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Polycombing the Genome: PcG, trxG, and Chromatin Silencing
... All these observations suggest that PREs are able to interact through the PcG complexes, therefore, discreet arrays of PREs could cooperate to establish a silenced structure either by creating a three-dimensional compact structure or just relaying the repressive activity as it has been proposed for the subtelomeric silencing elements in yeast (Fourel et al., 1999;reviewed in Simon, 1995;Pirrotta, 1995Pirrotta, , 1998. ...
... These sequences could be some minor PREs or PRE helpers. Such observation support a mechanism by which silencing complexes would be formed through the interaction of proteins bound to discreet sequences on the DNA that create a compact globular folded structure responsible for the silencing (Hop-and-skip model;Pirrotta, 1995Pirrotta, , 1998 Similarly, we observed a better maintenance with construct 8XS∆HS1∆196, 8XS∆HS1∆192, 8XS∆HS1∆193 than with construct 8XS∆HS1∆iab-8. This is probably the result of the presence of sequences of varying strength, which cooperate with the PRE in the distal fragment to strengthen the maintenance by freezing the initiated state. ...
The first part of this document explains the basics of the developmental genetics of Drosophila: why it is a model organism for more than a century, which genes are involved in its development, what is the function of the HOX genes (and their relevance in Human development) and how is organized the bithorax complex (BX-C) in Drosophila melanogaster.
The second part describes the results obtained thanks to the research I carried out during my doctoral studies which aimed to scan the entire Abd-B cis-regulatory area, molecularly and genetically. New regulatory elements (initiators, boundaries, enhancers…) have been identified and localized molecularly (e.g. Fab-8) via transgenic molecular constructs using reporter genes, and have been validated thanks to Drosophila mutants (genomic deletions, translocations…)
The third and last part of the document proposes a model of molecular regulation of the Abd-B gene based on the new regulatory elements discovered.
... H3K27 methylation and EZH2 in health and cancer SET domain containing EZH2 (Enhancer-of-zeste homolog 2) and its close homolog EZH1 catalyze mono-, diand tri-methylation of H3K27 [118][119][120]. EZH2 was originally identified as a member protein of the Polycomb Repressive Complex 2 (PRC2), which functions as a transcription repressor of Hox gene clusters important to the development [121][122][123]. In 2002, it was further determined to be a methyltransferase of H3K27 [118][119][120]. ...
... Complexation with EED and SUZ12, two other members in PRC2, is required to methylate H3K27 [124,125]. The biology of EZH2-containing PRC2 as well as their mediated H3K27 methylation has been reviewed [121][122][123]126]. Briefly, EZH2 is essential for embryonic development and plays important roles in normal physiology. ...
Post-translational methylation of histone lysine or arginine residues plays important roles in gene regulation and other physiological processes. Aberrant histone methylation caused by a gene mutation, translocation, or overexpression can often lead to initiation of a disease such as cancer. Small molecule inhibitors of such histone modifying enzymes that correct the abnormal methylation could be used as novel therapeutics for these diseases, or as chemical probes for investigation of epigenetics. Discovery and development of histone methylation modulators are in an early stage and undergo a rapid expansion in the past few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Several compounds have been in clinical trials for safety, pharmacokinetics, and efficacy, targeting several types of cancer. This review summarizes the biochemistry, structures, and biology of cancer-relevant histone methylation modifying enzymes, small molecule inhibitors and their preclinical and clinical antitumor activities. Perspectives for targeting histone methylation for cancer therapy are also discussed.
... In Drosophila and mammals, long-term repression of homeotic genes requires the activity of Polycomb group proteins (Pirrotta, 1998). WD Polycomb proteins play an important role in the suppression of gene transcription during insect and mammal embryo development. ...
... Our results suggest that in the female gametophyte, the FIE protein functions to repress the transcription of genes required for replication of the central cell nucleus and subsequent endosperm development. Most likely, FIE, like insect and animal WD Polycomb proteins (Pirrotta, 1998), suppresses gene transcription by forming complexes with other Polycomb group proteins ( Figure 6B). We propose that when fertilization occurs, alteration of complexes containing the FIE Polycomb protein may allow initiation of endosperm gene transcription. ...
A fundamental problem in biology is to understand how fertilization initiates reproductive development. Higher plant reproduction is unique because two fertilization events are required for sexual reproduction. First, a sperm must fuse with the egg to form an embryo. A second sperm must then fuse with the adjacent central cell nucleus that replicates to form an endosperm, which is the support tissue required for embryo and/or seedling development. Here, we report cloning of the Arabidopsis FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) gene. The FIE protein is a homolog of the WD motif–containing Polycomb proteins from Drosophila and mammals. These proteins function as repressors of homeotic genes. A female gametophyte with a loss-of-function allele of fie undergoes replication of the central cell nucleus and initiates endosperm development without fertilization. These results suggest that the FIE Polycomb protein functions to suppress a critical aspect of early plant reproduction, namely, endosperm development, until fertilization occurs.
... 4,5 Subsequently, BMI-1 was found to be a transcriptional repressor belonging to the mouse polycomb protein (PcG) family. 6,7 An epigenetic gene silencing factor, PcG regulates gene activity at the chromatin level by forming at least two multimeric complexes, namely PRC1 and PRC2. Many studies have shown that BMI-1 is frequently upregulated in various human cancer types, and is associated with poor prognosis in solid tumors including lung cancer, 8 medulloblastoma, 9 neuroblastoma, 10 hepatocellular carcinoma, 11 nasopharyngeal carcinoma, 12 and prostate cancer. ...
Breast cancer is among the most common malignant cancers in women. B-cell-specific Moloney murine leukemia virus integration site 1 (BMI-1) is a transcriptional repressor that has been shown to be involved in tumorigenesis, the cell cycle, and stem cell maintenance. In our study, increased expression of BMI-1 was found in both human triple negative breast cancer and luminal A-type breast cancer tissues compared with adjacent tissues. We also found that knockdown of BMI-1 significantly suppressed cell proliferation and migration in vitro and vivo. Further mechanistic research demonstrated that BMI-1 directly bound to the promoter region of CDKN2D/BRCA1 and inhibited its transcription in MCF-7/MDA-MB-231. More importantly, we discovered that knockdown of CDKN2D/BRCA1 could promote cell proliferation and migration after repression by PTC-209. Our results reveal that BMI-1 transcriptionally suppressed BRCA1 in TNBC cell lines, whereas in luminal A cell lines, CDKN2D was the target gene. This provides a reference for the precise treatment of different types of breast cancer in clinical practice.
... Die segmentale Entwicklung in Insekten erfolgt durch die transkriptionelle Aktivierung von Homeobox-(HOX) Domänen enthaltenden Genen (García-Bellido 1975;McGinnis und Krumlauf 1992). In Drosophila sind diese Gene in Gewebe-spezifischen Mustern durch zahlreiche Enhancer während der larvalen Entwicklung aktiviert (Beck et al. 2010 (Lanzuolo et al. 2012;Pirrotta 1998;Ringrose und Paro 2004;Schuettengruber et al. 2017). Komponenten der PcG Komplexe sind die PcG Faktoren Polycomb-like (Pcl) und Sex comb on midleg (Scm), Enhancer of zeste (E(z)) oder Supressor of zeste (Su(z)12). ...
To investigate the role of PCGF6 and E2F6 in murine embryonic stem cells (mESCs) and at the beginning of differentiation, knockout cell lines of both proteins and in combination were generated by the CRISPR/Cas9n system. Characterization of these knockout cell lines (KO) was performed by growth analysis in mESCs and differentiating murine stem cells (EBs). It was found that Pcgf6 KO cells formed smaller EBs that also could not be maintained in culture for an extended period. To resolve this specific phenotype, further molecular analyses were performed by flow cytometry (FACS). Cells of the Pcgf6 KO exhibited an increased proportion of cells in G1 phase during differentiation as well as an increased apoptotic frequency. Supporting the assumption of a cell cycle defect, RNASeq data were analysed. It could be shown that cells of the Pcgf6 KO differentiated in a temporally uncontrolled manner. Evaluation of differentially expressed genes revealed that expression of E2f6, a regulator of the cell cycle and another component of the non-canonical PRC1.6, was downregulated in mESC and EB cultures, whereas cell cycle-specific targets of E2F6-dependent gene regulation were upregulated at day 2 of differentiation. These results indicated that deletion of Pcgf6 at the beginning of differentiation must have effects on E2F6-dependent cell cycle regulation. Due to mycoplasma contamination in the cell culture at this time point, the Pcgf6 KO cell line had to be re-established. In addition, KO cell lines of E2f6 in Wt and in Pcgf6 KO mESCs were established. The replication of cellular characterization of the phenotype revealed that EB cultures of the Pcgf6 KO and the double knockout of Pcgf6 and E2f6 (dKOPcgf6/E2f6) exhibited reduced cell numbers during differentiation. Molecular characterizations of the phenotype revealed that the increased proportion of cells in the G1 phase of the Pcgf6 KO, which was detected before mycoplasma contamination, could not be reproduced. However, an increased frequency of cells in the G2 phase of dKOPcgf6/E2f6 was detected in mESC and EB culture. Analysis of apoptotic frequency in all KO cell lines indicated an increase during differentiation. RNASeq data from two publications of PCGF6 and E2F6 were used to support the analyses performed to this point (Qui et al, 2021; Dahlet et al, 2021). Gene Ontology Enrichment analyses of these data revealed that germline genes were independently upregulated in both KO cell lines in mESCs. However, both KO cell lines also showed an overlap of commonly upregulated germline genes. Following these publications, gene expression analysis of individual germline genes revealed that loss of E2f6 leads to de-repression of genes that have a binding site for E2F6. In contrast, loss of Pcgf6 had no effect on expression of these targets. These results, as well as previously published data, support the assumption that there are distinct subcomplexes that regulate the expression of germline genes in mESC and EB cultures.
