CGM - Department Dynamics & Stability of Genomes
More about the lab "Programmed genome rearrangements -
Mechanisms and regulation"
Group leader: Mireille BÉTERMIER
Last update: 30-Jun-2011
More about research
DNA elimination events programmed during development or cell differentiation have been described in many organisms and are sometimes involved in the assembly of open reading frames. This was reported for the sporulation-specific transcription factor s K gene in the bacterium Bacillus subtilis or, in vertebrates, for the genes encoding T cell receptors and immunoglobulins.
Remarkably, the whole germ line genome of ciliates undergoes large-scale DNA rearrangements during the process of nuclear differentiation that takes place at each sexual cycle. This system is based on nuclear dimorphism, which is a hallmark of these unicellular eukaryotes and results in the separation of germ line and somatic functions between the two types of nuclei that coexist in their cytoplasm (figure 1). Micronuclei (mic) are not transcribed during vegetative growth but they are essential because, at each sexual cycle, they undergo meiosis and transmit the germ line genome to the zygotic nucleus of the next sexual generation. Macronuclei (MAC) are responsible for virtually all gene transcription and can be viewed as somatic nuclei. They are, indeed, destroyed at each sexual cycle and, concomitantly, new macronuclei develop from mitotic products of the zygotic nucleus.
During macronuclear development, the germ line genome is entirely reorganized to yield the genome of the mature macronucleus (figure 2, right). This involves extensive DNA amplification from a diploid (in the germ line nucleus) to a highly polyploid state (800 to 1000n in the Paramecium macronucleus). In Paramecium tetraurelia, which is the model ciliate studied by the lab, two types of DNA rearrangements take place during macronuclear development, in a reproducible manner from one sexual generation to the next. On the one hand, repeated sequences (transposons and minisatellites) are eliminated imprecisely, in association with chromosome fragmentation. On the other hand, around 60,000 short sequences, the IESs (Internal Eliminated Sequences), each single copy in the germ line genome, are excised precisely at the nucleotide level: their excision allows the assembly of functional open reading frames and involves the introduction of double strand breaks at IES boundaries.
The main focus of the lab is the study of the molecular mechanisms that participate in IES excision and could account for its high precision and accuracy. Current research projects include (i) the molecular characterization of intermediate products of the reaction and (ii) a search for protein partners involved in IES end cleavage and in the repair of excision sites on the chromosomes.
The design of experimental strategies will greatly benefit from highly efficient tools available for RNA interference-mediated gene silencing in Paramecium and from the sequence of the P. tetraurelia macronuclear genome that has been completed recently at the Genoscope in collaboration with a consortium of French labs.
Collaborations
J. Cohen (CGM, Gif-sur-Yvette)
L. Duret (IPBL, Lyon, France)
J. Forney (Purdue Univ. West Lafayette, Indiana, USA)
R. Gromadka, M. Zagulski (IBB, Warsaw, Poland)
E. Meyer (ENS, Paris, France)
Grants
Ligue contre le Cancer – Comité de Paris (2006)
CNRS – Programme ATIP Génétique (2006-2009)
Mireille Bétermier's publications
Kapusta, A., Matsuda, A., Marmignon, A., Ku, M., Silve, A., Meyer, E., Forney, JD., Malinsky, S., Bétermier, M. (2011) Highly Precise and Developmentally Programmed Genome Assembly in Paramecium Requires Ligase IV-Dependent End Joining. PLoS Genet, 7 (4) :e1002049.
Nowak, J. K., Gromadka, R., Juszczuk, M., Jerka-Dziadosz, M., Maliszewska, K., Mucchielli, M. H., Gout, J. F., Arnaiz, O., Agier, N., Tang, T., Aggerbeck, L. P., Cohen, J., Delacroix, H., Sperling, L., Herbert, C. J., Zagulski, M., Betermier, M. (2011) A functional study of genes essential for autogamy and nuclear reorganization in Paramecium. Eukaryot Cell, 10 (3) 363-72.
Bouhouche, K., Gout, J-F., Kapusta, A., Bétermier, M., Meyer, E. (2011) Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling. Nucleic Acids Res, 39 (10) 4249-4264.
Arnaiz, O., Gout, J-F., Bétermier, M., Bouhouche, K., Cohen, J., Duret, L., Kapusta, A., Meyer, E. and Sperling, L. (2010) Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. BMC Genomics, 11:547.
Beisson, J., Bétermier, M., Bré, M.-H., Cohen, J., Duharcourt , S., Duret, L., Kung, C., Malinsky, S., Meyer, E., Preer, J.-R. and Sperling, L. (2010) Paramecium tetraurelia: The Renaissance of an Early Unicellular Model. CSH Protoc, 2010 (1) pdb.emo140.
Complements to this publication may be found at the following URL: http://paramecium.cgm.cnrs-gif.fr/parawiki/Protocols
Baudry, C., Malinsky, S., Restituito, M., Kapusta, A., Rosa, S., Meyer and E., Bétermier, M. (2009). PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia. Genes & Dev, 23 (21) 2478-83.
Lepère, G., Bétermier, M., Meyer, E. and Duharcourt, S. (2008) Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia. Genes Dev, 22 (11) 1501-12.
Gratias, A., Lepère, G., Garnier, O., Rosa, S., Duharcourt, S., Malinsky, S., Meyer, E. and Bétermier, M. (2008) Developmentally programmed DNA splicing in Paramecium reveals short-distance crosstalk between DNA cleavage sites. Nucleic Acids Res, 36 (10) 3244-51.
