for every gene

Author

Cuppen, Edwin, Gort, Eelke;, Hazendonk, Esther, Mudde, Josine, van de Belt, Jose, Nijman, Isaac J., Guryev, Victor, and Plasterk, Ronald H. A.

Subjects
Caenorhabditis elegans -- Genetic aspects, Gene mutations -- Research, Mutagenesis -- Research, Health
Abstract

A target-selected knockout approach, based on the random chemical mutagenesis is employed to study the efficient targeted-selected mutagenesis in Caenorhabditis elegans (C.elegans). The use of a nonsense introducing mutations (NIMs) genotyping approach for high-density microarrays is found to be extremely helpful for the genome-wide identification of C.elegans knockout.

Published
2007

37. Efficient target-selected mutagenesis in zebrafish

Author

Wienholds, Erno, Eeden, Freek van, Kosters, Marit, Mudde, Josine, Plasterk, Ronald H. A., and Cuppen, Edwin

Subjects
Genetic research -- Analysis, Genomes -- Physiological aspects, Genomes -- Research, Mutagenesis -- Analysis, Zebra fish -- Genetic aspects, Health
Abstract

Research has been conducted on zebrafish. The authors describe the modifications to the method developed to perform the target-selected mutagenesis in zebrafish which now allow to generate knockouts in zebrafish.

Published
2003

38. Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

Author

Howe, Kerstin, primary, Clark, Matthew D., additional, Torroja, Carlos F., additional, Torrance, James, additional, Berthelot, Camille, additional, Muffato, Matthieu, additional, Collins, John E., additional, Humphray, Sean, additional, McLaren, Karen, additional, Matthews, Lucy, additional, McLaren, Stuart, additional, Sealy, Ian, additional, Caccamo, Mario, additional, Churcher, Carol, additional, Scott, Carol, additional, Barrett, Jeffrey C., additional, Koch, Romke, additional, Rauch, Gerd-Jörg, additional, White, Simon, additional, Chow, William, additional, Kilian, Britt, additional, Quintais, Leonor T., additional, Guerra-Assunção, José A., additional, Zhou, Yi, additional, Gu, Yong, additional, Yen, Jennifer, additional, Vogel, Jan-Hinnerk, additional, Eyre, Tina, additional, Banerjee, Ruby, additional, Chi, Jianxiang, additional, Fu, Beiyuan, additional, Langley, Elizabeth, additional, Maguire, Sean F., additional, Laird, Gavin, additional, Lloyd, David, additional, Kenyon, Emma, additional, Donaldson, Sarah, additional, Sehra, Harminder, additional, Almeida-King, Jeff, additional, Loveland, Jane, additional, Trevanion, Stephen, additional, Jones, Matt, additional, Quail, Mike, additional, Willey, Dave, additional, Hunt, Adrienne, additional, Burton, John, additional, Sims, Sarah, additional, McLay, Kirsten, additional, Plumb, Bob, additional, Davis, Joy, additional, Clee, Chris, additional, Oliver, Karen, additional, Clark, Richard, additional, Riddle, Clare, additional, Elliott, David, additional, Threadgold, Glen, additional, Harden, Glenn, additional, Ware, Darren, additional, Begum, Sharmin, additional, Mortimore, Beverley, additional, Kerry, Giselle, additional, Heath, Paul, additional, Phillimore, Benjamin, additional, Tracey, Alan, additional, Corby, Nicole, additional, Dunn, Matthew, additional, Johnson, Christopher, additional, Wood, Jonathan, additional, Clark, Susan, additional, Pelan, Sarah, additional, Griffiths, Guy, additional, Smith, Michelle, additional, Glithero, Rebecca, additional, Howden, Philip, additional, Barker, Nicholas, additional, Lloyd, Christine, additional, Stevens, Christopher, additional, Harley, Joanna, additional, Holt, Karen, additional, Panagiotidis, Georgios, additional, Lovell, Jamieson, additional, Beasley, Helen, additional, Henderson, Carl, additional, Gordon, Daria, additional, Auger, Katherine, additional, Wright, Deborah, additional, Collins, Joanna, additional, Raisen, Claire, additional, Dyer, Lauren, additional, Leung, Kenric, additional, Robertson, Lauren, additional, Ambridge, Kirsty, additional, Leongamornlert, Daniel, additional, McGuire, Sarah, additional, Gilderthorp, Ruth, additional, Griffiths, Coline, additional, Manthravadi, Deepa, additional, Nichol, Sarah, additional, Barker, Gary, additional, Whitehead, Siobhan, additional, Kay, Michael, additional, Brown, Jacqueline, additional, Murnane, Clare, additional, Gray, Emma, additional, Humphries, Matthew, additional, Sycamore, Neil, additional, Barker, Darren, additional, Saunders, David, additional, Wallis, Justene, additional, Babbage, Anne, additional, Hammond, Sian, additional, Mashreghi-Mohammadi, Maryam, additional, Barr, Lucy, additional, Martin, Sancha, additional, Wray, Paul, additional, Ellington, Andrew, additional, Matthews, Nicholas, additional, Ellwood, Matthew, additional, Woodmansey, Rebecca, additional, Clark, Graham, additional, Cooper, James D., additional, Tromans, Anthony, additional, Grafham, Darren, additional, Skuce, Carl, additional, Pandian, Richard, additional, Andrews, Robert, additional, Harrison, Elliot, additional, Kimberley, Andrew, additional, Garnett, Jane, additional, Fosker, Nigel, additional, Hall, Rebekah, additional, Garner, Patrick, additional, Kelly, Daniel, additional, Bird, Christine, additional, Palmer, Sophie, additional, Gehring, Ines, additional, Berger, Andrea, additional, Dooley, Christopher, additional, Ersan-Ürün, Zübeyde, additional, Eser, Cigdem, additional, Geiger, Horst, additional, Geisler, Maria, additional, Karotki, Lena, additional, Kirn, Anette, additional, Konantz, Judith, additional, Konantz, Martina, additional, Oberländer, Martina, additional, Rudolph-Geiger, Silke, additional, Teucke, Mathias, additional, Lanz, Christa, additional, Raddatz, Günter, additional, Osoegawa, Kazutoyo, additional, Zhu, Baoli, additional, Rapp, Amanda, additional, Widaa, Sara, additional, Langford, Cordelia, additional, Yang, Fengtang, additional, Schuster, Stephan C., additional, Carter, Nigel P., additional, Harrow, Jennifer, additional, Ning, Zemin, additional, Herrero, Javier, additional, Searle, Steve M. J., additional, Enright, Anton, additional, Geisler, Robert, additional, Plasterk, Ronald H. A., additional, Lee, Charles, additional, Westerfield, Monte, additional, de Jong, Pieter J., additional, Zon, Leonard I., additional, Postlethwait, John H., additional, Volhard, Christiane Nüsslein-, additional, Hubbard, Tim J. P., additional, Crollius, Hugues Roest, additional, Rogers, Jane, additional, and Stemple, Derek L., additional