... These proteins were first discovered in the fruit fly Drosophila melanogaster as transcriptional regulators of key developmental genes known as homeobox (Hox) genes [4][5][6]. PcG proteins are highly conserved from Drosophila to human, and thus their function as transcriptional regulators of mammalian embryonic development and cell differentiation is well recognized [7,8], impacting the expression of genes important for cell fate decisions [9,10], embryogenesis [5,[11][12][13], proliferation and stem cell self-renewal [14,15]. Of note, the balance between homeotic gene silencing and activation is maintained by another heterogeneous group of proteins called the trithorax group (TrxG) [16]. ...
The polycomb group (PcG) proteins are a class of transcriptional repressors that mediate gene silencing through histone post-translational modifications. They are involved in the maintenance of stem cell self-renewal and proliferation, processes that are often dysregulated in cancer. Apart from their canonical functions in epigenetic gene silencing, several studies have uncovered a function for PcG proteins in DNA damage signaling and repair. In particular, members of the poly-comb group complexes (PRC) 1 and 2 have been shown to recruit to sites of DNA damage and mediate DNA double-strand break repair. Here, we review current understanding of the PRCs and their roles in cancer development. We then focus on the PRC1 member BMI1, discussing the current state of knowledge of its role in DNA repair and genome integrity, and outline how it can be targeted pharmacologically.
... Similar to the DNA methylation, SAM was used as the methyl group donor by histone methyltransferases (HMTs), and is removed by histone demethylases (HDMs) (86). Among the HMTs, the polycomb repressive complex 2 (PRC2) is widely known as an H3K27 methyltransferase, which is composed of four core subunits including EZH1/2, SUZ12, EED, and RbAp46/48 (87,88). Notably, H3K4me3 and H3K27me3 are reported to coexist in the promoters as a bivalent mark to fine-tune gene expression (89)(90)(91). ...
Epstein-Barr virus (EBV) infection is associated with a variety of malignancies including Burkitt’s lymphoma (BL), Hodgkin’s disease, T cell lymphoma, nasopharyngeal carcinoma (NPC), and ∼10% of cases of gastric cancer (EBVaGC). Disruption of epigenetic regulation in the expression of tumor suppressor genes or oncogenes has been considered as one of the important mechanisms for carcinogenesis. Global hypermethylation is a distinct feature in NPC and EBVaGC, whereas global reduction of H3K27me3 is more prevalent in EBVaGC and EBV-transformed lymphoblastoid cells. In BL, EBV may even usurp the host factors to epigenetically regulate its own viral gene expression to restrict latency and lytic switch, resulting in evasion of immunosurveillance. Furthermore, in BL and EBVaGC, the interaction between the EBV episome and the host genome is evident with respectively unique epigenetic features. While the interaction is associated with suppression of gene expression in BL, the corresponding activity in EBVaGC is linked to activation of gene expression. As EBV establishes a unique latency program in these cancer types, it is possible that EBV utilizes different latency proteins to hijack the epigenetic modulators in the host cells for pathogenesis. Since epigenetic regulation of gene expression is reversible, understanding the precise mechanisms about how EBV dysregulates the epigenetic mechanisms enables us to identify the potential targets for epigenetic therapies. This review summarizes the currently available epigenetic profiles of several well-studied EBV-associated cancers and the relevant distinct mechanisms leading to aberrant epigenetic signatures due to EBV.
... H3K27 can also be mono-, di-and trimethylated (H3K27me1/me2/me3). H3K27me2/me3, catalyzed by the Polycomb repressive complex2 (PRC2) (Pirrotta, 1998), is enriched at promoters of silenced genes and plays an important role in the silencing of developmentally regulated genes during cell differentiation (Banaszynski et al., 2013;Cao et al., 2002;Margueron and Reinberg, 2011;Simon and Kingston, 2013). certified by peer review) is the author/funder. ...
The lysine 27 to methionine mutation of histone H3.3 (H3.3K27M) is detected in over 75% of diffuse intrinsic pontine glioma (DIPG). The H3.3K27M mutant proteins inhibit H3K27 methyltransferase complex PRC2, resulting in a global reduction of tri-methylation of H3K27 (H3K27me3). Paradoxically, high levels of H3K27me3 were also detected at hundreds of genomic loci. However, it is not known how and why H3K27me3 is redistributed in DIPG cells. Here we show that lower levels of H3.3K27M mutant proteins at some genomic loci contribute to the retention of H3K27me3 peaks. But more importantly, Jarid2, a PRC2-associated protein, strongly correlates the presence of H3K27me3 and relieves the H3.3K27M-mediated inhibition in vivo and in vitro. Furthermore, we show that H3K27me3-mediated silencing of tumor suppressor gene Wilms Tumor 1 (WT1) supports the proliferation of DIPG cells and reaction of WT1 inhibits DIPG proliferation. Together, these studies reveal mechanisms whereby H3K27me3 is retained in the environment of global loss of this mark, and how persistence of this mark contributes to DIPG tumorigenesis.
... Several reports on epigenetic mutants indicate that this regulation occurs through changes in the chromatin state of the corresponding loci, such as post-translational modifications of histones [Engelhorn, 2014 #169]. Histone 3 trimethylation at lysine 27 (H3K27me3) is a repressive modification targeting developmental regulators in all higher eukaryotes and is catalysed by Polycomb Group (PcG) proteins [Pirrotta, 1998Schuettengruber, 2007 #518; Morey, 2010 #395]. Genome-wide studies of H3K27me3 distribution in whole seedlings revealed that this mark targets more than one fourth of all Arabidopsis genes [Zhang, 2007Oh, 2008 #2408;Roudier, 2011 #2385], comprising tissue-or stage-specific regulators of the vegetative to reproductive transition, floral meristem identity genes and all above-mentioned floral homeotic genes. ...
Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes, respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related H3K4me3. However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with transcriptional changes, in a developmental series including Arabidopsis leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prime over changes in H3K27me3 and quantitatively correlate with transcription changes, while H3K27me3 changes occur after prolonged expression changes. Notably, early activation of PcG target genes is dominated by increases in H3K4me3 while H3K27me3 remains present at the locus. Our results reveal H3K4me3 as greater predictor over H3K27me3 for transcription dynamics, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.
... Polycomb repressive complex 1 and 2 (PRC1 and PRC2) function as epigenetic repressors [16]; PRC2 is a histone methyltransferase complex that tri-methylates histone 3 on lysine 27 to produce H3K27me3 [17]. H3K27me3 is a hallmark of transcriptional repression [11]. ...
Epigenetic modifications regulate normal physiological, as well as pathological processes in various organs, including the uterus and placenta. Both organs undergo dramatic and rapid restructuring that depends upon precise orchestration of events. Epigenetic changes that alter transcription and translation of gene-sets regulate such responses. Histone modifications alter the chromatin structure, thereby affecting transcription factor access to gene promoter regions. Binding of histones to DNA is regulated by addition or removal of subunit methyl and other groups, which can inhibit or stimulate transcription. Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PRC2) that catalyzes tri-methylation of histone H3 at Lys 27 (H3K27me3) and subsequently suppresses transcription of genes bound by such histones. Uterine EZH2 expression exerts a critical role in development and function of this organ with deletion of this gene resulting in uterine hyperplasia and expression of cancer-associated transcripts. Elucidating the roles of EZH2 in uterus and placenta is essential as EZH2 dysregulation is associated with several uterine and placental pathologies. Herein, we discuss EZH2 functions in uterus and placenta, emphasizing its physiological and pathological importance.
... Consistent with impaired cellular proliferation, homozygous-null embryos are smaller in size than wild-type embryos and do not survive past midgestation (Faust et al. 1995;O'Carroll et al. 2001;Cao and Zhang 2004;Pasini et al. 2004). Classically, PcG components were described in Drosophila as suppressors of the homeotic HOX gene cluster, which control body segmentation and morphology during embryogenesis (Lewis 1978;Pirrotta 1998). PRC2 has retained conserved functions across phyla, binding to genes involved in development, morphogenesis, organogenesis, and neurogenesis in both human and murine embryonic stem cells Bracken et al. 2006;Lee et al. 2006). ...
Within histone H3, lysine 27 (H3K27) is one of the residues that functions as a molecular switch, by virtue of being subject to mutually exclusive post-translational modifications that have reciprocal effects on gene expression. Whereas acetylation of H3K27 is associated with transcriptional activation, methylation at this residue causes transcriptional silencing; these two modifications are mutually exclusive. Establishment of these epigenetic marks is important in defining cellular identity and for maintaining normal cell function, as evidenced by rare genetic disorders of epigenetic writers involved in H3K27 post-translational modification. Polycomb repressive complex (PRC2)-related overgrowth and Rubinstein-Taybi syndrome (RSTS) are respectively associated with impaired H3K27 methylation and acetylation. Whereas these syndromes share commonalities like intellectual disability and susceptibility to cancers, they are generally divergent in their skeletal growth phenotypes, potentially through dysregulation of their opposing H3K27 writer functions. In this review, we discuss the requirement of H3K27 modifications for successful embryogenesis, highlighting data from relevant mouse knockout studies. Although such gene ablation studies are integral for defining fundamental biological roles of methyl- and acetyltransferase function in vivo, studies of partial loss-of-function models are likely to yield more meaningful translational insight into progression of PRC2-related overgrowth or RSTS. Thus, modeling of rare human PRC2-related overgrowth and RSTS variants in mice is needed to fully understand the causative role of aberrant H3K27 modification in the pathophysiology of these syndromes.
