Ronald H.A. Plasterk

Ronald Plasterk received his PhD from the University in Leiden in 1984, where he studied transposable elements. For his postdoctoral training he worked in the group of Mel Simon at the California Institute of Technology and subsequently in the group of John Sulston at the MRC-LMB, where he initiated his studies of the nematode Caenorhabditis elegans. From 1987 to 2000 he was group leader at the Netherlands Cancer Institute in Amsterdam and from 1993 to 2003 he was also Professor at the Free University of Amsterdam (Molecular Microbiology) and University of Amsterdam (Molecular Genetics) respectively. Since February 2000 he is director of the Hubrecht Laboratory / Netherlands Institute for Developmental Biology in Utrecht, and Professor of Developmental Genetics at the University of Utrecht. He is a member of the Royal Netherlands Academy of Arts and Sciences, the European Molecular Biology Organization, and the Board of Governors of The Wellcome Trust. Plasterk’s research interests are in the areas of genetics and functional genomics, mainly studying the nematode C. elegans (and more recently also the zebrafish). He focuses on the mechanism and regulation of DNA transposition, and on the mechanism of RNAi and miRNAs.

Group Members
Address
RNA as the immune system of the genome
miRNAs in animal development
Facilities and Expertise
Future projects
Goals
Selected publications

 

Group members

Marcel Tijsterman, postdoctoral fellow
Titia Sijen, postdoctoral fellow
Eugene Berezikov, postdoctoral fellow
Ellen Nollen, postdoctoral fellow
Victor Guriev, postdoctoral fellow
Brandon Ason, postdoctoral fellow
Erno Wienholds, PhD student
Nadine Vastenhouw, PhD student
Bastiaan Tops, PhD student
Gijs van Haaften, PhD student
Wigard Kloosterman, PhD student
Karin Brouwer, PhD student
Florian Steiner, PhD student
Tjakko van Ham, PhD student
Josien van Wolfswinkel, PhD student
Sam Linsen, PhD student
Esther Hazendonk, technician
Karen Thijssen, technician
Anja Bathoorn, technician
Ewart de Bruijn, technician
Evelien Kruisselbrink, technician

Address
Hubrecht Laboratory of Developmental Biology
Uppsalalaan 8
3584 CT Utrecht
Tel: +31-30-2121963
Fax: +31-30-2516554
E-mail: plasterk@niob.knaw.nl
Homepage: http://www.niob.knaw.nl/researchpages/plasterk


RNA as the immune system of the genome

Our lab, initially based at the Netherlands Cancer Institute in Amsterdam, The Netherlands, and since five year at the Hubrecht Laboratory in Utrecht, The Netherlands, discovered the role of small regulatory RNAs in one specific function, the protection of the genome of the nematode Caenorhabditis elegans against jumping of transposable elements.

The history of this is the following. The nematode is known to contain in its genome multiple transposons of quite different sequences. These transposons can jump, as witnessed by excision and insertion in somatic cells. Strikingly, the germ line of the animal seems protected against transposition: one can culture such an animal for many generations, and all progeny will have precisely the same transposon insertions as their parents. Therefore our lab concluded that most likely there was an active protection system in the germ line, and we undertook a genetic screen to isolate mutants defective in transposon silencing. We found multiple mutants. Surprisingly, these mutants had lost the silencing of all transposable elements at once, showing that there was one common mechanism that silenced all transposons of different sequence. The second surprise was that most of these mutants, isolated for their loss of transposon silencing, were found to be also deficient in the phenomenon of RNA interference or RNAi. This phenomenon had at that time just been discovered by Mello and Fire, as a means to silence genes by injection of double-stranded RNA. In follow-up studies our lab showed that most likely these transposons, which contained long terminal inverted repeats, produce RNA that can fold into double-stranded RNA, which triggers activity of the RNAi-system, resulting in silencing of the expression of the transposon-encoded protein transposase. Given the strong interrelation between RNAi and transposon silencing we then initiated mechanistic studies on the mechanism of RNAi, resulting in the discovery of an active amplification system, in which an RNA dependent RNA polymerase can generate secondary silencing signals.

