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Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex

Nature Cell Biology volume 9, pages 1167–1174 (2007)Cite this article

Abstract

In Drosophila, the function of the Polycomb group genes (PcGs) and their target sequences (Polycomb response elements (PREs)) is to convey mitotic heritability of transcription programmes — in particular, gene silencing. As part of the mechanisms involved, PREs are thought to mediate this transcriptional memory function by building up higher-order structures in the nucleus. To address this question, we analysed in vivo the three-dimensional structure of the homeotic locus bithorax complex (BX-C) by combining chromosome conformation capture (3C) with fluorescent in situ hybridization (FISH) and FISH immunostaining (FISH-I) analysis. We found that, in the repressed state, all major elements that have been shown to bind PcG proteins, including PREs and core promoters, interact at a distance, giving rise to a topologically complex structure. We show that this structure is important for epigenetic silencing of the BX-C, as we find that major changes in higher-order structures must occur to stably maintain alternative transcription states, whereas histone modification and reduced levels of PcG proteins determine an epigenetic switch that is only partially heritable.

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Figure 1: Repressed PREs colocalize in PC bodies.
Figure 2: BX-C conformation in staged embryos.
Figure 3: PC depletion affects long-range interactions.
Figure 4: Different BX-C conformations in constitutively active cells.
Figure 5: The BX-C adopts different spatial conformations relative to its transcription state.

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Acknowledgements

We thank G. Cavalli for providing lab space and funding to perform the work done by F.B. and V.R., stimulating discussions and constructive criticisms about this manuscript. We thank A. Breiling, G. Oliva, N. Hornig, M. Vivo, Z. Jasencakova, M. Matarazzo and F. Cernilogar for helpful comments on the manuscript and technical advice. We are grateful to A. Ambesi-Impiombato, D. Di Bernardo, A. Buonocore, E. Pirozzi and A. Mas for statistical analysis, and to D. Romano for modelling the 3D image. This work was supported by grants from Fondazione Telethon (TCP00094), La Compagnia di San Paolo, Associazione Italiana Ricerca sul Cancro AIRC, VolkwagenStiftung (I77 996) and The Epigenome Network of Excellence (LSHG-CT-2004-503433) to V.O.; by the National Institutes of Health (HG03143) to J.D. V.R. is supported by the Ministère de la Recherche, F.B. is supported by the CNRS. C.L. and V.O. would like to dedicate this work to the heart and soul of Maria Graziella Persico.

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Authors and Affiliations

  1. Dulbecco Telethon Institute at IGB CNR, Epigenetics and Genome Reprogramming, Via Pietro Castellino 111, Naples, 80131, Italy

    Chiara Lanzuolo & Valerio Orlando

  2. Institute of Human Genetics, Chromatin and Cell Biology lab, UPR 1142 — CNRS, 141 rue de la Cardonille, Montpellier, Cedex 5, 34396, France

    Virginie Roure & Frédéric Bantignies

  3. Department of Biochemistry and Molecular Pharmacology, Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, 01605, Massachusetts, USA

    Job Dekker

Authors
  1. Chiara Lanzuolo
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  2. Virginie Roure
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  3. Job Dekker
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  4. Frédéric Bantignies
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  5. Valerio Orlando
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Contributions

C.L. performed all 3C experiments, FISH analysis on Drosophila S2 and S3 cells and part of statistical analysis. V.R. and F.B. performed FISH experiments on embryos and helped C.L. with FISH analysis in S2 and S3 cells. J.D. provided unpublished protocols on 3C technology and suggested crucial control experiments. V.O. designed the experiments, participated in data analysis and presentation, and prepared the manuscript together with C.L. At all stages, all authors discussed the results and gave a substantial contribution to the final manuscript.

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Correspondence to Valerio Orlando.

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Lanzuolo, C., Roure, V., Dekker, J. et al. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol 9, 1167–1174 (2007). https://doi.org/10.1038/ncb1637

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