... In stem cells, the polycomb group (PcG) proteins, a particular family of transcriptional repressors, are key regulators of cell self-renewal and cell fate commitment [71][72][73][74][75]. PcG possess several stable gene repressing functions, among which these proteins establish a repressive chromatin structure, inhibit the chromatin remodeling system, prevent the transcriptional initiation organization and also inhibit the interactions of enhancer/promoter that enable transcription [76]. PRC1 and PRC2, two distinct PRCs, cooperate at the initial site of repression and induce epigenetic modifications of chromatin to enable gene silencing [77,78]. PRC1 includes Cbx, Mph, Ring, Bmi-1, and Me118. ...
Adult stem/progenitor are a small population of cells that reside in tissue-specific niches and possess the potential to differentiate in all cell types of the organ in which they operate. Adult stem cells are implicated with the homeostasis, regeneration, and aging of all tissues. Tissue-specific adult stem cell senescence has emerged as an attractive theory for the decline in mammalian tissue and organ function during aging. Cardiac aging, in particular, manifests as functional tissue degeneration that leads to heart failure. Adult cardiac stem/progenitor cell (CSC) senescence has been accordingly associated with physiological and pathological processes encompassing both non-age and age-related decline in cardiac tissue repair and organ dysfunction and disease. Senescence is a highly active and dynamic cell process with a first classical hallmark represented by its replicative limit, which is the establishment of a stable growth arrest over time that is mainly secondary to DNA damage and reactive oxygen species (ROS) accumulation elicited by different intrinsic stimuli (like metabolism), as well as external stimuli and age. Replicative senescence is mainly executed by telomere shortening, the activation of the p53/p16INK4/Rb molecular pathways, and chromatin remodeling. In addition, senescent cells produce and secrete a complex mixture of molecules, commonly known as the senescence-associated secretory phenotype (SASP), that regulate most of their non-cell-autonomous effects. In this review, we discuss the molecular and cellular mechanisms regulating different characteristics of the senescence phenotype and their consequences for adult CSCs in particular. Because senescent cells contribute to the outcome of a variety of cardiac diseases, including age-related and unrelated cardiac diseases like diabetic cardiomyopathy and anthracycline cardiotoxicity, therapies that target senescent cell clearance are actively being explored. Moreover, the further understanding of the reversibility of the senescence phenotype will help to develop novel rational therapeutic strategies.
... Fraser and Grosveld, 1998;Festenstein and Kioussis, 2000). Grunstein, 1997aGrunstein, , 1998 Pirrotta, 1998;Jacobs and van Lohuizen, 1999). ...
HIRA was isolated during positional cloning of the region of chromosome 22ql1 commonly deleted in DiGeorge Syndrome (DGS), a complex developmental anomaly thought to arise from the failure of neural crest cells to migrate or interact properly during early development. HIRA is a good candidate for a gene contributing to DGS, since Hira expression is particularly high in the developing neuroepithelium and the rostral neural crest. Hira -/- knockout mice indicate a critical role for Hira during development, demonstrating embryonic lethality by E10 with a wide range of malformation. HIRA encodes a WD40 repeat protein with strong similarity to two yeast transcriptional co-repressors HIR1 and HIR2, and the chromatin assembly factor CAF1 p60 subunit. HIRA also has similarity to the transcriptional co-repressor TUP1. Such homologies suggested HIRA might function as part of a protein complex, and a yeast two-hybrid screen of an early mouse embryonic library identified a number of potential HIRA interactors. Among these were several homeodomain-containing transcription factors including Pax3, Pax7 and Otx2, as well as core histones H3 and H2B. These interactions have been confirmed in vitro and the Pax3 interaction domain mapped. The effect of HIRA on Pax3- and Otx2-mediated transcription at target promoters has been investigated in cell transfection experiments. HIRA is able to stimulate Pax3-driven expression from the MITF promoter, yet a ternary complex between HIRA, Pax3 and DNA cannot be demonstrated by EMSA. HIRA has also been shown to stimulate transcription from several other unrelated promoters, suggesting that HIRA may effect transcription of a whole range of genes, although the mechanism by which this is achieved is unclear. Preliminary studies have been performed to examine HIRA-containing complexes to try to elucidate the mode of action of HIRA in transcriptional regulation. Sucrose gradient sedimentation analysis has revealed the presence of large HIRA- containing complexes and future work will focus on the analysis of these. Immunofluorescence studies in transfected cells reveal that HIRA shows a varied localisation pattern that may be under some sort of control. Preliminary data indicates that this may be related to the cell cycle, and this will be further investigated.
... Polycomb group (PcG) proteins were originally identified in Drosophila and are involved in silencing homeotic genes by maintaining the repressed chromatin state [24,25]. PcG proteins recognize and interact with polycomb response elements (PREs) that are scattered throughout the genome to silence expression of genes containing PREs and nearby genes in Drosophila [26]. Most PcG proteins form two major polycomb repressive complexes (PRC)-PRC1 and PRC2 [27]. ...
Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important transcriptional regulators during seed development. Histone modifications and small RNA pathways add another layer of complexity in regulating seed development. In summary, multiple epigenetic pathways are pivotal in regulating seed development. It remains to be elucidated how these epigenetic pathways interplay to affect dynamic chromatin structure and control reproduction.
... Polycomb-group (PcG) proteins play essential roles in epigenetically repressing or activating genes transcription in animals and plants, and are implicated in stable and heritable transcriptional silencing or activating of target genes during organism development [1][2][3][4][5]. PcG proteins are evolutionarily conserved and are involved in various aspects of plant development, such as the timing of flowering and seed development [3,[6][7][8], and response to abiotic and biotic stresses [9]. ...
Background:
Polycomb group (PcG) proteins play important roles in animal and plant development and stress response. Polycomb repressive complex 1 (PRC1) and PRC2 are the key epigenetic regulators of gene expression, and are involved in almost all developmental stages. PRC1 catalyzes H2A monoubiquitination resulting in transcriptional silencing or activation. The PRC1 components in the green lineage were identified and evolution and conservation was analyzed by bioinformatics techniques. RING Finger Protein 1 (RING1), B lymphoma Mo-MLV insertion region 1 homolog (BMI1), Like Heterochromatin Protein 1 (LHP1) and Embryonic Flower 1 (EMF1) are the PRC1 core components and Vernalization 1 (VRN1), VP1/ABI3-Like 1/2/3 (VAL1/2/3), Alfin-like 1-7 (AL1-7), Inhibitor of growth 1/2 (ING1/2), and Early Bolting in Short Days (EBS) / Short Life (SHL) are the associated factors.
Results:
Each PRC1 subunit possesses special domain organizations, such as RING and the ring finger and WD40-associated ubiquitin-like (RAWUL) domains for RING1 and BMI1, chromatin organization modifier (CHROMO) and chromo shadow (ChSh) domains for LHP1, one or two B3 DNA binding domain(s) for VRN1, B3 and zf-CW domains for VAL1/2/3, Alfin and Plant HomeoDomain (PHD) domains for AL1-7, ING and PHD domains for ING1/2, Bromoadjacent homology (BAT) and PHD domains for EBS/SHL. Six new motifs are uncovered in EMF1. The PRC1 core components RING1 and BMI1, and the associated factors VAL1/2/3, AL1-7, ING1/2, and EBS/SHL exist from alga to higher plants, whereas LHP1 only occurs in higher plants. EMF1 and VRN1 are present only in eudicots. PRC1 components undergo duplication in the plant evolution. Most of plants carry the homologous core component LHP1, the associated factor EMF1, and several homologs in RING1, BMI1, VRN1, AL1-7, ING1/2/3, and EBS/SHL. Cabbage, cotton, poplar, orange and maize often exhibit more gene copies than other species. Domain organization analysis shows that duplicated gene functions may be of diverse.
Conclusions:
The PRC1 core components RING1 and BMI1, and the associated factors VAL1/2/3, AL1-7, ING1/2, and EBS/SHL originate from algae. The core component LHP1 is from moss and the associated factors EMF1 and VRN1 are from dicotyledon. PRC1 components are of functional redundancy and diversity in evolution.
... B cell-specific Moloney murine leukemia virus integration site 1 (BMI1) which was identified as a c-myc-cooperating oncogene, is a critical transcriptional repressor for maintenance of proper gene expression during development [164][165][166]. INK4a locus, which encodes p16 and p19 Arf , is an important target of BMI1 and overexpression of BMI1 extends replicative lifespan of human fibroblasts, probably through suppressing the p16-mediated senescence pathway [167,168]. ...
Cellular senescence is a major hurdle for primary cell-based tissue engineering and regenerative medicine. Telomere erosion, oxidative stress, the expression of oncogenes and the loss of tumor suppressor genes all may account for the cellular senescence process with the involvement of various signaling pathways. To establish immortalized cell lines for research and clinical use, strategies have been applied including internal genomic or external matrix microenvironment modification. Considering the potential risks of malignant transformation and tumorigenesis of genetic manipulation, environmental modification methods, especially the decellularized cell-deposited extracellular matrix (dECM)-based preconditioning strategy, appear to be promising for tissue engineering-aimed cell immortalization. Due to few review articles focusing on this topic, this review provides a summary of cell senescence and immortalization and discusses advantages and limitations of tissue engineering and regeneration with the use of immortalized cells as well as a potential rejuvenation strategy through combination with the dECM approach.
... The Drosophila Homeotic/Hox genes are activated in a tissue-specific pattern by numerous enhancers during early embryonic development. Their transcriptional status are then maintained by epigenetic mechanisms mediated by the Polycomb Group (PcG) and Trithorax Group (Trx-G) complexes in late development [39][40][41][42][43] . As both enhancer-and chromatin-mediated transcriptional regulation are influences by the formation of chromatin loops, the homeotic/Hox complexes provide a good model for elucidating the mechanism and regulation of genomic loops. ...
