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.
Bibliographical noteFunding Information:
URLs. Vienna Campus Support Facility (CSF), http://www.csf. ac.at/; Austrian Academy of Sciences, http://www.oeaw.ac.at/; European Union Framework Programme 6 Network of Excellence ‘The Epigenome’, http://www.epigenome-noe.net/; European Union Framework Programme 7 Network of Excellence ‘Epigenesys’, http://www.epigenesys.eu/; FWF Austrian Science Fund, http://www. fwf.ac.at/en/; Definiens XD software, http://www.definiens.com/ product-services/definiens-xd-product-suite.html; Vienna Drosophila Resource Center (VDRC), http://stockcenter.vdrc.at/; modENCODE, http://www.modencode.org/; FANTOM3 CAGE summary data set, http://fantom31p.gsc.riken.jp/cage_analysis/export/mm5/; liftOver tool, https://genome.ucsc.edu/cgi-bin/hgLiftOver; R/Bioconductor, http://www.R-project.org/; dm3 and mm9 RefSeq gene annotation, http://genome.ucsc.edu/.
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)øGFP 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.).