Polycomb in Transcriptional Phase Transition of Developmental Genes

doi:10.1016/j.tibs.2015.11.005

Trends in Biochemical Sciences

Volume 41, Issue 1, January 2016, Pages 9-19

https://doi.org/10.1016/j.tibs.2015.11.005 Get rights and content

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Polycomb group factors form mainly two distinct protein complexes, Polycomb repressive complex (PRC)1 and PRC2; both of which are central players in transcriptional repression of developmental genes.

PRCs are highly diversified and form many functionally different complexes. Particularly, PRC1 exists as at least six different stable complexes. Recent research supports a new model for PRC recruitment to chromatin, in which variant PRC1.1 initiates PRC recruitment and transcriptional repression.

Emerging data show that PRCs are involved in regulation of higher-order chromatin organization, by which PRCs could contribute to both induced activation and repression of target gene transcription by regulating promoter–enhancer association.

PRC1 subcomplexes could be differentially used to confer reversibility and robustness to PcG-dependent transcriptional regulation of developmental genes.

Combinatorial associations between distinct chromatin domains, namely promoters and cis-regulatory elements, determine transcriptional status. Developmental regulatory gene expression, mostly regulated by the Polycomb/Trithorax group of chromatin regulators, is often temporally and spatially specific, and sometimes changes repeatedly within the same cell lineage. Dysregulated expression of these genes causes morphological and/or functional disorganization of tissues and organs. Therefore, maintenance of both the active and negative states of transcription is equally important. In this review, we summarize the mechanisms of transition between transcriptional status of developmental regulators, including complex processes for enhancer activation and promoter–enhancer association. In particular, we propose testable models in which Polycomb group factors contribute to promoter–enhancer associations and thus proper gene expression.

Section snippets

Expression of Developmental Regulatory Factors: Spatiotemporal Precision and Reversibility

Developmental regulators are generally expressed in a tissue- and stage-specific manner to modulate patterning, differentiation, and proliferation. Morphological and/or functional defects in loss-of-function and gain-of-function mutants suggest that both the repression and activation of these genes are equally crucial for normal development and lifelong tissue homeostasis 1, 2, 3, 4. Notably, this also implies that there could be evolutionarily conserved mechanisms to ensure the developmental

PcG Factors Repress Expression of Developmental Genes

PcG factors were first identified in Drosophila melanogaster as a group of regulators for the Hox (homeotic) cluster genes 15, 16. Remarkably, mutation of these factors caused mis-specification of anterior–posterior segments because of aberrant expression of Hox genes. Since then, a vast number of studies have shown that PcG proteins mediate repressive chromatin structures, at Hox and other target genes, which can be inherited across multiple rounds of cell division [17].

PcG factors mediate

PcG Factors Balance Robust Repression and Activation of Genes

Although PcG factors bind promoter regions of genes, they also mediate interactions between distantly separated genomic regions, which could contribute not only to repression but also activation of genes in a spatiotemporal manner 6, 23, 35, 36, 37, 38. One study used transgenic mice to shows that binding of PcG factors at a CGI in the promoter of human α-globin is regulated by tissue-specific enhancers [39]. In addition, a recent study demonstrated that PcG factors are required to mediate

Activation of Tissue-Specific Enhancers

Activation of tissue-specific enhancers may require two distinct classes of transcription factors (TFs) that cooperate with various epigenetic modifiers to endorse stepwise progression towards enhancer activation (Figure 3, Table 1). The first class is the pioneering TFs, which bind to their target sites; the second class is the inductive TFs, which bring coactivators to target sites for gene activation. In the inactive state, a prospective enhancer sequence, possibly along with methylated

Activation of PcG-Repressed Promoters by Active Enhancers

In general, promoter activation is considered to follow enhancer activation [64]. Repressed promoters of developmental regulator genes are bound by PcG factors and some TrxG factors (i.e., MLL1/2) and consequently marked by H3K27me3, H2AK119u1 and H3K4me3 in ES cells (Figure 4A) 65, 66. This may imply that promoters of developmental regulator genes are already bound by PcG factors and are predisposed to inducible activation by activated enhancers as early as the epiblast stage. Therefore, both

Targeting of PcG Factors by Active Enhancers

To the best of our knowledge, functional and substantial interactions between putative bridging factors and PcG factors during transcriptional regulation have not been reported. However, a functional link between Cohesin complexes and PcG factors has been shown to mediate sister chromatid interactions during Drosophila meiosis [73]. Furthermore, another recent study in Drosophila showed PcG-mediated gene silencing induced by heat shock stress was closely associated with changes in higher-order

Silencing of Active Promoters by PcG Factors

One of the important functions of developmental regulators is to maintain the multipotent and/or premature status of stem or precursor cells. However, since persistent expression of such genes even could affect cellular differentiation 82, 83, they also have to be silenced upon progression of developmental processes or terminal differentiation.