The three-dimensional organization of the eukaryotic genome is important for its structure and function. Recent studies indicate that hierarchies of chromatin loops underlie important aspects of both genomic organization and gene regulation. Looping between insulator or boundary elements interferes with enhancer-promoter communications and limits the spread active or repressive organized chromatin. We have used the SF1 insulator in the Drosophila Antennapedia homeotic gene complex (ANT-C) as a model to study the mechanism and regulation of chromatin looping events. We reported previously that SF1 tethers a transient chromatin loop in the early embryo that insulates the Hox gene Sex comb reduce from the neighbor non-Hox gene fushi tarazu for their independent regulation. To further probe the functional range and connectivity of SF1, we used high-resolution chromosomal conformation capture (3C) to search for SF1 looping partners across ANT-C. We report here the identification of three distal SF1 Tether Elements (STEs) located in the labial, Deformed and Antennapedia Hox gene regions, extending the range of SF1 looping network to the entire complex. These novel STEs are bound by four different combinations of insulator proteins and exhibit distinct behaviors in enhancer block, enhancer-bypass and boundary functions. Significantly, the six STEs we identified so far map to all but one of the major boundaries between repressive and active histone domains, underlining the functional relevance of these long-range chromatin loops in organizing the Hox complex. Importantly, SF1 selectively captured with only 5 STEs out of ~20 sites that display similar insulator binding profiles, indicating that presence of insulator proteins alone is not sufficient to determine looping events. These findings suggest that selective interaction among diverse STE insulators organize the Drosophila Hox genes in the 3D nuclear space.
... In general, histone acetylation at lysine positions, such as H3K9, 14, and 56, signifies transcription initiation [22,23]; trimethylation at H3K36 is a hallmark of transcription elongation [23], while H3K27 trimethylation (H3K27me3) is a key repressive histone mark which plays an important role during brain development, neuron specification, and function [24][25][26][27]. The H3K27 methylation mark is set up by the polycomb repressive complex 2 (PRC2) [28,29]. Mammalian PRC2 consists of four core components: enhancer of zeste (EZH), embryonic ectoderm development (EED), suppressor of zeste 12 homolog (SUZ12), and RbAp46/48 [30]. ...
Testis-specific protein, Y-encoded-like 2 (TSPYL2) is an X-linked gene in the locus for several neurodevelopmental disorders. We have previously shown that Tspyl2 knockout mice had impaired learning and sensorimotor gating, and TSPYL2 facilitates the expression of Grin2a and Grin2b through interaction with CREB-binding protein. To identify other genes regulated by TSPYL2, here, we showed that Tspyl2 knockout mice had an increased level of H3K27 trimethylation (H3K27me3) in the hippocampus, and TSPYL2 interacted with the H3K27 methyltransferase enhancer of zeste 2 (EZH2). We performed chromatin immunoprecipitation (ChIP)-sequencing in primary hippocampal neurons and divided all Refseq genes by k-mean clustering into four clusters from highest level of H3K27me3 to unmarked. We confirmed that mutant neurons had an increased level of H3K27me3 in cluster 1 genes, which consist of known EZH2 target genes important in development. We detected significantly reduced expression of genes including Gbx2 and Prss16 from cluster 1 and Acvrl1, Bdnf, Egr3, Grin2c, and Igf1 from cluster 2 in the mutant. In support of a dynamic role of EZH2 in repressing marked synaptic genes, the specific EZH2 inhibitor GSK126 significantly upregulated, while the demethylase inhibitor GSKJ4 downregulated the expression of Egr3 and Grin2c. GSK126 also upregulated the expression of Bdnf in mutant primary neurons. Finally, ChIP showed that hemagglutinin-tagged TSPYL2 co-existed with EZH2 in target promoters in neuroblastoma cells. Taken together, our data suggest that TSPYL2 is recruited to promoters of specific EZH2 target genes in neurons, and enhances their expression for proper neuronal maturation and function.
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... How these modifications are assembled in a temporal sense is not clear, nor is it clear how precise recruitment of the dizzying numbers of catalytic activities that shape the landscape is enabled. Abundant evidence demonstrates the fact that numerous epigenome regulators exist within multiprotein complexes such as polycomb, trithorax, SAGA which regulate silencing, expression capacity and nucleosome remodeling to name but three (21)(22)(23). ...
The use of epigenome editing is set to expand our knowledge of how epigenetic landscapes facilitate gene expression capacity within a given cell. As epigenetic landscape profiling in health and disease becomes more commonplace, so does the requirement to assess the functional impact that particular regulatory domains and DNA methylation profiles have upon gene expression capacity. That functional assessment is particularly pertinent when analyzing epigenomes in disease states where the reversible nature of histone and DNA modification might yield plausible therapeutic targets. In this review we discuss first the nature of the epigenetic landscape, secondly the types of factors that deposit and erase the various modifications, consider how modifications transduce their signals and lastly address current tools for experimental epigenome editing with particular emphasis on the immune system.
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... This model has been supported by various lines of evidence, with our recent work and others showing that a reduction in condensed heterochromatin promotes DSB repair (Goodarzi et al., 2008;Chiolo et al., 2011;Chen et al., 2015;An et al., 2017). Histone H3 with hyper-methylation at lysine 27 causes another type of repressive chromatin and is often associated with gene silencing via polycomb group protein (PcG) repression (Pirrotta, 1998(Pirrotta, , 1997Kingston, 2009, 2013). The PRC2 complex has been reported to be related to DSB repair (Campbell et al., 2013;Chou et al., 2010;Kakarougkas et al., 2014;Vierra et al., 2017), however, it is not clear whether the aberrant changes in H3K27me2/3 levels caused by pathological events, such as mutations in EZH2 or presence of H3.1K27M, may directly affect DSB repair efficiency, thus altering genome stability and potentially leading to carcinogenesis. ...
Dysregulation of the homeostatic balance of histone H3 di- and tri-methyl lysine 27 (H3K27me2/3) levels caused by the mis-sense mutation of histone H3 (H3K27M) is reported to be associated with various types of cancers. In this study, we found that reduction in H3K27me2/3 caused by H3.1K27M, a mutation of H3 variants found in patients with diffuse intrinsic pontine glioma (DIPG), dramatically attenuated the presence of 53BP1 (also known as TP53BP1) foci and the capability of non-homologous end joining (NHEJ) in human dermal fibroblasts. H3.1K27M mutant cells showed increased rates of genomic insertions/deletions and copy number variations, as well as an increase in p53-dependent apoptosis. We further showed that both hypo-H3K27me2/3 and H3.1K27M interacted with FANCD2, a central player in the choice of DNA repair pathway. H3.1K27M triggered the accumulation of FANCD2 on chromatin, suggesting an interaction between H3.1K27M and FANCD2. Interestingly, knockdown of FANCD2 in H3.1K27M cells recovered the number of 53BP1-positive foci, NHEJ efficiency and apoptosis rate. Although these findings in HDF cells may differ from the endogenous regulation of the H3.1K27M mutant in the specific tumor context of DIPG, our results suggest a new model by which H3K27me2/3 facilitates NHEJ and the maintenance of genome stability.
This article has an associated First Person interview with the first author of the paper.
... PcG proteins mediate transcription repression via binding to conserved DNA sequence elements known as Polycomb response elements (PREs). PREs contain binding sites for the sequence-specific DNA-binding proteins Pleiohomeotic (PHO) and Pleiohomeotic-like (Phol), which are homologs of the ubiquitous mammalian transcription factor Yin Yang-1 (YY1) [14,[16][17][18][19][20][21][22]. PcG recruitment functions via the multifunctional transcription factor YY1. ...
Triple-negative breast cancer (TNBC) has a higher potential for invasion and metastasis than other types of breast cancer. Enhancer of zeste homolog 2 (EZH2) is the catalytic core protein in the polycomb repressive complex 2 (PRC2), which catalyzes the trimethylation of histone H3 at lysine 27 (H3K27me3) and mediates gene silencing of the target genes that are involved in fundamental cellular processes, such as the cell fate decision, cell cycle regulation, senescence, cell differentiation, and cancer formation. A consistent association between TNBC metastasis and EZH2 has not been confirmed. The aim of this study was to investigate the role of EZH2 in the regulation of tissue inhibitor of metalloproteinase (TIMPs) and matrix metalloproteinases (MMPs) to promote metastasis of TNBC cells and to characterize the metastasis-associated genes regulated by EZH2 in TNBC cells. We found that high levels of EZH2 expression induce repression of TIMP2 transcription, leading to increased activity of MMP-2 and MMP-9 and thus to increased invasive activity of TNBC cells.
... Bmi1 is a transcriptional repressor that belongs to the polycomb group family of proteins, which are involved in axial patterning, hematopoiesis, the regulation of proliferation and senescence. [96][97][98][99] Bmi1 was found to be more highly expressed in bladder cancer than it was in adjacent normal tissues, and was related to tumor aggressiveness and patient survival. 99 Furthermore, studies on head and neck cancers showed the direct regulation of Bmi1 by the EMT regulator, Twist1; and Twist1 as well as Bmi1 were found to both be essential to promoting the EMT and tumor-initiating capability, and were associated with a worse prognosis. ...
