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. 2016 Nov;48(11):1436-1442.
doi: 10.1038/ng.3671. Epub 2016 Sep 19.

Coordinate Redeployment of PRC1 Proteins Suppresses Tumor Formation During Drosophila Development

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Free PMC article

Coordinate Redeployment of PRC1 Proteins Suppresses Tumor Formation During Drosophila Development

Vincent Loubière et al. Nat Genet. .
Free PMC article

Abstract

Polycomb group proteins form two main complexes, PRC2 and PRC1, which generally coregulate their target genes. Here we show that PRC1 components act as neoplastic tumor suppressors independently of PRC2 function. By mapping the distribution of PRC1 components and trimethylation of histone H3 at Lys27 (H3K27me3) across the genome, we identify a large set of genes that acquire PRC1 in the absence of H3K27me3 in Drosophila larval tissues. These genes massively outnumber canonical targets and are mainly involved in the regulation of cell proliferation, signaling and polarity. Alterations in PRC1 components specifically deregulate this set of genes, whereas canonical targets are derepressed in both PRC1 and PRC2 mutants. In human embryonic stem cells, PRC1 components colocalize with H3K27me3 as in Drosophila embryos, whereas in differentiated cell types they are selectively recruited to a large set of proliferation and signaling-associated genes that lack H3K27me3, suggesting that the redeployment of PRC1 components during development is evolutionarily conserved.

Conflict of interest statement

Competing Financial Interests Statement

The authors declare that they have no competing financial interests.

Figures

Fig. 1
Fig. 1. Differential effects of PRC1 and PRC2 mutations on tumorigenesis
A- DAPI staining shows that PRC1 mutants (phdel, PcXT109 and Psc-Su(z)21.b8) overgrow while PRC2 mutants (E(z)731 and Su(z)121) exhibit small eye phenotype. B- Double staining of PH or H3K27me3 and of the ELAV neuronal differentiation marker. Dashed squares indicate higher magnification. C- Staining of the F-actin polarity marker. White dashed lines indicate the positions of the XZ and YZ cross-sections shown respectively below and to the right of each panel. D- Staining of the Hox UBX protein in PRC1 and PRC2 mutants, as indicated. E- Staining of PH or H3K27me3 and of N in PRC1 and PRC2 mutants, as indicated. Scale bars are 50 µm in B, C, E and 100 µm in A, D. The morphogenetic furrow (MF) is indicated by arrowheads and discs are oriented with the posterior on the right side.
Fig. 2
Fig. 2. Massive redeployment of PRC1 from canonical to neo PRC1 gene targets during development
A- Venn diagram showing the overlap of PcG PRC1-PRC2 target genes in embryos and in eye imaginal discs. B- Venn diagram representing the overlap of genes marked only by PC/PH in the absence of the H3K27me3 mark (PRC1 only targets) in wild type embryos and in third instar eye imaginal discs. C- ChIP-Seq for PC, PH and H3K27me3 in embryos and eye imaginal discs for PRC1-PRC2 targets illustrated at the Bithorax complex (BXC), at chinmo, danr and dan. Significantly enriched regions are shown as horizontal bars under each ChIP-Seq track. D- Distribution of PC/PH and of H3K27me3 mark in embryos and eye imaginal discs at neo PRC1 target genes. E- Scatter plots showing the ChIP-Seq signal levels of PC or PH versus H3K27me3 on their targets in embryos and larval eye discs. Regions that were already enriched in embryos are shown in orange, whereas green indicates targeting in larval stage only. A control random set of H3K27me3 negative regions is represented in grey. F- qChIP for PC, PH and PSC from the PRC1 complex, SU(Z)12 from the PRC2 complex and for H3K27me3. Results are normalized using the PGRP-LE gene (negative control). Error bars represent the s.d of three experiments. G- Comparative Gene Ontology (GO) analysis of the maintained versus neo PcG targets in eye imaginal discs. The number of PcG target genes in each GO category is indicated in brackets. The fraction of bound genes and p-values are indicated by the size and color of each spot.
Fig. 3
Fig. 3. PRC1 represses transcriptionally active neo PRC1 targets.
A- ChIP-Seq profiles for PC, PH, H3K27me3 and H3K27Ac in the BXC locus in eye imaginal discs. Enriched regions are shown under each ChIP-Seq track. B- ChIP-Seq profiles as above in a set of neo PRC1 target loci. C- qChIP against H3K27Ac on a set of canonical and neo PRC1 target genes. Results are normalized using the Antp gene (negative control). Error bars represent the s.d of three experiments. D- Scatter plot showing the ChIP-Seq distribution of H3K27me3 and H3K27Ac. PRC1-PRC2 target sites (in black) mainly carry H3K27me3 while neo PRC1 target sites (in red) carry H3K27Ac. The H3K27Ac and H3K27me3 enrichments are anti-correlated with a spearman’s rank correlation coefficient ρ of –0,79. E- Venn diagram showing the overlap of the different classes of PcG target genes with the H3K27Ac mark, based on genome-wide ChIP-Seq data analysis in eye imaginal discs. F- Percentage of upregulated genes in RNA-seq of PRC1 (ph505 and Psc1.b8) or PRC2 (E(z)731 and Su(z)121) mutant eye discs. G- Comparative Gene Ontology (GO) analysis of genes upregulated in PRC1 (ph505 and Psc1.b8) or PRC2 (E(z)731 and Su(z)121 ) mutants, stratified by categories of PcG ChIP-Seq targets. The total number of upregulated genes in each GO category is indicated in brackets. The fraction of bound genes that are upregulated in each category of PcG targets and the p-values are indicated by the size and the color of each spot.
Fig. 4
Fig. 4. PcG proteins localize to a large set of DNA-unmethylated CpG islands in the absence of H3K27me3 in differentiated human cells.
A- Venn diagram showing the overlap of RING1B target genes (in red) and genes carrying H3K27me3 (in white) in human ES cells (ES), K562 myelogenous leukemia cells and foreskin fibroblasts (Hs68). B- ChIP-Seq profiles for RING1B and H3K27me3 in ES at the HOXD complex. Significantly enriched regions are shown as horizontal bars under each ChIP-Seq track C- ChIP-Seq profiles for RING1B and H3K27me3 at a set of PRC1 loci in K562 cells. D- ChIP-Seq profiles for RING1B and H3K27me3 at a set of PRC1 loci in Hs68 cells. E- Comparative Gene Ontology (GO) analysis of canonical versus non-canonical PcG targets in ES, K562 and Hs68 cells. The total number of PcG target genes in each GO category is indicated in brackets. The fraction of bound genes and the p-values are indicated by the size and the color of each spot, respectively. F- KEGG pathways enriched in the non-canonical targets in K562 cells. G- KEGG pathways enriched in the non-canonical targets in Hs68 cells. H- Heat maps and profiles of percentage of DNA methylation, occupancies of RING1B, BMI1, EZH2, SUZ12, H3K27me3 and H3K27Ac within -/+ 5kb from RING1B peaks in K562 cells.

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