Histone H2A Mono-Ubiquitination Is a Crucial Step to Mediate PRC1-Dependent Repression of Developmental Genes to Maintain ES Cell Identity

Two distinct Polycomb complexes, PRC1 and PRC2, collaborate to maintain epigenetic repression of key developmental loci in embryonic stem cells (ESCs). PRC1 and PRC2 have histone modifying activities, catalyzing mono-ubiquitination of histone H2A (H2AK119u1) and trimethylation of H3 lysine 27 (H3K27me3), respectively. Compared to H3K27me3, localization and the role of H2AK119u1 are not fully understood in ESCs. Here we present genome-wide H2AK119u1 maps in ESCs and identify a group of genes at which H2AK119u1 is deposited in a Ring1-dependent manner. These genes are a distinctive subset of genes with H3K27me3 enrichment and are the central targets of Polycomb silencing that are required to maintain ESC identity. We further show that the H2A ubiquitination activity of PRC1 is dispensable for its target binding and its activity to compact chromatin at Hox loci, but is indispensable for efficient repression of target genes and thereby ESC maintenance. These data demonstrate that multiple effector mechanisms including H2A ubiquitination and chromatin compaction combine to mediate PRC1-dependent repression of genes that are crucial for the maintenance of ESC identity. Utilization of these diverse effector mechanisms might provide a means to maintain a repressive state that is robust yet highly responsive to developmental cues during ES cell self-renewal and differentiation

Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity

10 páginas, 7 figuras, 1 tabla -- PAGS nros. 1513-1524The Polycomb group (PcG) proteins mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes 1 (PRC1) and 2 (PRC2). Although PRC2 has been shown to share target genes with the core transcription network, including Oct3/4, to maintain embryonic stem (ES) cells, it is still unclear whether PcG proteins and the core transcription network are functionally linked. Here, we identify an essential role for the core PRC1 components Ring1A/B in repressing developmental regulators in mouse ES cells and, thereby, in maintaining ES cell identity. A significant proportion of the PRC1 target genes are also repressed by Oct3/4. We demonstrate that engagement of PRC1 at target genes is Oct3/4-dependent, whereas engagement of Oct3/4 is PRC1-independent. Moreover, upon differentiation induced by Gata6 expression, most of the Ring1A/B target genes are derepressed and the binding of Ring1A/B to their target loci is also decreased. Collectively, these results indicate that Ring1A/B-mediated Polycomb silencing functions downstream of the core transcriptional regulatory circuitry to maintain ES cell identityThis work was supported in part by a grant from the Genome Network Project (to H.K.) and a grant-in-aid for Scientific Research on Priority Areas (17045038, to M.E.) from the Ministry of Education, Culture, Sports, Science and Technology, JapanPeer reviewe

H2A ubiquitination activity of Ring1B is essential for the maintenance of ESC identity and repression of target gene expression.

<p>(A) Morphology of OHT-untreated and –treated (day 8) <i>Ring1A^−/−; Ring1B^fl/fl; R26::CreERT2</i> ESC lines expressing the indicated transgene. The images were acquired under a phase-contrast microscope. Scale bars indicate 200 µm. (B) Histograms showing the expression changes of H2AK119u1+ and H2AK119u1− genes in <i>Ring1A^−/−; Ring1B^fl/fl; Rosa26::CreERT2</i> ESCs expressing mock (blue line), WT Ring1B (red line), or mutant Ring1B (green dotted line) following OHT treatment. (C) Expression levels of <i>Hoxa9</i>, <i>Hoxb13</i>, <i>Hoxd11</i>, <i>Zic1</i>, <i>Pax3</i> and <i>Pou5f1</i> in <i>Ring1A^−/−; Ring1B^fl/fl; Rosa26::CreERT2</i> ESCs expressing mock, WT, I53S, or I53A Ring1B before (−) or after (+) OHT treatment (day 2). Expression levels were normalized to a <i>Gapdh</i> control and are depicted as fold changes relative to mock (OHT-untreated) ESCs. Error bars represent standard deviation determined from at least three independent experiments. (D) Local levels of trimethylated H3K4 (H3K4me3) at promoter regions of representative target genes in <i>Ring1A^−/−; Ring1B^fl/fl; R26::CreERT2</i> ESCs stably expressing mock, WT, I53S, or I53A Ring1B before (−) or after (+) OHT treatment (day 2) were determined by ChIP and site-specific real-time PCR. The relative amount of immunoprecipitated DNA is depicted as a percentage of input DNA. Error bars represent standard deviation determined from at least three independent experiments. (E) As in (D), but showing local levels of RNA polymerase II (RNAP) detected with the 8WG16 antibody.</p

Global mapping of Ring1B-dependent H2AK119u1 deposition in ESCs reveals that genes occupied by H2AK119u1 represent central targets of PRC1.

