Aline PROBST

Principal Investigator

Resume

Aline PROBSTprofile picture
  • Directrice de Recherche, CNRS, since 2018
  • Principal Investigator, 2013
  • Chargée de Recherche, CNRS, GReD, 2009-13
  • Postdoctoral Fellow, Curie Institute, Paris, 2005-09, team G. Almouzni
  • PhD, Friedrich Miescher Institute, Basel, Switzerland, 2001-04, team J. Paszkowski
  • Master in Biotechnology, ESBS, Strasbourg, 1997- 2000

Research

 

 

 

 

 

GENOME PLASTICITY: EXAMPLE OF 5S RIBOSOMAL RNA GENES

5S ribosomal RNAs (rRNAs) are critical components of the ribosomes, molecular machineries that translate genetic information into proteins. Due to the essential role of these RNAs and the requirement to be produced in large quantities, 5S rRNA genes are highly repeated in the genome. Given their repetitive nature and their localization in the pericentromeric regions of the genome, 5S rRNA genes are only partly assembled in the reference genome, which has rendered detailed analyses of their organization, dynamics and epigenetic regulation difficult. Nevertheless, 5S rRNA genes show small variations in sequence and not all copies are transcribed, inciting the question how expression of these quasi-identical sequences is regulated.

Using next generation sequencing of DNA and 5S ribosomal RNA we have shown that specific DNA signatures distinguish the 5S rRNA gene copies from the three major 5S rDNA loci. Using these sequence signatures, we have built bioinformatics pipelines and developed specific probes for DNA Fluorescence in situ hybridization specific for a particular locus. With these tools, we revealed sequence polymorphisms between the different 5S rRNA gene copies and between loci as well as differential enrichment in epigenetic marks linked to differential gene expression. We further showed important variation in copy number and position of 5S rRNA genes between ecotypes of Arabidopsis thaliana, the latter influencing genome organization within the nucleus. Finally, our results indicate important plasticity among ecotypes in 5S rRNA gene expression both between 5S rDNA loci and within a particular locus.

Simon L, Rabanal FA, Dubos T, Oliver C, Lauber D, Poulet A, Vogt A, Mandlbauer A, Le Goff S, Sommer A, Duborjal H, Tatout C, Probst AV (2018) Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana. Nucleic Acids Research. 46:3019-3033. doi: 10.1093/nar/gky163.

Simon L, Probst AV (2018) High-Affinity LNA-DNA Mixmer Probes for Detection of Chromosome-Specific Polymorphisms of 5S rDNA Repeats in Arabidopsis thaliana. In: Bemer M., Baroux C. (eds) Plant Chromatin Dynamics. Methods in Molecular Biology Humana Press, New York, NY; 1675:481-491. doi: 10.1007/978-1-4939-7318-7_28.

