Polycomb domain formation depends on short and long distance regulatory cues

PLoS One. 2013;8(2):e56531. doi: 10.1371/journal.pone.0056531. Epub 2013 Feb 20.

Abstract

Background: Polycomb group (PcG) proteins dynamically define cellular identities through the epigenetic repression of key developmental genes. In Drosophila, cis-regulatory regions termed PcG response elements (PREs) act as nucleation sites for PcG proteins to create large repressive PcG domains that are marked by trimethylation of lysine 27 on histone H3 (H3K27me3). In addition to an action in cis, PREs can interact over long distances, thereby enhancing PcG dependent silencing. How PcG domains are established, which factors limit their propagation in cis, and how long range interactions of PREs in trans affect the chromatin structure is largely unknown.

Principal findings: We demonstrate that the insertion of a PRE-containing transgene in the Drosophila genome generates an artificial PcG domain and we analyze its organization by quantitative ChIP and ChIP-on-chip experiments. Intriguingly, a boundary element and known insulator proteins do not necessarily interfere with spreading of H3K27me3. Instead, domain borders correlate with the presence of promoter regions bound by RNA Polymerase II and active chromatin marks. In contrast, genes that are silent during early fly development get included within the PcG domain and this incorporation interferes with gene activation at later developmental stages. Moreover, trans-interaction of the transgenic PRE with its homologous endogenous PRE results in increased PcG binding, correlating with reinforced silencing of genes within the domain borders.

Conclusions: Our results suggest that higher-order organization of PcG-bound chromatin can stabilize gene silencing within PcG domains. Further we propose that multi-protein complexes associated with active promoters are able to define the limits of PcG domains. Future work aimed to pinpoint the factors providing this barrier function will be required to understand the precise molecular mechanism by which active promoter regions can act as boundaries to stop spreading of H3K27me3.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / genetics*
  • DNA-Binding Proteins / genetics
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / growth & development
  • Gene Expression Regulation, Developmental
  • Histone Demethylases / genetics*
  • Histone Demethylases / metabolism
  • Histones / genetics
  • Histones / metabolism
  • Homeodomain Proteins / genetics
  • Polycomb-Group Proteins / genetics*
  • Promoter Regions, Genetic
  • Protein Structure, Tertiary / genetics
  • Response Elements / genetics

Substances

  • Chromatin
  • DNA-Binding Proteins
  • Histones
  • Homeodomain Proteins
  • Polycomb-Group Proteins
  • Histone Demethylases

Grant support

Research in the lab of GC was funded by the Centre National de la Recherche Scientifique, the Human Frontiers in Science Program Organization, the European Union FP 6 (Network of Excellence “The Epigenome”) and FP 7 (Network of Excellence EpigeneSys), the Association pour la Recherche sur le Cancer, the Agence Nationale pour la Recherche (ANR - iPolycomb) and the European Research Council (Advanced Investigator grant FlyingPolycomb). BS was supported by a fellowship of the Fondation de la Recherche Médicale and by the Institut National de la Santé et de la Recherche Médicale. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.