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Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

Nature Structural & Molecular Biology volume 20, pages 332–338 (2013)Cite this article

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Abstract

How a more plastic chromatin state is maintained and reversed during development is unknown. Heterochromatin-mediated silencing of repetitive elements occurs in differentiated cells. Here, we used repetitive elements, including retrotransposons, as model loci to address how and when heterochromatin forms during development. RNA sequencing throughout early mouse embryogenesis revealed that repetitive-element expression is dynamic and stage specific, with most repetitive elements becoming repressed before implantation. We show that LINE-1 and IAP retrotransposons become reactivated from both parental genomes after fertilization. Chromatin immunoprecipitation for H3K4me3 and H3K9me3 in 2- and 8-cell embryos indicates that their developmental silencing follows loss of activating marks rather than acquisition of conventional heterochromatic marks. Furthermore, short LINE-1 RNAs regulate LINE-1 transcription in vivo. Our data indicate that reprogramming after mammalian fertilization comprises a robust transcriptional activation of retrotransposons and that repetitive elements are initially regulated through RNA.

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Figure 1: Expression of repetitive elements is abundant, highly dynamic and stage specific.
Figure 2: Repetitive elements are reactivated after fertilization, and their expression decreases as development proceeds.
Figure 3: Silencing of repetitive elements follows loss of active histone marks rather than acquisition of repressive marks.
Figure 4: RNA from LINE-1s can form triple helices in vitro.
Figure 5: Short LINE-1 RNAs regulate LINE-1 transcription in vivo after fertilization.

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Acknowledgements

We thank L. Tora for support during the initial part of this work, S. Bour for graphic work, Y. Miyanari for advice on RNA FISH, E. Heard (Curie Institute, Paris, France) for the full-length LINE-1 probe, M. Dewannieux and T. Heidmann (Gustave Roussy Institute, Villejuif, France) for the IAP probe, D. Stollar, T. Ye and members of the Torres-Padilla lab for helpful discussions and A.J. Bannister and A. Burton for critical reading of the manuscript. M.-E.T.-P. acknowledges funding from AVENIR/INSERM, ANR-09-Blanc-0114, Epigenesys NoE and ERC-2011-StG 280840 “NuclearPotency.” Work in P.C.'s laboratory is supported by a Research Grant for RIKEN Omics Science Center from MEXT and a Funding Program for the Next Generation World Leading Researchers. A.F. was supported by a post-doctoral fellowship from the Fondation pour la Recherche Medicale.

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  1. Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Illkirch, France

    Anas Fadloun, Stéphanie Le Gras, Bernard Jost, Céline Ziegler-Birling & Maria-Elena Torres-Padilla

  2. Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan

    Hazuki Takahashi & Piero Carninci

  3. Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Cidade Universitária, São Paulo, Brazil

    Eduardo Gorab

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Contributions

A.F. designed, performed and analyzed most of the experiments in this study; S.L.G. performed all bioinformatic analyses; B.J. and H.T. generated libraries; C.Z.-B. performed experiments; E.G. provided the triplex antibody; P.C. supervised library generation. M.-E.T.-P. conceived of the project, designed and supervised the study and performed experiments. A.F., S.L.G. and M.-E.T.-P. wrote the manuscript.

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Correspondence to Maria-Elena Torres-Padilla.

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Fadloun, A., Le Gras, S., Jost, B. et al. Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nat Struct Mol Biol 20, 332–338 (2013). https://doi.org/10.1038/nsmb.2495

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