Publications

  • 2019
    • S. Le Goff, B. Nur Keceli, H. Jerabkova, S. Heckmann, T. Rutten, S. Cotterell, V. Schubert, E. Roitinger, K. Mechtler, F. Franklin, C. Tatout, A. Houben, D. Geelen, A. Probst and I. Lermontova, “The H3 histone chaperone NASP(SIM) (3) escorts CenH3 in Arabidopsis.”, Plant J., 2019.
  • 2018
    • M. Benoit, L. Simon, S. Desset, C. Duc, S. Cotterell, A. Poulet, S. Le Goff, C. Tatout and A. Probst, “Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development.”, The New phytologist, 2018.
    • G. Parry, A. Probst, C. Baroux and C. Tatout, “Meeting report - INDEPTH kick-off meeting.”, Journal of cell science, vol. 131 (12) , 2018.
    • L. Simon, F. Rabanal, T. Dubos, C. Oliver, D. Lauber, A. Poulet, A. Vogt, A. Mandlbauer, S. Le Goff, A. Sommer, H. Duborjal, C. Tatout and A. Probst, “Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.”, Nucleic Acids Res., 2018.
    • A. Probst, “A Compendium of Methods to Analyze the Spatial Organization of Plant Chromatin.”, Meth. Mol. Biol., vol. 1675 , pp. 397–418, 2018.
    • L. Simon and A. Probst, “High-Affinity LNA-DNA Mixmer Probes for Detection of Chromosome-Specific Polymorphisms of 5S rDNA Repeats in Arabidopsis thaliana.”, Meth. Mol. Biol., vol. 1675 , pp. 481–491, 2018.
  • 2017
  • 2016
    • A. Poulet, A. Probst, K. Graumann, C. Tatout and D. Evans, “Exploring the evolution of the proteins of the plant nuclear envelope.”, Nucleus, pp. 0, 2016.
  • 2015
  • 2014
    • K. Graumann, E. Vanrobays, S. Tutois, A. Probst, D. Evans and C. Tatout, “Characterization of two distinct subfamilies of SUN-domain proteins in Arabidopsis and their interactions with the novel KASH-domain protein AtTIK.”, J. Exp. Bot., vol. 65 (22) , pp. 6499–512, 2014.
    • A. Poulet, I. Arganda-Carreras, D. Legland, A. Probst, P. Andrey and C. Tatout, “NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei.”, Bioinformatics (Oxford, England), 2014.
    • C. Tatout, D. Evans, E. Vanrobays, A. Probst and K. Graumann, “The plant LINC complex at the nuclear envelope.”, Chromosome Res., 2014.
    • M. Thomas, L. Pingault, A. Poulet, J. Duarte, M. Throude, S. Faure, J. Pichon, E. Paux, A. Probst and C. Tatout, “Evolutionary history of Methyltransferase 1 genes in hexaploid wheat.”, BMC genomics, vol. 15 , pp. 922, 2014.
  • 2013
    • M. Casanova, M. Pasternak, F. El Marjou, P. Le Baccon, A. Probst and G. Almouzni, “Heterochromatin reorganization during early mouse development requires a single-stranded noncoding transcript.”, Cell Rep, vol. 4 (6) , pp. 1156–67, 2013.
    • M. Benoit, E. Layat, S. Tourmente and A. Probst, “Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci.”, Gene, vol. 526 (1) , pp. 39–45, 2013.
  • 2012
    • E. Layat, A. Probst and S. Tourmente, “Structure, function and regulation of Transcription Factor IIIA: From Xenopus to Arabidopsis.”, Biochim. Biophys. Acta, vol. 1829 (3-4) , pp. 274–82, 2012.
  • 2011
    • G. Almouzni and A. Probst, “Heterochromatin maintenance and establishment: lessons from the mouse pericentromere.”, Nucleus, vol. 2 (5) , pp. 332–8, 2011.
    • A. Probst and G. Almouzni, “Heterochromatin establishment in the context of genome-wide epigenetic reprogramming.”, Trends Genet., vol. 27 (5) , pp. 177–85, 2011.
    • C. Maison, D. Bailly, D. Roche, R. Montes de Oca, A. Probst, I. Vassias, F. Dingli, B. Lombard, D. Loew, J. Quivy and G. Almouzni, “SUMOylation promotes de novo targeting of HP1alpha to pericentric heterochromatin.”, Nat. Genet., vol. 43 (3) , pp. 220–7, 2011.
    • C. Maison, J. Quivy, A. Probst and G. Almouzni, “Heterochromatin at mouse pericentromeres: a model for de novo heterochromatin formation and duplication during replication.”, Cold Spring Harb. Symp. Quant. Biol., vol. 75 , pp. 155–65, 2011.
  • 2010
    • A. Probst, I. Okamoto, M. Casanova, F. El Marjou, P. Le Baccon and G. Almouzni, “A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development.”, Dev. Cell, vol. 19 (4) , pp. 625–38, 2010.
  • 2009
    • A. Probst, E. Dunleavy and G. Almouzni, “Epigenetic inheritance during the cell cycle.”, Nat. Rev. Mol. Cell Biol., vol. 10 (3) , pp. 192–206, 2009.
  • 2007
    • A. Probst and G. Almouzni, “Pericentric heterochromatin: dynamic organization during early development in mammals.”, Differentiation, vol. 76 (1) , pp. 15–23, 2007.
    • A. Probst, F. Santos, W. Reik, G. Almouzni and W. Dean, “Structural differences in centromeric heterochromatin are spatially reconciled on fertilisation in the mouse zygote.”, Chromosoma, vol. 116 (4) , pp. 403–15, 2007.
  • 2006
    • Y. Habu, O. Mathieu, M. Tariq, A. Probst, C. Smathajitt, T. Zhu and J. Paszkowski, “Epigenetic regulation of transcription in intermediate heterochromatin.”, EMBO Rep., vol. 7 (12) , pp. 1279–84, 2006.
    • M. Houlard, S. Berlivet, A. Probst, J. Quivy, P. Hery, G. Almouzni and M. Gerard, “CAF-1 is essential for heterochromatin organization in pluripotent embryonic cells.”, PLoS Genet., vol. 2 (11) , pp. e181, 2006.
    • N. Schonrock, V. Exner, A. Probst, W. Gruissem and L. Hennig, “Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana.”, J. biol. chem., vol. 281 (14) , pp. 9560–8, 2006.
  • 2005
    • O. Mathieu, A. Probst and J. Paszkowski, “Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis.”, EMBO J., vol. 24 (15) , pp. 2783–91, 2005.
    • A. Pecinka, N. Kato, A. Meister, A. Probst, I. Schubert and E. Lam, “Tandem repetitive transgenes and fluorescent chromatin tags alter local interphase chromosome arrangement in Arabidopsis thaliana.”, Journal of cell science, vol. 118 (Pt 16) , pp. 3751–8, 2005.
  • 2004
    • C. Bowler, G. Benvenuto, P. Laflamme, D. Molino, A. Probst, M. Tariq and J. Paszkowski, “Chromatin techniques for plant cells.”, Plant J., vol. 39 (5) , pp. 776–89, 2004.
    • A. Probst, M. Fagard, F. Proux, P. Mourrain, S. Boutet, K. Earley, R. Lawrence, C. Pikaard, J. Murfett, I. Furner, H. Vaucheret and O. Mittelsten Scheid, “Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats.”, Plant Cell, vol. 16 (4) , pp. 1021–34, 2004.
    • S. Takeda, Z. Tadele, I. Hofmann, A. Probst, K. Angelis, H. Kaya, T. Araki, T. Mengiste, O. Mittelsten Scheid, K. Shibahara, D. Scheel and J. Paszkowski, “BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis.”, Genes Dev., vol. 18 (7) , pp. 782–93, 2004.
  • 2003
    • M. Tariq, H. Saze, A. Probst, J. Lichota, Y. Habu and J. Paszkowski, “Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin.”, Proc. Natl. Acad. Sci. U.S.A., vol. 100 (15) , pp. 8823–7, 2003.
    • A. Probst, P. Fransz, J. Paszkowski and O. Mittelsten Scheid, “Two means of transcriptional reactivation within heterochromatin.”, Plant J., vol. 33 (4) , pp. 743–9, 2003.
  • 2002
    • O. Mittelsten Scheid, A. Probst, K. Afsar and J. Paszkowski, “Two regulatory levels of transcriptional gene silencing in Arabidopsis.”, Proc. Natl. Acad. Sci. U.S.A., vol. 99 (21) , pp. 13659–62, 2002.