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A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element

Nature Genetics volume 46, pages 973981 (2014) | Download Citation


Polycomb/Trithorax response elements (PRE/TREs) can switch their function reversibly between silencing and activation by mechanisms that are poorly understood. Here we show that a switch in forward and reverse noncoding transcription from the Drosophila melanogaster vestigial (vg) PRE/TRE switches the status of the element between silencing (induced by the forward strand) and activation (induced by the reverse strand). In vitro, both noncoding RNAs inhibit PRC2 histone methyltransferase activity, but, in vivo, only the reverse strand binds PRC2. Overexpression of the reverse strand evicts PRC2 from chromatin and inhibits its enzymatic activity. We propose that the interaction of RNAs with PRC2 is differentially regulated in vivo, allowing regulated inhibition of local PRC2 activity. Genome-wide analysis shows that strand switching of noncoding RNAs occurs at several hundred Polycomb-binding sites in fly and vertebrate genomes. This work identifies a previously unreported and potentially widespread class of PRE/TREs that switch function by switching the direction of noncoding RNA transcription.

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We thank S. Gasser for discussions and for critical reading of the manuscript. We thank M. Rehmsmeier and members of our laboratories for discussions, P. Pasierbek for advice and training on imaging, P.A. Steffen (IMBA) for the GFP and E(z)GFP constructs, C. Ehrhardt and E. Dworschak for technical assistance, B. Dickson (Janelia Farm) for the enGAL4 driver line, J.M. Dura (Institute of Human Genetics, Montpelier, France) for the daGAL4 driver line, I. Tamir (CSF Vienna) for the bioinformatics analysis of ChIP-seq data and sharing the 'Fuge' algorithm, F. Bantignies (Institute of Human Genetics, Montpelier, France) for advice on three-dimensional DNA FISH, R. Jones (Dedman College, Southern Methodist University) for providing antibody to E(Z) and the Vienna Campus Support Facility (CSF) for library preparation, deep sequencing and the purification of Drosophila PRC2. This work was funded by the Austrian Academy of Sciences, by European Community grants European Union Framework Programme 6 Network of Excellence 'The Epigenome' (to L.R.) and the European Union Framework Programme 7 Network of Excellence 'Epigenesys' (to L.R.), and by an FWF Austrian Science Fund grant (P21525-B20 to L.R.).

Author information

Author notes

    • Veronika A Herzog
    •  & Adelheid Lempradl

    These authors contributed equally to this work.


  1. IMBA (Institute of Molecular Biotechnology), Vienna, Austria.

    • Veronika A Herzog
    • , Adelheid Lempradl
    • , Johanna Trupke
    • , Helena Okulski
    • , Christina Altmutter
    • , Frank Ruge
    • , Andrew Dimond
    • , Hasene Basak Senergin
    •  & Leonie Ringrose
  2. Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.

    • Adelheid Lempradl
    • , Marius Ruf
    •  & Andrew Pospisilik
  3. CeMM (Research Center for Molecular Medicine), Vienna, Austria.

    • Bernd Boidol
    •  & Stefan Kubicek
  4. IMP (Institute of Molecular Pathology), Vienna, Austria.

    • Gerald Schmauss
    •  & Karin Aumayr
  5. The Babraham Institute, Babraham Research Campus, Cambridge, UK.

    • Andrew Dimond
  6. Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA.

    • Marcus L Vargas
    •  & Jeffrey A Simon


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A.L. and L.R. initiated the project. L.R., V.A.H. and A.L. designed the experiments. J.T. performed bioinformatics analysis of genome-wide data sets. G.S. and K.A. performed automated image analysis of three-dimensional DNA FISH. V.A.H., A.L., H.O., C.A., F.R., B.B., A.D., M.R., H.B.S. and L.R. conducted the experiments and analyzed the data. S.K. supervised B.B. A.P. supervised M.R. M.L.V. and J.A.S. provided purified Drosophila PRC2 and polynucleosome substrates. L.R. prepared the manuscript with input from V.A.H., J.T., A.L., B.B. and H.O.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Leonie Ringrose.

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–10 and Supplementary Tables 1 and 3.

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  1. 1.

    PcG-bound regions in fly and mouse that show convergent or divergent transcripts.

    Genomic coordinates of PcG-bound regions with the identity of the closest gene. See the Online Methods and legend in the table for details. (a) mouse_CAGE. Mouse ES cell PcG peaks from ref. 34 that overlap with convergent or divergent CAGE tags from the FANTOM3 CAGE dataset32. In mouse, the CAGE data provide tags from multiple developmental stages and tissues, and the majority of the PcG-bound peaks have multiple tags. Individual tags are not listed in the table, and the coordinates of these are available on request. (b) Fly_modENCODE_MACE. Fly PcG peaks from ref. 21 that overlap with convergent or divergent MACE tags from ref. 20. (c) Fly_modENCODE_MACE_tags. Fly PcG peaks from ref. 21 that overlap with convergent or divergent MACE tags from ref. 20 showing all MACE tags overlapping with each peak. (d) Fly_modENCODE_CAGE. Fly PcG peaks from ref. 21 that overlap with convergent or divergent CAGE tags from ref. 31. (e) Fly_modENCODE_CAGE_tags. Fly PcG peaks from ref. 21 that overlap with convergent or divergent CAGE tags from ref. 31 showing all CAGE tags overlapping with each peak. The source of tag data is listed as 'peaks' (indicating data from CAGE peaks in Supplemental Data File 4 of ref. 31), or 'file 3' (indicating RACE and other annotated transcript start sites from Supplemental Data File 3 of ref. 31). (f) Fly_Enderle_MACE. Fly PcG peaks from ref. 20 that overlap with convergent or divergent MACE tags from the same study. (g) Fly_Enderle_MACE_tags. Fly PcG peaks from ref. 20 that overlap with convergent or divergent MACE tags from the same study showing all MACE tags overlapping with each peak. (h) Fly_Enderle_CAGE. Fly PcG peaks from ref. 20 that overlap with convergent or divergent CAGE tags from ref. 31. (i) Fly_Enderle_CAGE_tags. Fly PcG peaks from ref. 20 that overlap with convergent or divergent CAGE tags from ref. 31 showing all CAGE tags overlapping with each peak.


  1. 1.

    Three-dimensional animation of vg mRNA showing downregulation upon noncoding RNA expression.

    The animation shows the three-dimensional reconstruction of the z stack from the double in situ hybridizations shown in Figure 3l-n. The animation shows a transgenic 3rd instar larval wing disc overexpressing the forward strand from pKC27vg.fwd′ under the control of the enGAL4 driver, which expresses in the posterior half of the disc. At the start of the animation, posterior is to the left, anterior is to the right. The domain of enGAL4 expression was defined in three dimensions using the noncoding RNA signal and is shown in green at the start of the animation, with the remaining ones shown in blue. As the animation plays, first the blue mask and then the green mask is removed, showing the in situ signals: green, forward noncoding RNA; red, vg mRNA; blue, DAPI. Subsequently, the noncoding RNA and DAPI channels are removed, leaving the vg mRNA signal in the red channel. The image is then rotated to show the downregulation of vg mRNA in the posterior part of the disc. See also Figure 3l-p.

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