There is growing evidence of the presence of cancer stem cells in urothelial carcinoma. Cancer stem cells have the ability to self-renew and to differentiate into all cell types of the original heterogeneous tumor. A panel of diverse cancer stem cell markers might be suitable for simulation studies of urothelial cancer stem cells and for the development of optimized treatment protocols. The present review focuses on the advances in recognizing the markers of urothelial cancer stem cells and possible therapeutic targets. The commonly reported markers and pathways that were evaluated include CD44, CD133, ALDH1, SOX2 & SOX4, BMI1, EZH1, PD-L1, MAGE-A3, COX2/PGE2/STAT3, AR, and autophagy. Studies on the epithelial-mesenchymal transition-related pathways (Shh, Wnt/β-catenin, Notch, PI3K/Akt, TGF-β, miRNA) are also reviewed. Most of these markers were recognized through the expression patterns of cancer stem cell-rich side populations. Their regulative role in the development and differentiation of urothelial cancer stem cells was confirmed in vitro by functional analyses (e.g. cell migration, colony formation, sphere formation), and in vivo in xenograft experiments. Although a small number of these pathways are targeted by currently available drugs or drugs that are the currently being tested in clinical trials, a clear treatment approach has not been developed for most pathways. A greater understanding of the mechanisms that control the proliferation and differentiation of cancer stem cells is expected to lead to improvements in targeted therapy.
... Several reports on epigenetic mutants indicate that this regulation occurs through changes in the chromatin state of the corresponding loci, such as post-translational modifications of histones [4]. Histone 3 trimethylation at lysine 27 (H3K27me3) is a repressive modification targeting developmental regulators in all higher eukaryotes and is catalysed by Polycomb Group (PcG) proteins [5][6][7]. Genome-wide studies of H3K27me3 distribution in whole seedlings revealed that this mark targets more than one fourth of all Arabidopsis genes [8][9][10], comprising tissue-or stage-specific regulators of the vegetative to reproductive transition, floral meristem identity genes and all above-mentioned floral homeotic genes. Activation of PcG-repressed genes is conducted by the conserved trithorax Group (trxG) proteins, involved in three main activation processes: (i) removal of repressive H3K27me3 marks; (ii) deposition of activation-associated Histone 3 trimethylation at lysine 4 (H3K4me3) marks; and (iii) chromatin remodelling to allow access of the transcriptional machinery [4,11,12]. ...
Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.
... Interestingly, distinct epigenetic mechanisms distinguish TMPRSS2eERG fusion-positive and -negative prostate cancers (Alumkal and Herman, 2012) and, as previously discussed, DNA methylation and histone modifications are two epigenetic mechanisms responsible for the de-regulation of microRNAs expression (Lujambio et al., 2008). Interestingly, one of the highly upregulated genes during prostate cancer progression is the human homologue of the Drosophila protein Enhancer of Zeste 2 (EZH2), which belongs to the group of polycomb proteins and is involved in silencing of homeobox genes through methylation (Pirrotta, 1998;Hoffmann et al., 2007). ...
Prostate cancer (PCa) is the most common malignancy detected in males and the second most common cause of cancer death in western countries. The development of the prostate gland, is finely regulated by androgens which modulate also its growth and function. Importantly, androgens exert a major role in PCa formation and progression and one of the hypothesized mechanism proposed has been linked to the chromosomal rearrangement of the androgen regulated gene TMPRSS2 with ERG. Androgens have been therefore used as main target for therapies in the past. However, despite the development of endocrine therapies (e.g. androgen ablation), when PCa progress, tumors become resistant to this therapeutic castration and patients develop incurable metastases. A strategy to better understand how patients respond to therapy, in order to achieve a better patient stratification, consists in monitoring the levels of small noncoding RNAs (microRNAs). microRNAs are a class of small molecules that regulate protein abundance and their application as biomarkers to monitor disease progression has been intensely studied in the last years. In this review, we highlight the interactions between microRNAs and endocrine-related aspects of PCa in tissues. We focus on the modulation of TMPRSS2-ERG and Glucocorticoid Receptor (GR) by microRNAs and detail the influence of steroidal hormonal therapies on microRNAs expression.
... PcG proteins regulate the Hox expression pattern required for development [78,79]. Recent studies showed that PcG proteins are essential for the regulation of normal gene expression during cell differentiation and embryonic development [80,81]. Two major PcG protein complexes, PRC1 and PRC2, are recruited to target sites in the genome [82] to modulate the chromatin structure and repress gene expression. ...
Retinoblastoma protein (pRB) interacts with E2F and other protein factors to play a pivotal role in regulating the expression of target genes that induce cell cycle arrest, apoptosis, and differentiation. pRB controls the local promoter activity and has the ability to change the structure of nucleosomes and/or chromosomes via histone modification, epigenetic changes, chromatin remodeling, and chromosome organization. Functional inactivation of pRB perturbs these cellular events and causes dysregulated cell growth and chromosome instability, which are hallmarks of cancer cells. The role of pRB in regulation of nucleosome/chromatin structures has been shown to link to tumor suppression. This review focuses on the ability of pRB to control nucleosome/chromatin structures via physical interactions with histone modifiers and chromatin factors and describes cancer therapies based on targeting these protein factors.
... Genes that are frequently hypermethylated in cancers often carry the repressive mark H3K27me3 in normal tissues and it has been suggested that many of the CpG islands undergoing methylation are in a repressed state before transformation (Schlesinger et al., 2007). Polycomb group (PcG) proteins play important roles in maintaining the silent state of HOX genes (Pirrotta, 1998). Recent reports implicated histone methylation in long-term gene silencing (Ng, 2002;Zhang, 2001). ...
The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies. We conclude that sample heterogeneity masks DNA methylation signatures in subpopulations of cells and thus believe that beside a genetic evaluation, extensive epigenomic screening should become a standard procedure to ensure hiPSCs state before they are used for genome editing and differentiation into neurons of interest. In particular, we suggest that exploitation of the single-cell composition of the epigenome will provide important insights into heterogeneity within hiPSCs subpopulations to fast forward development of reliable hiPSC-based analytical platforms in neurological disorders modelling and before completed hiPSC technology will be implemented in clinical approaches.
... Several studies have shown that dSet1 and mammalian Set1a/b are responsible for bulk H3K4 di-and trimethylation across the genome (Wu et al. 2008;Ardehali et al. 2011;Mohan et al. 2011;Hallson et al. 2012), whereas Trx and MLL1/MLL2 are necessary for gene-specific H3K4 trimethylation, including Hox gene promoters (Wang et al. 2009) and bivalent promoters ( promoters marked by concurrent trimethylation of H3K4 and H3K27 and poised to express developmental genes) in mouse embryonic stem (mES) cells (Hu et al. 2013b). Trx was initially discovered as a regulator of the developmental expression of Hox genes in Drosophila, specifically being required for maintaining Hox gene activation (Breen and Harte 1991;Pirrotta 1998;Mahmoudi and Verrijzer 2001;Poux et al. 2002;Klymenko and Muller 2004;Shilatifard 2012). It is through shared protein homology with Trx that Trr was cloned (Sedkov et al. 1999 Figure 1. ...
During development, precise spatiotemporal patterns of gene expression are coordinately controlled by cis-regulatory modules known as enhancers. Their crucial role in development helped spur numerous studies aiming to elucidate the functional properties of enhancers within their physiological and disease contexts. In recent years, the role of enhancer malfunction in tissue-specific tumorigenesis is increasingly investigated. Here, we direct our focus to two primary players in enhancer regulation and their role in cancer pathogenesis: MLL3 and MLL4, members of the COMPASS family of histone H3 lysine 4 (H3K4) methyltransferases, and their complex-specific subunit UTX, a histone H3 lysine 27 (H3K27) demethylase. We review the most recent evidence on the underlying roles of MLL3/MLL4 and UTX in cancer and highlight key outstanding questions to help drive future research and contribute to our fundamental understanding of cancer and facilitate identification of therapeutic opportunities.
... Polycomb group (PcG) proteins play major roles in the epigenetic repression of gene transcription in animals and plants [1]. PcGs are implicated in silencing target genes during development and in differentiated cells or mammalian cancer cells [2][3][4][5][6][7]. In mammals, the PcG protein polycomb repressive complex 1 (PRC1) regulates genes expression through controlling chromatin compaction and catalysing monoubiquitylation histone H2A, whereas polycomb repressive complex 2 (PRC2) is responsible for chromatin structure and methylation of histone H3K27 [8]. ...
The polycomb group (PcG) proteins are key epigenetic regulators of gene expression in animals and plants. They act in multiprotein complexes, of which the best characterized is the polycomb repressive complex 2 (PRC2), which catalyses the trimethylation of histone H3 at lysine 27 (H3K27me3) at chromatin targets. InArabidopsis thaliana, PRC2 proteins are involved in the regulation of diverse developmental processes, including cell fate determination, vegetative growth and development, flowering time control and embryogenesis. Here, we systematically analysed the evolutionary conservation and diversification of PRC2 components in lower and higher plants. We searched for and identified PRC2 homologues from the sequenced genomes of several green lineage species, from the unicellular green algaOstreococcus lucimarinusto more complicated angiosperms. We found that some PRC2 core components, e.g. E(z), ESC/FIE and MSI/p55, are ancient and have multiplied coincidently with multicellular evolution. For one component, some members are newly formed, especially in the Cruciferae. During evolution, higher plants underwent copy number multiplication of various PRC2 components, which occurred independently for each component, without any obvious co-amplification of PRC2 members. Among the amplified members, usually one was well-conserved and the others were more diversified. Gene amplification occurred at different times for different PcG members during green lineage evolution. Certain PRC2 core components or members of them were highly conserved. Our study provides an insight into the evolutionary conservation and diversification of PcG proteins and may guide future functional characterization of these important epigenetic regulators in plants other thanArabidopsis.
... D uring development of metazoans, different cells become committed to different fates, in part through heritable, quasi-stable changes in gene expression. Two families of proteins, the trithorax (trx) group and the polycomb (Pc) group, have been demonstrated to play important roles in this process (1,2). These two chromatinassociated classes of proteins are known to function by activating or repressing transcription. ...