Published
2013
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39. Mapping determinants of gene expression plasticity by genetical genomics in C-elegans

Author

Li, Yang, Gutteling, Evert W., Tijsterman, Marcel, Fu, Jingyuan, Riksen, Joost A. G., Hazendonk, Esther, Prins, Pjotr, Plasterk, Ronald H. A., Jansen, Ritsert C., Breitling, Rainer, Kammenga, Jan E., Álvarez, Olga Alda, Li, Yang, Gutteling, Evert W., Tijsterman, Marcel, Fu, Jingyuan, Riksen, Joost A. G., Hazendonk, Esther, Prins, Pjotr, Plasterk, Ronald H. A., Jansen, Ritsert C., Breitling, Rainer, Kammenga, Jan E., and Álvarez, Olga Alda

Published
2006

40. Long-term gene silencing by RNAi

Author

Vastenhouw, Nadine L., Brunschwig, Karin, Okihara, Kristy L., Müller, Fritz, Tijsterman, Marcel, Plasterk, Ronald H. A., Vastenhouw, Nadine L., Brunschwig, Karin, Okihara, Kristy L., Müller, Fritz, Tijsterman, Marcel, and Plasterk, Ronald H. A.

Abstract

Small RNA molecules participate in a variety of activities in the cell: in a process known as RNA interference (RNAi), double-stranded RNA triggers the degradation of messenger RNA that has a matching sequence; the small RNA intermediates of this process can also modify gene expression in the nucleus¹. Here we show that a single episode of RNAi in the nematode Caenorhabditis elegans can induce transcriptional silencing effects that are inherited indefinitely in the absence of the original trigger. Our findings may prove useful in the ongoing development of RNAi to treat disease.

Published
2006

41. Sydney Brenner: A Biography

Author

Plasterk, Ronald H. A.

Subjects
Sydney Brenner: A Biography (Biography) -- Friedberg, Errol C. -- Book reviews, Books -- Book reviews, Humanities
Abstract

Brenner, Sydney Sydney Brenner: A Biography. Errol C. Friedberg. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 2010. 379 p. $39.00. 'Friedberg (a pathologist at the University of Texas Southwestern [...]

Published
2011

49. Long-term gene silencing by RNAi

Author

Vastenhouw, Nadine L., primary, Brunschwig, Karin, additional, Okihara, Kristy L., additional, Müller, Fritz, additional, Tijsterman, Marcel, additional, and Plasterk, Ronald H. A., additional

Published
2006
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