The role of PcG in such processes has been studied in developing neural precursors, in which PcG factors contribute to progressive repression of

Concluding Remarks

In this review, we summarized how PcG factors regulate developmental regulatory genes with an emphasis on their potential roles in promoter–enhancer interactions. The molecular actions of PcG factors at CGI promoters of developmental regulators may be closely linked to enhancer activity particularly during phase transition of transcriptional status. We propose that PcG factor function can be divided into two distinct aspects: robust maintenance of repression, and transition between active and

Acknowledgments

We would like to thank the members of RIKEN-Koseki and KAST laboratories for daily helpful discussions; and Kit-Wan Ma and Jafar Sharif for critical reading of the manuscript. H.K. and T.K. are supported by SIP from the government cabinet office and a Grant-in-Aid from NEXT. T.K. is also funded by the Regional Innovation Program from NEXT.

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The polycomb group protein Bmi1 maintains hematopoietic stem cell (HSC) functions. We previously reported that Bmi1-deficient mice exhibited progressive fatty changes in bone marrow (BM). A large portion of HSCs reside in the perivascular niche created partly by endothelial cells and leptin receptor⁺ (LepR⁺) BM stromal cells. To clarify how Bmi1 regulates the HSC niche, we specifically deleted Bmi1 in LepR⁺ cells in mice. The Bmi1 deletion promoted the adipogenic differentiation of LepR⁺ stromal cells and caused progressive fatty changes in the BM of limb bones with age, resulting in reductions in the numbers of HSCs and progenitors in BM and enhanced extramedullary hematopoiesis. This adipogenic change was also evident during BM regeneration after irradiation. Several adipogenic regulator genes appeared to be regulated by Bmi1. Our results indicate that Bmi1 keeps the adipogenic differentiation program repressed in BM stromal cells to maintain the integrity of the HSC niche.
Ezh1 Targets Bivalent Genes to Maintain Self-Renewing Stem Cells in Ezh2-Insufficient Myelodysplastic Syndrome
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Citation Excerpt :
In the well-established model, PRC2-induced H3K27me3 recruits canonical PRC1, containing CBX as the H3K27me3-binding module. On the other hand, recent studies have reported the existence of variant PRC1s, which lack CBX proteins but bind to a stretch of unmethylated CpG sites and induce H2AK119ub1, independently of PRC2 (Blackledge et al., 2015; Holoch and Margueron, 2017; Kondo et al., 2016). Comprehensive genome sequencing studies identified change-of-function mutations in EZH2, which increase H3K27me3 levels and reduce H3K27me2 levels, in patients with follicular and diffuse large B-cell lymphomas (Morin et al., 2010).
Polycomb repressive complex (PRC) 2 represses transcription through histone H3K27 trimethylation (H3K27me3). We previously reported that the hematopoietic-cell-specific deletion of Ezh2, encoding a PRC2 enzyme, induced myelodysplastic syndrome (MDS) in mice, whereas the concurrent Ezh1 deletion depleted hematopoietic stem and progenitor cells (HSPCs). We herein demonstrated that mice with only one Ezh1 allele (Ezh1^+/-Ezh2^Δ/Δ) maintained HSPCs. A chromatin immunopreciptation sequence analysis revealed that residual PRC2 preferentially targeted genes with high levels of H3K27me3 and H2AK119 monoubiquitination (H2AK119ub1) in HSPCs (designated as Ezh1 core target genes), which were mostly developmental regulators, and maintained H3K27me3 levels in Ezh1^+/-Ezh2^Δ/Δ HSPCs. Even upon the complete depletion of Ezh1 and Ezh2, H2AK119ub1 levels were largely retained, and only a minimal number of Ezh1 core targets were de-repressed. These results indicate that genes marked with high levels of H3K27me3 and H2AK119ub1 are the core targets of polycomb complexes in HSPCs as well as MDS stem cells.
Polycomb group RING finger proteins 3/5 activate transcription via an interaction with the pluripotency factor Tex10 in embryonic stem cells
2017, Journal of Biological Chemistry
Citation Excerpt :
A canonical PRC1 complex contains one of five different Cbx protein subunits (Cbx2/4/6/7/8) that specifically interact with H3K27me3 via its chromodomain and enable PRC1 recruitment to its target loci (38). Despite the recent advances made in understanding the role of PcG complexes in the epigenetic regulation of gene repression involved in various developmental processes (7, 39), how some of these complexes may interact with the general transcription machinery to contribute to the transcriptional activation remains elusive. In this study, we found that, in contrast to the canonical role of PRC1 in gene repression, Pcgf3/5 predominantly act as transcriptional activators driving expression of a number of genes involved in mesoderm differentiation.