... In contrast to the complex situation in mammals, methylation is not detectable in Drosophila (Urieli-Shoval et al., 1982), and embryonic gene silencing in ies is dependent on altered chromatin structures or silencing factors. For example, the Polycomb group (Pc-G) genes are silencing factors that maintain patterns of repression established in the early embryo (Pirrotta, 1998). Reversal of such Pc-G silencing is accompanied by H4 hyperacetylation (Cavalli and Paro, 1999). ...
Retrovirus vectors are de novo methylated and trans-criptionally silent in mammalian stem cells. Here, we identify epigenetic modi®cations that mark retrovirus-silenced transgenes. We show that murine stem cell virus (MSCV) and human immunode®ciency virus type 1 (HIV-1) vectors dominantly silence a linked locus control region (LCR) b-globin reporter gene in transgenic mice. MSCV silencing blocks LCR hyper-sensitive site formation, and silent transgene chroma-tin is marked differentially by a histone code composed of abundant linker histone H1, deacetylated H3 and acetylated H4. Retrovirus-transduced embry-onic stem (ES) cells are silenced predominantly 3 days post-infection, with a small subset expressing enhanced green ¯uorescent protein to low levels, and silencing is not relieved in de novo methylase-null [dnmt3a±/±;dnmt3b±/±] ES cells. MSCV and HIV-1 sequences also repress reporter transgene expression in Drosophila, demonstrating establishment of silencing in the absence of de novo and maintenance methylases. These ®ndings provide mechanistic insight into a conserved gene silencing mechanism that is de novo methylase independent and that epigenetically marks retrovirus chromatin with a repressive histone code.
... Most epigenetic factors involved in gene regulation have been identified in Drosophila as the regulators of homeotic genes. These factors are formally grouped into two categories: the Polycomb group of proteins involved in gene silencing, and the antagonistic trithorax group of proteins, which are activators of homeotic gene expression (Kennison 1995;Pirrotta 1998). Their DNA targets have been identified, and named PRE (Polycomb Response Element) ( Simon et al. 1993) and TRE (Trithorax Response Element), respectively ( Rozovskaia et al. 1999). ...
In this review, we discuss how studying the Drosophila immune system contributes to a better understanding of the basic principles of innate immunity. We describe the homologies between the insect and the vertebrate immune-regulatory mechanisms and convergent evolutionary traits of the Drosophila and the vertebrate immune system.
... Genetic studies established that PcG genes are key regulators of early development in metazoans (Breiling et al., 2007;Faust et al., 1998;O'Carroll et al., 2001;Pasini et al., 2004). Later studies revealed that PcG proteins repress gene expression, in part by methylating and ubiquitylating histone tails (Orlando, 2003;Pirrotta, 1998;Ringrose and Paro, 2004;Schuettengruber et al., 2007;Schwartz and Pirrotta, 2007). In ES cells, PcG proteins occupy and silence genes encoding developmental regulators (Bernstein et al., 2006;Lee et al., 2006;Pan et al., 2007;Yeap et al., 2009;Zhao et al., 2007). ...
Cell state is established and maintained through the combined action of transcription factors, chromatin regulators and signaling pathways, which all contribute to a transcriptional regulatory circuitry. Embryonic stem (ES) cells are capable of self-renewal and can give rise to nearly all differentiated cell-types, making them an ideal system in which to address the challenges of understanding gene expression and cell state. Valuable insights into the control of cell state have been revealed by recent studies of the ES cell transcriptional regulatory circuitry. Here I present work contributing to the understanding of transcriptional regulatory mechanisms that control ES cell state, specifically signaling pathways and proteins that affect chromatin structure.
... TRX-G members are responsible for epigenetic gene regulation by establishing a transcriptionally active, 'open' state of chromatin that can be inherited through cell division. Thus, TRX is necessary for the continued maintenance, but not initiation, of a characteristic temporal and spatial expression pattern of the Hox-cluster genes (HOM-C) (reviewed in [4][5][6]. ...
Alterations of the proto-oncogene MLL (mixed lineage leukemia) are characteristic for a high proportion of acute leukemias, especially those occurring in infants.
The activation of MLL is achieved either by an internal tandem duplication of 5′ MLL exons or by chromosomal translocations that create chimeric proteins with the N-terminus of MLL fused to a variety of different
partner proteins. A domain of MLL with significant homology to the eukaryotic DNA methyltransferases (MT domain) has been
found to be essential for the transforming potential of the oncogenic MLL derivatives. Here we demonstrate that this domain
specifically recognizes DNA with unmethylated CpG sequences. In gel mobility shifts, the presence of CpG was sufficient for
binding of recombinant GST–MT protein to DNA. The introduction of 5-methylCpG on one or both DNA strands precluded an efficient
interaction. In surface plasmon resonance a KD of ∼3.3 × 10–8 M was determined for the GST–MT/DNA complex formation. Site selection experiments and DNase I footprinting confirmed CpG as the target of the MT domain.
Finally, this interaction was corroborated in vivo in reporter assays utilizing the DNA-binding properties of the MT domain in a hybrid MT–VP16 transactivator construct.
... Using the Target Scan program, we identified potential miR-494 targeting sites in the 3'UTR regions of Bmi1 and ADAM10. Bmi-1, a member of the Polycomb (PcG) family of transcriptional repressors, mediates gene silencing by regulating chromatin structure [43]. Bmi-1 was shown being involved in tumor initiation, self-renewal, and metastasis in malignant carcinomas including HNC [44]. ...
Tumor initiating cells (TICs) possessing cancer stemness were shown to be enriched after therapy, resulting in the relapse and metastasis of head and neck squamous cell carcinomas (HNC). An effective therapeutic approach suppressing the HNC-TICs would be a potential method to improve the treatments for HNC. We observed that the treatment of silibinin (SB) dose dependently down-regulated the ALDH1 activity, CD133 positivity, stemness signatures expression, self-renewal property, and chemoresistance in ALDH1+CD44+ HNC-TICs. Using miRNA-microarray and mechanistic studies, SB increased the expression of microRNA-494 (miR-494) and both Bmi1 and ADAM10 were identified as the novel targets of miR-494. Moreover, overexpression of miR-494 results in a reduction in cancer stemness. However, knockdown of miR-494 in CD44-ALDH1- non-HNC-TICs enhanced cancer stemness and oncogenicity, while co-knockdown of Bmi1 and ADAM10 effectively reversed these phenomena. Mice model showed that SB treatment by oral gavage to xenograft tumors reduced tumor growth and prolonged the survival time of tumor-bearing mice by activation of miR-494-inhibiting Bmi1/ADAM10 expression. Survival analysis indicated that a miR494highBmi1lowADAM10low phenotype predicted a favourable clinical outcome. We conclude that the inhibition of tumor aggressiveness in HNC-TICs by SB was mediated by up-regulation miR-494, suggesting that SB would be a valuable anti-cancer drug for treatment of HNC.
Head and neck cancer is a major health problem worldwide, with most cases arising in the oral cavity. Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer, accounting for over 90% of all cases. Compared to other types of cancer, OSCC, has the worse prognosis, with a 5-year survival rate of 50%. Additionally, OSCC is characterized by a high rate of resistance to chemotherapy treatment, which may be partly explained by the presence of cancer stem cells (CSC) subpopulation. CSC can adapt to harmful environmental condition and are highly resistant to both chemotherapy and radiotherapy treatments, thus contributing to tumor relapse. The aim of this review is to highlight the role of mitochondria in oral CSC as a potential target for oral cancer treatment. For this purpose, we reviewed some fundamental aspects of the most validated protein markers of stemness, autophagy, the mitochondrial function and energy metabolism in oral CSC. Moreover, a discussion will be made on why energy metabolism, especially oxidative phosphorylation in CSC, may offer such a diverse source of original pharmacological target for new drugs. Finally, we will describe some drugs able to disturb mitochondrial function, with emphasis on those aimed to interrupt the electron transport chain function, as novel therapeutic strategies in multidrug-resistant oral CSC. The reutilization of old drugs approved for clinical use as new antineoplastics, in cancer treatment, is also matter of revision.
Epigenetics has been well understood for its role in cell development; however, it is now known to regulate many processes involved in immune cell activation in a variety of cells. The skin maintains homeostasis via crosstalk between immune and non-immune cells. Disruption of normal epigenetic regulation in these cells may alter the transcription of immune-regulatory factors and affect the immunological balance in the skin. This review summarizes recent evidence for the epigenetic regulation of skin immunity. Much of what is known about epigenetic involvement in skin immunity is associated with DNA methylation. This review focuses on epigenetic regulation of histone modification and chromatin remodeling and describes their role in the transcriptional regulation of immune-regulatory factors. While much is still unknown regarding the regulation of skin immunity via histone modification or chromatin remodeling, these processes may underlie the pathogenesis of chronic cutaneous immune disorders.
The clinical use of molecular targeted therapy is rapidly evolving but has primarily focused on genomic alterations. Transcriptomic analysis offers an opportunity to dissect the complexity of tumors, including the tumor microenvironment (TME), a crucial mediator of cancer progression and therapeutic outcome. TME classification by transcriptomic analysis of >10,000 cancer patients identifies four distinct TME subtypes conserved across 20 different cancers. The TME subtypes correlate with patient response to immunotherapy in multiple cancers, with patients possessing immune-favorable TME subtypes benefiting the most from immunotherapy. Thus, the TME subtypes act as a generalized immunotherapy biomarker across many cancer types due to the inclusion of malignant and microenvironment components. A visual tool integrating transcriptomic and genomic data provides a global tumor portrait, describing the tumor framework, mutational load, immune composition, anti-tumor immunity, and immunosuppressive escape mechanisms. Integrative analyses plus visualization may aid in biomarker discovery and the personalization of therapeutic regimens.