miRNAs in animal development

The group of Greg Hannon (Cold Spring Harbor) demonstrated the central role of the Dicer enzyme as the nuclease that turns double-stranded RNA into small interfering RNAs (siRNAs). These approximately 21 nucleotide long RNA molecules are at the heart of all RNA-silencing systems. Almost immediately after the discovery of the Dicer enzyme, many researchers (including our lab) realized that the products of Dicer, RNA molecules of 21 bases, were strikingly similar to the small regulatory RNAs previously discovered by Ambros and Ruvkun (let-7 and lin-14). Therefore several researchers independently knocked-out the dicer gene in different systems, and indeed found that this resulted in the failure to make microRNAs. Our lab, in collaboration with Greg Hannon, first demonstrated this in C. elegans and then chose to further study the role of microRNAs in development of the vertebrate embryo of the zebrafish Danio rerio. Knock-out of the Dicer enzyme resulted indeed in failure to make microRNAs, which resulted in developmental arrest after two days. By bioinformatic studies we discovered that the list of microRNAs was probably significantly longer than the approximately 250 that had previously been recognized. What then is the specific role of microRNAs in animal development? This question is currently not answered yet. However, in a recent study our lab has initiated studies into roles of specific microRNAs in the vertebrate embryo by determining their expression patters in situ. A comprehensive set of all microRNAs known to be conserved between zebrafish and human was studied in situ, and the expression patterns were found to be strikingly tissue and organ specific.


Based on the timing of expression, and other arguments, it seems likely that microRNAs do not primarily act in switching on specific cell fates, but rather in maintaining these fates. One could say that microRNAs remind the cells of what they are. The beauty of the microRNA regulation system is that many different mRNAs can be regulated by the same microRNAs, while at the same time one messenger RNA can be regulated by different microRNAs. This provides a high degree of possible coordination, which is precisely what one requires of a system that maintains cell fates.

One of the new challenges in biology is now to determine the mechanism of microRNA action, dissect the roles of different microRNAs individually, and investigate the possible contribution of microRNA disfunction to human disease, and potentially even their therapeutic relevance.


Facilities and Expertise
Facilities for C. elegans research (transgenesis, Nomarski microscopy, dissecting microscopes, fluorescence microscopes) are availabe. In the context of the Hubrecht Laboratory all facilities for DNA research are also available.

Future projects
ß DNA transposition in animal cells: What is the mechanism of transposition, in particular which host factors are involved? How is transposition regulated?
ß Development of tools for functional genomics: How can transposable elements be used to study gene function in C. elegans? Can we develop similar technologies for higher animals (e.g. zebrafish and mice). More in general: with the genome sequence of animals such as C. elegans availabe, which new approaches can be developed to study gene function?
ß Using genetic analysis of C. elegans, can we understand how this animal perceives its environment (in particular taste), and respond appropriately? What is the molecular basis of memory effects?
All these three areas of research are, whenever possible, related to their medical relevance: transposons as possible tools for genetherapy, functional genomics to discover novel targets for drug development, and neurogenetics to understand human disease.

Goals
To study DNA transposition, and apply it in functional genome research.
To understand the action of the nervous system, using genetic model organisms, such as C. elegans.

Selected publications

Ketting, R., Haverkamp, Th.H.A., van Luenen, H.G.A.M., Plasterk, R.H.A. (1999). Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner Syndrome Helicase and RNaseD. Cell 99: 133-141.

Ketting, R.F., Plasterk, R.H.A. (2000). A genetic link between co-suppression and RNA interference in C. elegans. Nature, 404:296-298.

Ketting, R.F., Fischer, S.E.J., Bernstein, E., Sijen, T., Hannon, G.J., Plasterk R.H.A. (2001). Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes & Development 15: 2654-2659.

Sijen, T., Fleenor, J., Simmer, F., Thijssen, K.L., Parrish, S., Timmons, L., Plasterk, R.H.A., Fire, A. (2001). On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107: 465-476.

Tijsterman, M., Ketting, R.F., Okihara, K. L., Sijen, T., Plasterk, R. H. A. (2002) Short antisense RNAs can trigger gene silencing in C. elegans, depending on the RNA helicase MUT-14. Science 25;295 (5555): 694-697

Wienholds, E., Schulte-Merker, S., Walderich, B., Plasterk, R.H.A. (2002) Target-selected inactivation of the zebrafish rag1 gene. Science 297 (July 5): 99-102.

Wienholds, E., Koudijs, M.J., Van Eeden, F.J.M., Cuppen, E., Plasterk, R.H.A. (2003) The microRNA-producing enzyme Dicer 1 is essential for zebrafish development. Nature Genetics 35: 217-218.

Sijen, T., Plasterk, R.H.A. (2003) Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature 426: 310-314.

Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R.H.A., Cuppen, E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.

Robert, V.J.P., Sijen, T., van Wolfswinkel, J., Plasterk, R.H.A. (2005) Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences. Genes Dev. 19: 782-787.

Wienholds, E., Kloosterman, W.P., Miska, E., Alvarez-Saavedra, E. Berezikov, E., de Bruijn, E., Horvitz, H.R., Kauppinen, S., Plasterk, R.H.A. (2005) MicroRNA expression in zebrafish embryonic development. Science 309: 310-311.