Duret, L., Cohen, J., Jubin, C., Dessen, P., Gout, J., Mousset, S., Aury, J., Jaillon, O., Noel, B., Arnaiz, O., Betermier, M., Wincker, P., Meyer, E. and Sperling, L. (2008) Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germ line. Genome Res, 18 (4) 585-96.
Jaillon, O., Bouhouche, K., Gout, J., Aury, J., Noel, B., Saudemont, B., Nowacki, M., Serrano, V., Porcel, B., Ségurens, B., Le Mouël, A., Lepère, G., Schächter, V., Bétermier, M., Cohen, J., Wincker, P., Sperling, L., Duret, L. and Meyer, E. (2008) Translational control of intron splicing in eukaryotes. Nature, 451 (7176) 359-62.
Aury, J-M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, BM., Ségurens, B., Daubin, V., Anthouard, V., Aiach, N., Arnaiz, O., Billaut, A., Beisson, J., Blanc, I., Bouhouche, K., Câmara, F., Duharcourt, S., Guigo, R., Gogendeau, D., Katinka, M., Keller, A-M., Kissmehl, R., Klotz, C., Koll, F., Le Mouël, A., Lepère, G., Malinsky, S., Nowacki, M., Nowak, J-K., Plattner, H., Poulain, J., Ruiz, F., Serrano, V., Zagulski, M., Dessen, P., Bétermier, M., Weissenbach, J., Scarpelli, C., Schächter, V., Sperling, L., Meyer, E., Cohen, J., & Wincker, P. (2006) Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature, 2006 Nov 9;444(7116):171-178. Epub 2006 Nov 1.
Bétermier, M. (2004). Large-scale genome remodelling by the developmentally programmed elimination of germ line sequences in the ciliate Paramecium. Res. Microbiol. 155 : 399-408.
Gratias, A., Bétermier, M. (2003). Processing of double-strand breaks is involved in the precise excision of Paramecium IESs. Mol. Cell. Biol. 23 : 7152-7162.
Dessen, P., Zagulski, M., Gromadka, R., Plattner, H., Kissmehl, R., Meyer, E., Bétermier, M., Schultz, J.E., Linder, J.U., Pearlman, R.E., Kung, C., Forney, J., Satir, B., van Houten, J.L., Keller, A.M., Froissard, M., Sperling, L., Cohen, J. (2001). Paramecium genome survey : a pilot project. Trends Genet. 17 : 306-308.
Gratias, A., Bétermier, M. (2001). Developmentally programmed excision of internal DNA sequences in Paramecium aurelia. Biochimie. 83 : 1009-1022.
Bétermier, M., Duharcourt, S., Seitz, H., Meyer, E. (2000) Timing of developmentally programmed excision and circularization of Paramecium internal eliminated sequences. Mol. Cell. Biol. 20 : 1553-1561.
Haren, L., Bétermier, M., Polard, P., Chandler, M. (1997) IS911-mediated intramolecular transposition is naturally temperature-sensitive. Mol. Microbiol. 25 : 531-540.
Ton-Hoang, B., Bétermier, M., Polard, P., Chandler, M. (1997) Assembly of a strong promoter following IS911 circularization and the role of circles in transposition. EMBO J. 16 : 3357-3371. .
Polard, P., Ton-Hoang, B., Haren, L., Bétermier, M., Walczak, R., Chandler, M. (1996) IS911-mediated transpositional recombination in vitro. J. Mol. Biol. 264 : 68-81. .
Rousseau, P., Bétermier, M., Chandler, M., Alazard, R. (1996) Interactions between the repressor and the early operator region of bacteriophage Mu. J. Biol. Chem. 271 : 9739-9745 .
Bétermier, M., Rousseau, P., Alazard, R., Chandler, M. (1995) Mutual stabilisation of bacteriophage Mu repressor and histone-like proteins in a nucleoprotein structure. J. Mol. Biol. 249 : 332-341 .
Bétermier, M., Galas, D.J., Chandler, M. (1994) Interaction of FIS protein with DNA : Bending and specificity of binding. Biochimie 76 : 958-967. Bétermier, M ., Poquet, I., Alazard, R., Chandler, M. (1993) Involvement of Escherichia coli FIS protein in maintenance of bacteriophage Mu lysogeny by the repressor : control of early transcription and inhibition of transposition. J. Bacteriol. 175 : 3798-3811 .
Alazard, R., Bétermier, M., Chandler, M. (1992) Escherichia coli integration host factor stabilizes bacteriophage Mu repressor interactions with operator DNA in vitro. Mol. Microbiol. 6: 1707-1714 .
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Bétermier, M., Alazard, R., Ragueh, F., Roulet, E., Toussaint, A., Chandler, M. (1987) Phage Mu transposase : deletion of the carboxy-terminal end does not abolish DNA-binding activity. Mol. Gen. Genet. 210 : 77-85.
Colleaux, L., d’Auriol, L., Bétermier, M., Cottarel, G., Jacquier, A., Galibert, F., Dujon, B. (1986) Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E. coli as a specific double strand endonuclease. Cell 44 : 521-533.
Dujon, B., Cottarel, G., Colleaux, L., Bétermier, M., Jacquier, A., d’Auriol, L., Galibert, F. (1985). Mechanism of integration of an intron within a mitochondrial gene : a double strand break and the transposase function of an intron encoded protein as revealed by in vivo and in vitro assays. In « Achievements and perspectives of mitochondrial research. Volume II : Biogenesis », E. Quagliariello et al., eds. Elsevier and Science Publishers. p. 215-225.