The conversion from vegetative to inflorescence shoot apical meristem is one of the key developmental switches in flowering plants. This transition is modulated by various environmental and endogenous stimuli and is controlled by sophisticated regulatory networks. Regulation of flowering time and inflorescence architecture has a great impact on plant reproductive success and significantly influences plant biomass and fitness. FLOWERING LOCUS T (FT), a mobile protein identified as a major component of florigen, promotes the transition to flowering, whereas its homologous protein TERMINAL FLOWER 1 (TFL1) functions oppositely. Studies in various species have revealed that FT and TFL1 play universal and multifaceted roles in a wide range of developmental processes in plants. Hence, modulations of FT/TFL1 and their regulatory pathways have a considerable impact on plant development and crop domestication. This review provides an overview of the molecular basis underlying regulation of FT/TFL1 expression and modulation of their protein trafficking, and the relevant mechanisms in flowering time control and meristem development. Whenever applicable, we also discusses their functional conservation and divergence in various plant species.
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The sections in this article are
Introduction
Background
Nuclear Endosperm Development
Differentiation
Acknowledgments
The sections in this article are
Introduction
Morphological Aspects
Ovule Identity
Placenta Formation
The Formation of the Ovule Primordium
Integument Morphogenesis
Summary and Outlook
Note Added in Proof
Purpose
Neoadjuvant concurrent chemoradiotherapy (CCRT) is a gold standard treatment for patients with stage II/III rectal cancer. B-cell-specific Moloney murine leukemia virus insertion site 1 (BMI1) is a member of the polycomb group of proteins that are involved in regulating gene expression. High levels of BMI1 have been demonstrated to contribute to the malignant phenotypes of several cancers; however, its relevance in rectal cancer treated with CCRT is largely unknown.
Methods and materials
We used two patient cohorts to address the clinical relevance of BMI1 in human cancers. In addition, HT-29 and HCT-116 cells were chosen as our in vitro models to verify the role of BMI1 in cell response to ionizing radiation. Stemness-related proteins were analyzed by western blotting and cell survival was determined using clonogenic assays.
Results
BMI1 overexpression was found to significantly correlate with advanced pre-treatment nodal status (N1-N2; p < 0.001), post-treatment tumor stage (T1-T2; p = 0.015), inferior tumor regression grade (p = 0.001), and also an independent prognosis factor in 172 rectal cancer patients receiving CCRT. Serial cell-based functional examination indicated that BMI1 deficiency sensitized cells to radiation treatment by modulating the gene expression of Kruppel-like factor 4 (KLF4) and enhanced radiosensitivity in microsatellite stable (MSS) colorectal cancers. Overexpression of KLF4 partially overcame BMI1-deficiency-mediated γ-H2AX expression after ionizing radiation exposure. Consistent with in vitro data, an analysis of an additional 30 rectal cancer tissue specimens revealed a positive correlation between BMI1 and KLF4 (p = 0.02).
Conclusion
Higher levels of BMI1 are associated with poor therapeutic response and adverse outcomes in rectal cancer patients receiving CCRT.
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases (‘writers’) and demethylases (‘erasers’). In addition, distinct effector proteins (‘readers’) recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
Genes of the Drosophila Polycomb and trithorax groups (PcG and trxG, respectively) influence gene expression by modulating chromatin structure. Segmental expression of homeotic loci (HOM) initiated in early embryogenesis is maintained by a balance of antagonistic PcG (repressor) and trxG (activator) activities. Here we identify a novel trxG family member, taranis (tara), on the basis of the following criteria: (i) tara loss-of-function mutations act as genetic antagonists of the PcG genes Polycomb and polyhomeotic and (ii) they enhance the phenotypic effects of mutations in the trxG genes trithorax (trx), brahma (brm), and osa. In addition, reduced tara activity can mimic homeotic loss-of-function phenotypes, as is often the case for trxG genes. tara encodes two closely related 96-kD protein isoforms (TARA-alpha/-beta) derived from broadly expressed alternative promoters. Genetic and phenotypic rescue experiments indicate that the TARA-alpha/-beta proteins are functionally redundant. The TARA proteins share evolutionarily conserved motifs with several recently characterized mammalian nuclear proteins, including the cyclin-dependent kinase regulator TRIP-Br1/p34(SEI-1), the related protein TRIP-BR2/Y127, and RBTI, a partner of replication protein A. These data raise the possibility that TARA-alpha/-beta play a role in integrating chromatin structure with cell cycle regulation.
In the pupal stage, the fly body undergoes extensive metamorphic remodeling, in which programmed cell death plays a critical role. We studied two of the constituent processes in this remodeling, salivary gland degeneration and breakdown of the eclosion muscle, which are triggered by an increase and a decrease in the circulating steroid hormone ecdysone at the start and end of metamorphosis, respectively. We found that knockdown of zeste (z), a gene encoding a sequence-specific DNA-binding protein implicated in transvection, in salivary gland cells advances the initiation of their degeneration, whereas z knockdown in neurons delays muscle breakdown. We further showed that knockdown of an ecdysone-inducible gene, E74, retards salivary gland degeneration with little effect on eclosion muscle breakdown. We propose that Z tunes the sensitivity of ecdysone targets to this hormone in order to ensure a high safety margin so that the cell death program will be activated when the ecdysone titer is at a sufficiently high level that is reached only at a defined stage during metamorphosis.
Die vorliegende Arbeit ist auf die biologischen Funktionen des Mitglieds der E2F-Familie EMA/E2F-6 fokussiert. Die Familie von E2F-Trankriptionsfaktoren spielt eine wichtige Rolle in der Regulation des Zellzyklus, der Differenzierung und der Apoptose. EMA/E2F-6 wirkt als transkriptionaler Repressor durch die Rekrutierung eines großen, Polycomb-Gruppeproteine- (Pc-G) enthaltenden Proteinkomplexes an spezifische Zielgene, indem es deren Expression inaktiviert. Um die biologischen Funktionen von EMA/E2F-6 zu identifizieren, wurden Mäuse, denen dieser Faktor fehlt, generiert und analysiert. EMA/E2F-6-/--Mäuse wurden im erwarteten Verhältnis geboren, waren fruchtbar und entwickelten sich normal bis zu einem Alter von 18 Monaten. Dann entwickelten 25 % von ihnen eine Lähmung der Hinterbeine. Diese Mäuse hatten einen schwerwiegenden primären Myelinisierungsdefekt im Rückenmark und teilweise auch in den peripheren Nerven, der von einer massiven Makrophageninfiltration begleitet war. Es ist zu betonen, dass diese pathologischen Veränderungen auch - in einem geringen Ausmaß - in EMA/E2F-6-/--Mäusen gefunden wurden, die keine klinischen Symptome gezeigt hatten. Im Zusammenhang mit der Wechselwirkung mit Pc-G wurden keine signifikanten Veränderungen wie Skeletttransformationen in EMA/E2F-6-/--Mäusen festgestellt. Außerdem wurde nur ein schwacher Proliferationsdefekt von T-Lymphozyten beobachtet, die in einer deutlich stärkerem Form typisch für Mäuse mit Pc-G-Mutationen sind. Überraschenderweise haben EMA/E2F-6-/- embryonale Fibroblasten keinen offensichtlichen Zellzyklusdefekt. Die Genexpressionsprofile klassischer E2F-Zielgene waren in Übereinstimmung damit in diesen Zellen unverändert. Im Gegensatz dazu waren hier die normalerweise strikt Hoden-spezifisch exprimierten Gene alpha-Tubulin 3 und 7 stark exprimiert. Sie enthalten in ihren Promotoren eine konservierte E2F-Bindungsstelle, die sowohl für die EMA/E2F-6-abhänige Bindung als auch die Regulation notwendig ist.
The genes of the Polycomb-group (Pc-G) are responsible for maintaining the inactive expression state of homeotic genes. They act through specific cis-regulatory DNA elements termed PREs (Pc-G Response Elements). Multimeric complexes containing the Pc-G proteins are thought to induce heterochromatin-like structures, which stably and heritably inactivate transcription. We have tested the functional role of the FAB fragment, a PRE of the bithorax complex. We find that this element behaves as an orientation dependent silencer, capable of inducing mosaic gene expression on neighboring genes. Transgenic fly lines were constructed containing a PRE adjacent to a reporter gene inducible by the yeast GAL4 trans-activator. The competition between the activator and Pc-G-containing chromatin was visualized on polytene chromosomes using immunocytochemistry. The Pc-G protein Polycomb and GAL4 have mutually exclusive binding patterns, supporting the notion that Pc-G-induced chromatin structures can prevent activators from binding to their target sequences. However, this antagonistic function can be overcome by high doses of GAL4, even in the absence of DNA replication.
The Polycomb group (PcG) of genes are required for maintenance of the repressed state of the homeotic genes in Drosophila. There are similarities between the PcG repression and mating-type silencing in yeast or heterochromatic position effect in Drosophila, which suggest that PcG repression may involve a highly compacted chromatin structure. To test for such a structure, heterologous DNA- binding proteins were used as probes for DNA accessibility in Drosophila embryos. Binding sites for the yeast transcriptional activator GAL4 and for bacteriophage T7 RNA polymerase were inserted into the bithorax (bx) regulatory region of the endogenous Ultrabithorax (Ubx) gene, which is regulated by the PcG. Ubiquitously expressed GAL4 protein directs transcription through its binding sites only in the posterior segments where the bx region is active. The block to GAL4 activation in the more anterior segments is dependent on Polycomb (Pc) function. In contrast, T7 RNA polymerase can transcribe from its target promoter in all segments of the embryo. Thus, Pc-mediated repression blocks activated polymerase II transcription, but does not simply exclude all proteins.
