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

CONTROLLING HISTONE VARIANT DYNAMICS

Regulation of gene expression in the eukaryotic genome requires balance between packaging the large linear DNA molecules and permitting regulated access to protein complexes involved in DNA transcription, replication, and repair. This is achieved by its organization into chromatin, with nucleosomes as basic building blocks. Within a nucleosome, the double-stranded DNA helix wraps around an octamer of histone proteins. Most eukaryotic genomes encode different histone variants that can be deposited either in a DNA-synthesis dependent manner during DNA replication or in a DNA synthesis independent manner throughout the cell cycle. The incorporation of these histone variants can modify nucleosome stability or nucleosome-nucleosome as well as chromatin fiber interactions and in consequence influence higher-order chromatin structures and DNA accessibility. A sophisticated network of histone chaperones coordinates the timely and locus-specific deposition of these histone variants.

We aim to understand how the different histone variants are incorporated and how coordinated histone variant deposition contributes to chromatin organization and gene expression control.

Most eukaryotic genomes comprise different H3 variants including H3.1, the replacement variant H3.3, the centromere specific CenH3 variant as well as tissue-specific H3 variants. In mammals, H3.3 occupancy is associated with dynamic chromatin regions such as transcriptionally active genes and regulatory regions, with high nucleosome turnover, and DNA accessibility. In the plant Arabidopsis thaliana, H3.3 is enriched at active genes, promoters, and telomeric repeats.

            We showed that the histone chaperone HISTONE REGULATOR A (HIRA) and the Arabidopsis homologue of ALPHA THALASSEMIA-MENTAL RETARDATION X-LINKED (ATRX) function in complementary pathways of histone H3.3 deposition (Figure 1, Duc, 2015; 2017). We are currently aiming to understand the role of HIRA-mediated histone deposition in controlling transcriptional dynamics in response to environmental and developmental stimuli.

Duc C, Benoit M, Le Goff S, Simon L, Poulet A, Cotterell S, Tatout C, Probst AV (2015) The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF-1 complex mutants. Plant J, 81(5): 707-22

Duc C, Benoit M, Détourné G, Simon L, Poulet A, Jung M, Veluchamy A, Latrasse D, Le Goff S, Cotterell S, Tatout C, Benhamed M, Probst AV. (2017), Arabidopsis ATRX Modulates H3.3 Occupancy and Fine-Tunes Gene Expression. Plant Cell. 29(7):1773-1793.

Probst AV, Mittelsten Scheid O. (2015), Stress-induced structural changes in plant chromatin. Curr Opin Plant Biol. 27:8-16.

 

The centromere-specific histone variant CenH3 is a key component of centromeres and required for kinetochore function and correct chromosome segregation. In a collaborative effort with I. Lermontova (IPK Gatersleben, Germany) and D. Geelen (Ghent University, Belgium), we have provided evidence that the Arabidopsis NUCLEAR AUTOANTIGENIC SPERM PROTEIN (NASP) escorts the centromeric histone variant, CenH3, in plants (Figure 1, Le Goff, 2019).

Le Goff S, Nur Keçeli B, Jerabkova H, Heckmann S, Rutten T, Cotterell S, Schubert V, Roitinger E, Mechtler K, Franklin FCH, Tatout C, Houben A, Geelen D, Probst AV, Lermontova I (2019), The H3 histone chaperone NASPSIM3 escorts CenH3 in Arabidopsis. Plant J, doi: 10.1111/tpj.14518.

 

 

HISTONE VARIANT DYNAMICS DURING DEVELOPMENT

Developmental phase transitions involve important changes in higher order chromatin organization. During early seedling development the transition from hetero- to autotrophic growth coincides with the progressive clustering of repetitive sequences into chromocenters. Chromocenter formation involves changes in histone variant composition namely increasing enrichment in H3.1 as well as H2A.W histone variants (Benoit, 2019), hallmarks of heterochromatin. The clustering of repetitive sequences, H3.1 and H2A.W enrichment as well as enrichment in H3K9me2 are affected in mutants impaired in replication-coupled histone deposition mediated by CHROMATIN ASSEMBLY FACTOR 1 (CAF-1).    

Chromocenter formation during post-germination development therefore requires dynamic changes in nucleosome composition and histone post-translational modifications orchestrated by the replication-coupled H3.1 deposition machinery.

Benoit M, Simon L, Desset S, Duc C, Cotterell S, Poulet A, Le Goff S, Tatout C, Probst AV. (2019) Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development. New Phytol. 221:385-398.

 

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

  • 2020
    • A. Probst, B. Desvoyes and C. Gutierrez, “Similar yet Critically Different: The distribution, dynamics and function of Histone Variants.”, J. Exp. Bot., 2020.
  • 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.