Polycomb group (PcG) proteins are epigenetic transcriptional repressors that orchestrate numerous developmental processes and have been implicated in the maintenance of embryonic stem (ES) cell state. More recent evidence suggests that a subset of PcG proteins engages in transcriptional activation in some cellular contexts, but how this property is exerted remains largely unknown. Here, we generated ES cells with single or combined disruption of polycomb group RING finger protein 3 (Pcgf3) and Pcgf5 with the CRISPR-Cas9 technique. We report that although these mutant cells maintained their self-renewal and colony-forming capacity, they displayed severe defects in mesoderm differentiation in vitro and in vivo. Using RNA-seq to analyze transcriptional profiles of ES cells with single or combined Pcgf3/5 deficiencies, we found that in contrast to the canonical role of the related polycomb repressive complex 1 (PRC1) in gene repression, Pcgf3/5 mainly function as transcriptional activators driving expression of many genes involved in mesoderm differentiation. Proteomic approaches and promoter occupancy analyses helped to establish an extended Pcgf3/5 interactome and identified several novel Pcgf3/5 interactors. These included testis-expressed 10 (Tex10), which may directly contribute to transcriptional activation via the transcriptional co-activator p300. Furthermore, Pcgf3/5 deletion in ES cells substantially reduced the occupancy of Tex10 and p300 at target genes. Finally, we demonstrated that Pcgf3/5 are essential for regulating global levels of the histone modifier H2AK119ub1 in ES cells. Our findings establish Pcgf3/5 as transcriptional activators that interact with Tex10 and p300 in ES cells and point to redundant activity of Pcgf3/5 in pluripotency maintenance.
PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation
2017, Cell Stem Cell
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Therefore, the PE chromatin signature was proposed to bookmark a limited set of regulatory sequences in pluripotent cells and facilitate their timely and lineage-specific activation once the appropriate differentiation cues become available (Rada-Iglesias et al., 2011). Following their original description, the relevance of PEs was questioned, as they were also found in non-pluripotent cells, where they were proposed to display an inactive rather than poised state or to act as silencers (Bonn et al., 2012; Entrevan et al., 2016; Kondo et al., 2016; Spitz and Furlong, 2012). Most importantly, the functional relevance of PEs for the induction of cognate genes and the execution of somatic differentiation programs remains to be formally demonstrated (Rada-Iglesias et al., 2011; Zentner et al., 2011).
Poised enhancers marked by H3K27me3 in pluripotent stem cells have been implicated in the establishment of somatic expression programs during embryonic stem cell (ESC) differentiation. However, the functional relevance and mechanism of action of poised enhancers remain unknown. Using CRISPR/Cas9 technology to engineer precise genetic deletions, we demonstrate that poised enhancers are necessary for the induction of major anterior neural regulators. Interestingly, circularized chromosome conformation capture sequencing (4C-seq) shows that poised enhancers already establish physical interactions with their target genes in ESCs in a polycomb repressive complex 2 (PRC2)-dependent manner. Loss of PRC2 does not activate poised enhancers or induce their putative target genes in undifferentiated ESCs; however, loss of PRC2 in differentiating ESCs severely and specifically compromises the induction of major anterior neural genes representing poised enhancer targets. Overall, our work illuminates an unexpected function for polycomb proteins in facilitating neural induction by endowing major anterior neural loci with a permissive regulatory topology.
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Activation of the Meis2 gene requires a topological switch mediated by RING1B resulting in an association between the Meis2 gene promoter and an enhancer. In the absence of RING1B, the enhancer can no longer contact the promoter region, resulting in impaired Meis2 gene expression (Box 2) [105]. Here, in contrast to the study of Schoenfelder et al., RING1B is thus required to mediate promoter–enhancer interactions to activate Meis2 gene expression.
Polycomb group (PcG) proteins dynamically define cellular identities through the epigenetic repression of key developmental regulatory genes. PcG proteins are recruited to specific regulatory elements to modify the chromatin surrounding them. In addition, they regulate the organization of their target genes in the 3D space of the nucleus, and this regulatory function of the 3D genome architecture is involved in cell differentiation and the maintenance of cellular memory. In this review we discuss recent advances in our understanding of how PcG proteins are recruited to chromatin to induce local and global changes in chromosome conformation and regulate their target genes.
The Complex Macromolecular Complex
2016, Trends in Biochemical Sciences

