Local effect of enhancer of zeste-like reveals cooperation of epigenetic and cis-acting determinants for zygotic genome rearrangements

PLoS Genet. 2014 Sep 25;10(9):e1004665. doi: 10.1371/journal.pgen.1004665. eCollection 2014 Sep.

Abstract

In the ciliate Paramecium tetraurelia, differentiation of the somatic nucleus from the zygotic nucleus is characterized by massive and reproducible deletion of transposable elements and of 45,000 short, dispersed, single-copy sequences. A specific class of small RNAs produced by the germline during meiosis, the scnRNAs, are involved in the epigenetic regulation of DNA deletion but the underlying mechanisms are poorly understood. Here, we show that trimethylation of histone H3 (H3K27me3 and H3K9me3) displays a dynamic nuclear localization that is altered when the endonuclease required for DNA elimination is depleted. We identified the putative histone methyltransferase Ezl1 necessary for H3K27me3 and H3K9me3 establishment and show that it is required for correct genome rearrangements. Genome-wide analyses show that scnRNA-mediated H3 trimethylation is necessary for the elimination of long, repeated germline DNA, while single copy sequences display differential sensitivity to depletion of proteins involved in the scnRNA pathway, Ezl1- a putative histone methyltransferase and Dcl5- a protein required for iesRNA biogenesis. Our study reveals cis-acting determinants, such as DNA length, also contribute to the definition of germline sequences to delete. We further show that precise excision of single copy DNA elements, as short as 26 bp, requires Ezl1, suggesting that development specific H3K27me3 and H3K9me3 ensure specific demarcation of very short germline sequences from the adjacent somatic sequences.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Transposable Elements
  • Epigenesis, Genetic*
  • Gene Rearrangement*
  • Genome, Protozoan*
  • Histones / metabolism
  • Macronucleus
  • Methylation
  • Paramecium tetraurelia / classification
  • Paramecium tetraurelia / genetics*
  • Paramecium tetraurelia / metabolism
  • Phylogeny
  • Polyploidy
  • Protein Interaction Domains and Motifs
  • Protein Transport
  • Protozoan Proteins / chemistry
  • Protozoan Proteins / genetics
  • Protozoan Proteins / metabolism
  • Sequence Deletion
  • Zygote / metabolism*

Substances

  • DNA Transposable Elements
  • Histones
  • Protozoan Proteins

Grant support

This work was supported by the ANR-2010-BLAN-1603 “GENOMAC”, the ANR-12-BSV6-0017 “INFERNO”, a CNRS ATIP-Plus grant to SD. MLA, AF, CDW were supported by Ph.D. fellowships from the Ministère de l’Enseignement Supérieur et de la Recherche, and MLA was recipient of a fellowship from the Fondation de la Recherche Médicale. We acknowledge the ImagoSeine facility, member of the France BioImaging infrastructure supported by the ANR-10-INSB-04. The sequencing benefited from the facilities and expertise of the high-throughput sequencing platform of IMAGIF (Centre de Recherche de Gif - www.imagif.cnrs.fr). This study was carried out in the context of the CNRS-supported European Research Group “Paramecium Genome Dynamics and Evolution”, the European COST Action BM1102 and the LABEX “Who am I?” supported by the ANR-11-LABX-0071_WHOAMI and the ANR-11-IDEX-0005-02. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.