Abstract

In the ciliate Paramecium, transposable elements and their single-copy remnants are deleted during the development of somatic macronuclei from germline micronuclei, at each sexual generation. Deletions are targeted by scnRNAs, small RNAs produced from the germ line during meiosis that first scan the maternal macronuclear genome to identify missing sequences, and then allow the zygotic macronucleus to reproduce the same deletions. Here we show that this process accounts for the maternal inheritance of mating types in Paramecium tetraurelia, a long-standing problem in epigenetics. Mating type E depends on expression of the transmembrane protein mtA, and the default type O is determined during development by scnRNA-dependent excision of the mtA promoter. In the sibling species Paramecium septaurelia, mating type O is determined by coding-sequence deletions in a different gene, mtB, which is specifically required for mtA expression. These independently evolved mechanisms suggest frequent exaptation of the scnRNA pathway to regulate cellular genes and mediate transgenerational epigenetic inheritance of essential phenotypic polymorphisms.

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Accessions

Primary accessions

European Nucleotide Archive

GenBank/EMBL/DDBJ

Gene Expression Omnibus

Data deposits

Microarray data have been deposited at the Gene Expression Omnibus database49 under accession number GSE43436. RNA-seq data (transcriptomes of mtBO and mtCO mutants) have been deposited in the European Nucleotide Archive (EBI) under accession number ERP002291. Small RNA sequences have been deposited at the EBI under accession number ERP001812. The mtA, mtB and mtC sequences of all strains and species studied have been deposited at GenBank under accession codes KJ748544KJ748569.

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Acknowledgements

We thank S. Malinsky, C. Ciaudo and M.-A. Félix for critical reading of the manuscript, and S. Marker and all other laboratory members for continuous support and discussions. This work was supported by the ‘Investissements d’Avenir’ program ANR-10-LABX-54 MEMO LIFE/ANR-11-IDEX-0001-02 Paris Sciences et Lettres* Research University and by grants ANR-08-BLAN-0233 ‘ParaDice’ and ANR-12-BSV6-0017 ‘INFERNO’ to E.M., L.S. and S.D., an ‘Equipe FRM’ grant to E.M., grants ANR-2010-BLAN-1603 ‘GENOMAC’ and CNRS ATIP-Avenir to S.D., and National Science Foundation grant MCB-1050161 to M. Lynch (JFG). D.P.S. was supported by Ph.D. fellowships from the Erasmus Mundus program and from the Ligue Nationale Contre le Cancer. M.L.-A. was supported by Ph.D. fellowships from the Ministère de l’Enseignement Supérieur et de la Recherche and from the Fondation de la Recherche Médicale. A.P. was supported by grant RFBR 13-04-01683a. Some strains used in this study are maintained at the Centre of Core Facilities ‘Culture Collection of Microorganisms’ in St Petersburg State University. The sequencing of the mtBO and mtCO MAC genomes benefited from the facilities and expertise of the high-throughput sequencing platform of IMAGIF (Centre de Recherche de Gif, http://www.imagif.cnrs.fr). The mtBO and mtCO transcriptomes were sequenced at the Genomic Paris Centre - IBENS platform, member of ‘France Gènomique’ (ANR10-INBS-09-08). This study was carried out in the context of the CNRS-supported European Research Group ‘Paramecium Genome Dynamics and Evolution’ and the European COST Action BM1102.

Author information

Author notes

    • Baptiste Saudemont
    • , Jean-François Goût
    •  & Khaled Bouhouche

    Present addresses: Laboratoire de Biochimie, Unité Mixte de Recherche 8231, École Supérieure de Physique et de Chimie Industrielles, 75231 Paris, France (B.S.); Department of Biology, Indiana University, Bloomington, Indiana 47405, USA (J.-F.G.); INRA, UMR 1061 Unité de Génétique Moléculaire Animale, Université de Limoges, IFR 145, Faculté des Sciences et Techniques, 87060 Limoges, France (K.B.).

Affiliations

  1. Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS; Inserm, U1024; CNRS, UMR 8197 Paris F-75005, France

    • Deepankar Pratap Singh
    • , Baptiste Saudemont
    • , Gérard Guglielmi
    • , Simran Bhullar
    • , Khaled Bouhouche
    • , Véronique Tanty
    • , Corinne Blugeon
    •  & Eric Meyer
  2. Sorbonne Universités, UPMC Univ., IFD, 4 place Jussieu, 75252 Paris cedex 05, France

    • Deepankar Pratap Singh
    • , Baptiste Saudemont
    •  & Maoussi Lhuillier-Akakpo
  3. CNRS UPR3404 Centre de Génétique Moléculaire, Gif-sur-Yvette F-91198, and Université Paris-Sud, Département de Biologie, Orsay F-91405, France

    • Olivier Arnaiz
    • , Anne Aubusson-Fleury
    •  & Linda Sperling
  4. CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 Novembre 1918, Villeurbanne F-69622, France

    • Jean-François Goût
  5. Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland

    • Malgorzata Prajer
    •  & Ewa Przybòs
  6. Department of Microbiology, Faculty of Biology, St Petersburg State University, Saint Petersburg 199034, Russia

    • Alexey Potekhin
  7. Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris F-75205, France

    • Maoussi Lhuillier-Akakpo
    •  & Sandra Duharcourt
  8. Commissariat à l’Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France

    • Adriana Alberti
    • , Karine Labadie
    •  & Jean-Marc Aury

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Contributions

D.P.S. did almost all of the experimental work presented here and contributed to the design of experiments. B.S. characterized mRNAs and contributed to silencing experiments and northern blot analyses. G.G. contributed to gene sequencing, plasmid construction, PCR analyses and cell line maintenance. J.-F.G. did the microarray analysis, and A.A.-F. the confocal analysis of mtA–GFP fusions. A.A., K.L. and J.-M.A. carried out the deep sequencing of small RNAs, and C.B. that of the mtBO and mtCO transcriptomes; O.A. and L.S. did the bioinformatic analyses. K.B., M.L.-A., V.T. and S.D. showed the role of scnRNA pathway genes in mtA promoter excision. S.B. did the mtA promoter dsRNA feeding experiment. A.P. contributed to the analysis of the mtAO mutant and provided P. octaurelia and septaurelia strains. M.P. contributed to the analysis of the mtBO mutant and prepared samples from the P. octaurelia cross, which was carried out by E.P. E.M. conceived the study and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Eric Meyer.

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https://doi.org/10.1038/nature13318

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