View all citing articles on Scopus

⁴: These authors contributed equally to this work.

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Trends in Biochemical Sciences

OpinionSpecial Issue: 40 Years of TiBSPolycomb in Transcriptional Phase Transition of Developmental Genes

Trends

Section snippets

Expression of Developmental Regulatory Factors: Spatiotemporal Precision and Reversibility

PcG Factors Repress Expression of Developmental Genes

PcG Factors Balance Robust Repression and Activation of Genes

Activation of Tissue-Specific Enhancers

Activation of PcG-Repressed Promoters by Active Enhancers

Targeting of PcG Factors by Active Enhancers

Silencing of Active Promoters by PcG Factors

Concluding Remarks

Acknowledgments

Transfection of a DNA locus that mediates the conversion of 10T1/2 fibroblasts to myoblasts

Cell

Craniofacial abnormalities induced by ectopic expression of the homeobox gene Hox-1.1 in transgenic mice

Cell

Regionally restricted developmental defects resulting from targeted disruption of the mouse homeobox gene hox-1.5

Nature

Mutations affecting segment number and polarity in Drosophila

Nature

The role of Hox genes during vertebrate limb development

Curr. Opin. Genet. Dev.

Polycomb potentiates meis2 activation in midbrain by mediating interaction of the promoter with a tissue-specific enhancer

Dev. Cell

What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory

Nat. Rev. Mol. Cell Biol.

Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes

Curr. Opin. Genet. Dev.

Locking in stable states of gene expression: transcriptional control during Drosophila development

Curr. Opin. Cell Biol.

Posterior transformation, neurological abnormalities, and severe hematopoietic defects in mice with a targeted deletion of the bmi-1 proto-oncogene

Genes Dev.

Altered Hox expression and segmental identity in Mll-mutant mice

Nature

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

Cell

Polycomb complexes repress developmental regulators in murine embryonic stem cells

Nature

Control of developmental regulators by Polycomb in human embryonic stem cells

Cell

A gene complex controlling segmentation in Drosophila

Nature

Polycomblike: a gene that appears to be required for the normal expression of the bithorax and antennapedia gene complexes of Drosophila melanogaster

Genetics

Mechanisms of polycomb gene silencing: knowns and unknowns

Nat. Rev. Mol. Cell Biol.

Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites

Cell

Histone methyltransferase activity of a Drosophila Polycomb group repressor complex

Cell

Role of histone H3 lysine 27 methylation in Polycomb-group silencing

Science

The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans

Mol. Cell. Biol.

Role of histone H2A ubiquitination in Polycomb silencing

Nature

SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing

Dev. Cell

The growth-suppressive function of the polycomb group protein polyhomeotic is mediated by polymerization of its sterile alpha motif (SAM) domain

J. Biol. Chem.

Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity

PLoS Genet.

PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes

Mol. Cell

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

Elife

Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation

Mol. Cell

Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes

Nat. Cell Biol.

Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation

Cell

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

Cell Rep.

Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression

Nat. Struct. Mol. Biol.

Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation

Genes Dev.

The E3 ubiquitin ligase activity of RING1B is not essential for early mouse development

Opinion
Special Issue: 40 Years of TiBS
Polycomb in Transcriptional Phase Transition of Developmental Genes