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A transcription factor–based mechanism for mouse heterochromatin formation

Nature Structural & Molecular Biology volume 19, pages 1023–1030 (2012)Cite this article

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A Corrigendum to this article was published on 05 February 2013

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Abstract

Heterochromatin is important for genome integrity and stabilization of gene-expression programs. We have identified the transcription factors Pax3 and Pax9 as redundant regulators of mouse heterochromatin, as they repress RNA output from major satellite repeats by associating with DNA within pericentric heterochromatin. Simultaneous depletion of Pax3 and Pax9 resulted in dramatic derepression of major satellite transcripts, persistent impairment of heterochromatic marks and defects in chromosome segregation. Genome-wide analyses of methylated histone H3 at Lys9 showed enrichment at intergenic major satellite repeats only when these sequences retained intact binding sites for Pax and other transcription factors. Additionally, bioinformatic interrogation of all histone methyltransferase Suv39h–dependent heterochromatic repeat regions in the mouse genome revealed a high concordance with the presence of transcription factor binding sites. These data define a general model in which reiterated arrangement of transcription factor binding sites within repeat sequences is an intrinsic mechanism of the formation of heterochromatin.

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Figure 1: The transcription factor Pax3 localizes to pericentric heterochromatin through a binding site within the major satellite repeats.
Figure 2: Pax3 represses transcription from major satellite repeats.
Figure 3: Pax3 and Pax9 have redundant functions in protecting mouse pericentric heterochromatin.
Figure 4: Pax3-deficient (shPax9) iMEFs show increased major satellite transcripts in the G1/S and G2 phase of the cell cycle.
Figure 5: ChIP-seq for H3K9me3 at pericentric and intergenic major satellite repeats.
Figure 6: Genome-wide analysis and bioinformatic interrogation of Suv39h-dependent H3K9me3 heterochromatin.
Figure 7: A transcription factor–based model for mouse heterochromatin formation.

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  • 27 December 2012

    In the version of this article initially published, Simone Meidhof's affiliations should have included Spemann Graduate School of Biology and Medicine (SGBM), Albert Ludwigs University Freiburg, Freiburg, Germany and the Faculty of Biology, Albert Ludwigs University Freiburg, Freiburg, Germany. Acknowledgement of the Excellence Initiative of the German Research Foundation (GSC-4, Spemann Graduate School) was omitted. The errors have been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We thank A. Copp (University College London Institute of Child Health) for providing Sp2H mice, A. Mansouri (Max Planck Institute for Biophysical Chemistry) for Pax3-null ESCs and M. Busslinger (Research Institute of Molecular Pathology) for the Pax5 antibody. The Pax3 monoclonal antibody developed by C. Ordahl was obtained from the Developmental Studies Hybridoma Bank, developed under the auspices of the US National Institute of Child Health and Human Development and maintained by the University of Iowa Department of Biological Sciences. We thank D. Gilbert (Florida State University) and R. Agrelo (Institut Pasteur de Montevideo) for advice on RNA-FISH protocols and S. Rudloff (Max Planck Institute of Immunobiology and Epigenetics) for providing the pCAGGs plasmid. ChIP-seq was performed at the Deep-Sequencing/Bioinformatics Unit of the Max Planck Institute of Immunobiology and Epigenetics. In particular, we would like to thank S. Diehl for processing and quality control of the raw data and N. Noureen and F. Ramirez for help with the genome-wide analyses. This work was supported by the Research Institute of Molecular Pathology through Boehringer Ingelheim (T.J.), the European Union Network of Excellence 'The Epigenome' (T.J., LSHG-CT-2004-503433), the Genome Research in Austria initiative (T.J.), the German Research Foundation (T.J. and T.B., CRC992 Medical Epigenetics) and the Max Planck Society (T.J.) and the Excellence Initiative of the German Research Foundation (GSC-4, Spemann Graduate School; S.M.).

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Author notes

  1. Johannes Popow & Borbala Gerle

    Present address: Present addresses: Institute of Molecular Biotechnology, Vienna, Austria (J.P.) and University College London Genetics Institute, London, UK (B.G.).,

  2. Aydan Bulut-Karslioglu and Valentina Perrera: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany

    Aydan Bulut-Karslioglu, Valentina Perrera, Inti Alberto de la Rosa-Velazquez, Suzanne van de Nobelen, Nicholas Shukeir, Thomas Manke, Monika Lachner & Thomas Jenuwein

  2. Research Institute of Molecular Pathology, Vienna, Austria

    Valentina Perrera, Manuela Scaranaro, Inti Alberto de la Rosa-Velazquez, Johannes Popow, Borbala Gerle, Susanne Opravil, Michaela Pagani & Thomas Jenuwein

  3. Department of Visceral Surgery, University of Freiburg Medical Center, Freiburg, Germany

    Simone Meidhof & Thomas Brabletz

  4. Spemann Graduate School of Biology and Medicine (SGBM), Albert Ludwigs University Freiburg, Freiburg, Germany

    Simone Meidhof

  5. Faculty of Biology, Albert Ludwigs University Freiburg, Freiburg, Germany

    Simone Meidhof

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Contributions

A.B.K. and V.P. designed and performed most of the experiments, analyzed the data and contributed equally to this manuscript. M.S. made the initial observation of Pax3 localization to major satellites, generated the Pax3-deficient MEFs and contributed to the analysis of RNA output in Pax3-deficient MEFs. I.A.d.l.R.-V. did ChIP-seq and contributed to the analysis of intergenic major satellites. S.v.d.N. carried out the Pax9 EMSA experiments, J.P. performed the northern blot analysis and B.G. conducted the dsRNA analysis. N.S., S.O. and M.P. provided excellent technical assistance. S.M. and T.B. shared expertise and reagents for the analysis of Zeb1 in mouse and human cells. T.M. did the TRAP analysis of all Suv39h-dependent heterochromatic regions. M.L. and T.J. advised on experimental design and interpretation of data and wrote the manuscript.

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Correspondence to Thomas Jenuwein.

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Bulut-Karslioglu, A., Perrera, V., Scaranaro, M. et al. A transcription factor–based mechanism for mouse heterochromatin formation. Nat Struct Mol Biol 19, 1023–1030 (2012). https://doi.org/10.1038/nsmb.2382

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