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. 2014 Jun 12;7(5):1456-1470.
doi: 10.1016/j.celrep.2014.04.012. Epub 2014 May 22.

Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment

Sarah Cooper  1 , Martin Dienstbier  2 , Raihann Hassan  1 , Lothar Schermelleh  3 , Jafar Sharif  4 , Neil P Blackledge  5 , Valeria De Marco  6 , Sarah Elderkin  7 , Haruhiko Koseki  4 , Robert Klose  5 , Andreas Heger  2 , Neil Brockdorff  8
Affiliations

Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment

Sarah Cooper et al. Cell Rep. .

Abstract

The mechanisms by which the major Polycomb group (PcG) complexes PRC1 and PRC2 are recruited to target sites in vertebrate cells are not well understood. Building on recent studies that determined a reciprocal relationship between DNA methylation and Polycomb activity, we demonstrate that, in methylation-deficient embryonic stem cells (ESCs), CpG density combined with antagonistic effects of H3K9me3 and H3K36me3 redirects PcG complexes to pericentric heterochromatin and gene-rich domains. Surprisingly, we find that PRC1-linked H2A monoubiquitylation is sufficient to recruit PRC2 to chromatin in vivo, suggesting a mechanism through which recognition of unmethylated CpG determines the localization of both PRC1 and PRC2 at canonical and atypical target sites. We discuss our data in light of emerging evidence suggesting that PcG recruitment is a default state at licensed chromatin sites, mediated by interplay between CpG hypomethylation and counteracting H3 tail modifications.