<p>(A) ChIP-on-chip analysis showing the average of H2AK119u1 distributions at the promoter regions (from −5 kb to +5 kb relative to TSS) of Ring1B-bound and –unbound genes in <i>Ring1A^−/−</i> (OHT−: green line) and <i>Ring1A/B</i>-dKO (OHT+: red line) ESCs. Enrichment of H2AK119u1 (obtained by E6C5 mAb) and H2A is expressed relative to input DNA, and H2AK119u1 is normalized to H2A. (B) Venn diagram representing the overlap among genes occupied by Ring1B, H2AK119u1 and H3K27me3. Numbers in parentheses represent the total number of genes occupied by each one. (C) Graphic representation of expression changes induced by <i>Ring1B</i> depletion (2 days after OHT treatment) for each subset of genes classified by the presence (+) or absence (−) of Ring1B, H2AK119u1 and H3K27me3 is shown. The average, deviation and distribution of the expression changes for the respective subsets of genes determined by microarray analysis are shown. The 95% Confidence interval (CI) and standard deviation (SD) for the average value of the expression change are indicated. Significant (<i>P</i><0.001) and insignificant (<i>P</i>≥0.01) expression changes were determined by the Student's <i>t</i>-test and are indicated in orange and grey, respectively. <i>P</i>-values for the difference of expression changes between the indicated 2 groups are calculated by the Student's <i>t</i>-test and are indicated above each graph.</p

Generation of ESCs expressing catalytically inactive Ring1B.

<p>(A) Schematic representation of 3xFlag-tagged Ring1B, showing wild-type and point-mutant derivatives. Each of these construct was stably transfected into <i>Ring1A^−/−; Ring1B^fl/fl; R26::CreERT2</i> ESCs. (B) Immunoblot analysis of Ring1A, Ring1B, Flag, H2AK119u1 and Lamin B protein levels in whole cell lysates of <i>wild-type</i> and <i>Ring1A^−/−; Ring1B^fl/fl; R26::CreERT2</i> ESC lines expressing mock, WT, I53S, or I53A Ring1B with or without OHT treatment (OHT+ and −, respectively). (C) Immunoprecipitation (IP) analysis showing the association of exogenous Ring1B WT, I53S or I53A with an endogenous PRC1 component Mel18. Extracts of OHT-untreated (−) and -treated [(+); day 2] <i>Ring1A^−/−; Ring1B^fl/fl; R26::CreERT2</i> ESC lines expressing each of the constructs were immunoprecipitated with anti-Flag antibody. Resulting precipitates (IP) and lysates (Input) were immunoblotted with antibodies against Flag, Ring1B and Mel18. (D) Association of Flag-tagged proteins in <i>Ring1A^−/−; Ring1B^fl/fl; R26::CreERT2</i> ESC lines stably expressing mock, Flag-tagged Ring1B WT, I53S, or I53A with promoter regions of their representative target genes before (−) or after (+) OHT treatment (day 2) as determined by ChIP and site-specific real-time PCR. Error bars represent standard deviations determined from three independent experiments. (E) 3D FISH with probe pairs at <i>Hoxb</i> locus (<i>Hoxb1</i> and <i>Hoxb13</i>) in PFA-fixed nuclei of <i>Ring1A^−/−; Ring1B^fl/fl; R26::CreERT2</i> ESC lines stably expressing mock, WT, I53S, or I53A Ring1B before (−) or after (+) OHT treatment (day 2). Scale bars indicate 1 µm. The boxes show the median and interquartile range of interprobe distances (µm) in the indicated cells. Open circles indicate outliers. The statistical significance of differences between the indicated two data was examined by the Mann-Whitney U test.</p

A schematic summary of this study demonstrating that PRC1-dependent repression of developmental genes in ES cells is mediated by multiple effector mechanisms.

<p>A schematic summary of this study demonstrating that PRC1-dependent repression of developmental genes in ES cells is mediated by multiple effector mechanisms.</p