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Figures

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Graphical abstract
Figure 1
Figure 1
PcG Complexes Localize to PCH in Response to Loss of DNA Methylation (A) IF of Dnmt TKO and WT cells stained for H2AK119u1 (PRC1) or H3K27me3 (PRC2), and DNA stained with DAPI. Yellow lines show total nuclear area (left) and PCH domains (right) based on DAPI staining defined by the ImageJ threshold algorithm Triangle. (B) Graph showing the percentage of cells with PCH foci positive for H2AK119u1 or H3K27me3 in WT or Dnmt TKO cells. Bars show average (n > 200 DAPI foci) ± SD (n = 3). (C) Box and whisker plot showing quantification of fluorescence intensities at PCH domains. The total nuclear area and PCH domains were defined as shown by the yellow lines in (A). Fluorescence intensity (H2AK119u1 or H3K27me3 staining) was calculated within the defined PCH domains in either WT or Dnmt TKO cells and is expressed relative to the fluorescence intensity within the total nuclear area of the cell (n = 20, p values Student’s t test, unpaired). Scale bars represent 5 μm. See also Figure S1.
Figure 2
Figure 2
PcG Complexes Are Dynamically Acquired at PCH upon Loss of DNA Methylation (A) Southern blot showing loss of DNA methylation over time upon loss of Uhrf1. Genomic DNA from WT, Dnmt TKO, or tamoxifen-induced deletion of Uhrf1 in conditional knockout cells (0–120 hr) was digested with the methylation-sensitive enzyme HpyCH41V and the blot was probed for major satellite repeats. (B) IF of conditional knockout Uhrf1−/− cells (72 hr, tamoxifen treatment) stained for H2AK119u1 or H3K27me3. Arrowheads indicate an example of staining within PCH. (C) Graph showing the percentage of cells with H3K27me3 or H2AK119u1 foci during the Uhrf1−/− deletion time course. Bars show average (n > 200 cells) ± SD (n = 3). (D) IF of Dnmt1−/− (and control) MEF cells stained for H2AK119u1 and H3K27me3. Arrowheads indicate a single PCH domain. Scale bars represent 5 μm. See also Figure S2.
Figure 3
Figure 3
H3K9me3 Antagonizes PRC2, but Not PRC1 (A) IF of Dnmt TKO cells costained for H2AK119u1 and HP1α. The graph shows a profile plot of fluorescence intensity (arbitrary units [A.U.]) across a single PCH domain (2 μM) defined by DAPI and marked on the merge image as a yellow bar. (B) As in (A), but costained for H3K27me3 and H3K9me3. (C) Superresolution 3D-SIM images of Dnmt TKO and WT cells stained with H3K27me3 (green), H3K9me3 (red), and DAPI (blue). Upper panels show a single xy plane and bottom panels show an orthogonal xz plane. Arrowheads indicate the cutting plane. Middle panels show a single PCH region (delineated with a white line), and merges show overlap of each color. Arrowheads mark H3K27me3 staining within PCH in Dnmt TKO cells. (D) Stable knockdown of Suv3-9h1/h2 or a scrambled control in Uhrf1−/− cells costained for H3K27me3 and H3K9me3. Profile plots as in (A) across a single PCH domain, marked on the merge image as a yellow bar. (E) Graph showing the percentage of DAPI foci staining for H3K27me3 in Uhrf1−/− cells with either scrambled control or stable knockdown (KD) of Suv3-9h1/h2. Bars show average (n > 200 DAPI foci) ± SD (n = 3). Scale bars represent 5 μm (unless otherwise stated). See also Figure S3 and Table S2.
Figure 4
Figure 4
Loss of DNA Methylation Redistributes PcG Complexes Away from Canonical Sites to New Sites Depending on CpG Content and H3K36me3 Occupancy (A) Graph showing at the indicated repeat regions the fold change of reads, normalized to total reads, from ChIP-seq analysis of Input, H3K27me3, Ring1B, and Suz12 in Dnmt TKO relative to WT cells. The %CpG of each repeat class is shown. Two bars represent biological repeats. (B) As in (A), but with fold change at BioCAP-seq positive regions (WT unmethylated CpG regions). (C) Screen shot of one biological repeat of ChIP-seq of H3K27me3, Ring1B, Suz12, and Input in WT and Dnmt TKO cells. (D) ChIP-qPCR of H3K27me3 or H2AK119u1 at canonical targets or new sites in WT and Dnmt TKO cells. Bars show average ± SD (n = 3). (E) Graphs showing a positive fold change in Dnmt TKO versus WT cells using a sliding-window analysis of H3K27me3, Ring1B, and Suz12 ChIP-seq of only BioCAP-seq-negative regions, binned according to CpG content. (F) As in (A), but with fold change at H3K36me3-positive or -negative exons, or introns. See also Figure S4 and Tables S1, S2, and S3.
Figure 5
Figure 5
DNA Methylation Does Not Inhibit PcG Activity Directly (A) Schematic showing in vitro methylation of 601 positioning DNA and reconstitution of dinucleosomes. (B) PRC2 histone methyltransferase assay using 3H SAM and either WT/H3Kc36me3 nucleosomes or WT/methylated DNA nucleosomes as substrate. Top and bottom panels: Coomassie-stained gel; middle panel: autoradiography of dried gel. (C) PRC1 ubiquitylation assay using WT/methylated DNA nucleosomes as substrate, and analyzed by western blot (probed for H2AK119u1 or H3). (D) Schematic of MBD tethering assay to target proteins of interest to regions of methylated DNA. (E) MBD-Ezh2-Flag transfected into E14 ESCs stained for Flag and H3K27me3. The percentage of cells that showed the illustrated phenotype is indicated (n > 200). (F) As in (E), but transfected with MBD-Ring1B-Flag and stained for Flag and H2AK119u1. (G) As in (E), but transfected with MBD-Ezh2-Flag and stained for Flag and H2AK119u1. (H) MBD-Ezh2-Flag transfected into MEFs and stained for Flag and H3K27me3. Scale bars represent 5 μm. See also Figure S5.
Figure 6
Figure 6
KDM2B and Ring1B Recruit PRC2 Activity to PCH Domains (A) Schematic of MBD-KDM2B-Flag indicating the positions of mutations in the JmjC domain (HID-AAA) and the CxxC domain (K-A). (B) MBD-KDM2B transfected into E14 ESCs stained for Flag and H2AK119u1 (left) and Flag and H3K27me3 (right). (C) MBD-KDM2B-Flag catalytic mutant (JmjC mutant HID-AAA) transfected into E14 ESCs stained for Flag and H2AK119u1 (left), and Flag and H3K27me3 (right). (D) Inducible stable line expressing MBD-Ring1B-Flag, stained for Flag and H2AK119u1 3 days after induction with doxycycline (left) and Flag and H3K27me3 (right). (E) Graph showing the percentage of transfected cells with H2AK119u1 (gray) or H3K27me3 (black) PCH foci in cells transfected with WT MBD-KDM2B and catalytically inactive JmjC domain mutant. Bars show average (n > 200 transfected cells) ± SD (n > 3). (F) Graph showing the percentage of cells with H2AK119u1 (gray) or H3K27me3 (black) PCH foci in stable MBD-KDM2B and stable MBD-Ring1B either with or without 3 days induction with doxycycline (n > 100 cells) ± SD (n > 3). Arrowheads indicate an example of staining within Flag domains at PCH. Scale bars represent 5 μm. See also Figures S5 and S6.
Figure 7
Figure 7
Ubiquitylated H2A Is Sufficient to Recruit PRC2 to PCH Domains (A) Structure of the minimal E3 and E2 complex (Bentley et al., 2011), showing the catalytic domain of Pcgf4 (yellow) and Ring1B (orange) interacting with E2 enzyme (blue). RPCD was made by fusing the C terminus (S116) of Ring1B to the N terminus (R3) of Pcgf4 using a 4x GGS flexible linker. Catalytic mutant (mut) RPCD comprised C51G (in Pcgf4) and I53A (in Ring1B). (B) Inducible stable line expressing MBD-RPCD-Flag or MBD-mut-RPCD-Flag, stained for Flag and H2AK119u1 3 days after induction with doxycycline (left) and Flag and H3K27me3 (right). Arrowheads indicate an example of staining within Flag domains at PCH. (C) Graph showing the percentage of cells with H2AK119u1 (gray) or H3K27me3 (black) PCH foci in stable MBD-Ring1B-Flag, MBD-RPCD-Flag, and MBD-mut-RPCD-Flag cell lines, either with or without 3 days induction with doxycycline (n > 100 cells) ± SD (n > 3). (D) Schematic to illustrate potential models of for PRC2 recruitment by H2AK119u1, either by direct/indirect protein interactions “reader” (top) or by “chromatin state” (bottom). Scale bars represent 5 μm. See also Figure S7.
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