Repression of yeast a cell-specific genes by the global repressor Ssn6/Tup1 has been linked to a specific organization of chromatin. We report here that Tup1 directly interacts with the amino-terminal tails of histones H3 and H4, providing a molecular basis for this connection. This interaction appears to be required for Tup1 function because amino-terminal mutations in H3 and H4 that weaken interactions with Tup1 cause derepression of both a cell-specific and DNA damage-inducible genes. Moreover, the Tup1 histone-binding domain coincides with the previously defined Tup1 repression domain. Tup1/histone interactions are negatively influenced by high levels of histone acetylation, suggesting a mechanism whereby the organization of chromatin may be modulated in response to changing environmental signals.
Transcriptional repression at the silent mating-type loci in yeast requires the targeting of silent information regulator (Sir) proteins through specific interactions formed at cis-acting silencer elements. We show here that a reporter gene flanked by two functional silencers is not repressed when integrated at >200 kb from a telomere. Repression is restored by creation of a new telomere 13 kb from the integrated reporter or by elevated expression of SIR1, SIR3, and/or SIR4. Coupled expression represses in an additive manner, suggesting that all three factors are in limiting concentrations. When overexpressed, Sir3 and Sir4 are dispersed throughout the nucleoplasm, in contrast to wild-type cells where they are clustered in a limited number of foci together with telomeres. Efficient silencer function thus seems to require either proximity to a pool of concentrated Sir proteins, that is, proximity to telomeres, or delocalization of the silencing factors.
The Polycomb group and trithorax group genes of Drosophila are required for maintaining the differential expression state of developmental regulators, such as the homeotic genes, in a stable and heritable manner throughout development. The Polycomb group genes have been suggested to act by regulating higher order chromatin and packaging repressed chromosomal domains in a heterochromatin-like structure. We have mapped, at high resolution, the distribution of Polycomb protein on the bithorax complex of Drosophila tissue culture cells, using an improved formaldehyde cross-linking and immunoprecipitation technique. Polycomb protein is not distributed homogeneously on the regulatory regions of the repressed Ultrabithorax and abdominal-A genes, but is highly enriched at discrete sequence elements, many of which coincide with previously mapped Polycomb group response elements (PREs). Our results further suggest that Polycomb protein spreads locally over a few kilobases of DNA surrounding PREs, perhaps to stabilize silencing complexes. GAGA factor/Trithorax-like, a member of the trithorax group, is also bound at those PREs which contain GAGA consensus-binding sites. Two modes of binding can be distinguished: a high level binding to elements in the regulatory domain of the expressed Abdominal-B gene, and a low level of binding to Polycomb-bound PREs in the inactive domains of the bithorax complex. We propose that GAGA factor binds constitutively to regulatory elements in the bithorax complex, which function both as PREs and as trithorax group response elements.
Transcriptional silencing by the Polycomb Group of genes maintains the position-specific repression of homeotic genes throughout Drosophila development. The Polycomb Group of genes characterized to date encode chromatin-associated proteins that have been suggested to form heterochromatin-like structures. By studying the expression of reporter genes, we have identified a 725 bp fragment, called MCP725, in the homeotic gene Abdominal-B, that accurately maintains position-specific silencing during proliferation of imaginal cells. Silencing by MCP725 requires the Polycomb and the Polycomblike genes, indicating that it contains a Polycomb response element To investigate the mechanisms of transcriptional silencing by MCP725, we have studied its temporal requirements by removing MCP725 from the transgene at various times during development. We have discovered that excision of MCP725 during larval stages leads to loss of silencing. Our findings indicate that the silencer is required for the maintenance of the repressed state throughout cell proliferation. They also suggest that propagation of the silenced state does not occur merely by templating of a heterochromatin structure by virtue of protein-protein interactions. Rather, they suggest that silencers play an active role in the maintenance of the position-specific repression throughout development.
The Dorsal morphogen acts as both an activator and a repressor of transcription in the Drosophila embryo to regulate the expression of dorsal/ventral patterning genes. Circumstantial evidence has suggested that Dorsal is an intrinsic activator and that additional factors (corepressors) convert it into a repressor. These corepressors, however, have previously eluded definitive identification. We show here, via the analysis of embryos lacking the maternally encoded Groucho corepressor and via protein-binding assays, that recruitment of Groucho to the template by protein:protein interactions is required for the conversion of Dorsal from an activator to a repressor. Groucho is therefore a critical component of the dorsal/ventral patterning system.
Polycomb group (Pc-G) proteins act to keep homeotic genes stably and heritably silenced during Drosophila development. Here, it is shown that Polycomb (Pc), one of the Pc-G proteins, acts as a transcriptional silencer in Drosophila embryos if tethered to reporter genes by the DNA binding domain of GAL4 (i.e. as a GAL-Pc fusion protein). The results suggest that silencing by GAL-Pc requires the C-terminal portion of Pc, but not the chromodomain. If a pulse of Gal-Pc is provided, synthetic reporter genes are repressed, though only transiently. In contrast, reporter genes containing homeotic gene sequences remain stably and heritably silenced in a Pc-G gene-dependent fashion, even when GAL-Pc is no longer present. This implies that GAL-Pc recruits Pc-G proteins to DNA and suggests that maintenance of silencing requires the anchoring of Pc-G proteins to specific cis-regulatory sequences present in homeotic genes. The extent of DNA over which the Pc-G machinery acts is quite selective, as silencing established on one enhancer does not necessarily 'spread' to a juxtaposed synthetic enhancer.
Heterochromatin is the highly compact, usually pericentromeric, region of eukaryotic chromosomes. Unlike the more gene-rich euchromatin, heterochromatin remains condensed during interphase, when it is sequestered to the periphery of the nucleus. Here we show, by using fluorescent in situ hybridization to interphase diploid nuclei of Drosophila, that the insertion of heterochromatin into a euchromatic gene, which results in position-effect variegation (PEV), also causes the aberrant association of the gene and its homologous copy with heterochromatin. In correlation with the gene's mutant variegating phenotype, the cytological association of the heterochromatic region is affected by chromosomal distance from heterochromatin and by genic modifiers of PEV. Proteins that are thought to be involved in the formation of heterochromatin can therefore influence the interphase nuclear position of a chromosomal region. This suggests that heterochromatin and proteins involved in its formation provide a structural framework for the interphase nucleus.
The distinction between soma and germline was recognized more than a century ago: somatic cells form the body of an organism, whereas germ cells serve to produce future generations. In Caenorhabditis elegans, the separation of some and germline occurs through a series of asymmetrical divisions, in which embryonic germline blastomeres divide unequally to produce one somatic daughter and one germline daughter. Here we show that after each asymmetrical division, embryonically transcribed RNAs are detected in somatic, but not germline, blastomeres. This asymmetry depends on the activity of the germline specific factor, PIE-1. In the absence of PIE-1, embryonically transcribed RNAs are detected in both somatic and germline blastomeres. Furthermore, ectopic expression of PIE-1 in somatic blastomeres can significantly reduce the accumulation of new transcripts in these cells. Taken together, these results suggest that germ-cell fate depends on an inhibitory mechanism that blocks new gene expression in the early embryonic germ lineage.
Telomeric genes and the HM loci in saccharomyces cerevisiae are transcriptionally repressed and adopt a heterochromatin-like structure. The trans-acting factors RAP1, SIR3 and SIR4 are required for telomeric and HM silencing, and are thought to be chromosomal, but how they contribute to histone-dependent repression of adjacent chromatin is unclear. SIR3 suppresses silencing defects in histones, is limiting for silencing adjacent to telomeres, and interacts with the H3 and H4 amino termini in vitro. Here we show that SIR3 co-immunoprecipitates SIR4, RAP1 and histones from cellular extracts, suggesting the presence of large chromatin-associated protein complexes. Crosslinking experiments show that SIR3 is present at HMRa, HMLalpha and telomeres in vivo, and that is spreads from telomeric regions into adjacent chromatin when overexpressed. Thus SIR3 is a structural component of yeast heterochromatin, repressing adjacent genes as it spreads along the chromosome.
Recent advances in fluorescence in situ hybridization and three-dimensional microscopy have revealed a high degree of large-scale order in the nucleus, indicating that the position of each gene within the nucleus is not random. As with any other biological phenomenon, this large-scale organization must ultimately be specified by molecular interactions. Biochemical and molecular investigations have revealed a small set of local molecular-scale interactions that can be used together in a combinatorial fashion to establish a global large-scale nuclear architecture.
Silencing complexes in yeast and in the fly have many similarities. This repressive complex is assembled by a chain of recruitment; its extent and stability depend on the concentration of components and affect an extended chromatin region, probably through interactions with nucleosomes. Recent results show that assembly of the complex is antagonized by transcriptional activity in the region but is favored by interactions with other complexes nearby or in other regions that associate in the same nuclear environment. How such a complex interferes with transcriptional activity is not entirely clear but current evidence suggests that they compete with the chromatin structure required for the binding of activators.
In recent years, molecular genetic studies of plant development, particularly flower development, have uncovered a number of homeotic gene.s 1,2. These genes specify cell fates. Are plant homeotic genes also regulated by the polycomb-trStborax group of genes? A recent Nature paper indicates that the answer is yes, at least for one floral homentic gene.
When two to six copies of a white promoter-Alcohol dehydrogenase (Adh) reporter fusion gene are introduced into the genome, the expression is progressively reduced both in larvae and adults rather than the expected gene dosage effect. In addition, multiple transgenes reduce endogenous Adh transcripts, a result that is strongly analogous to "cosuppression" phenomena described in many plant species but which has not been previously observed in animals. Silencing of the Adh gene is not influenced by zeste-dependent transvection but strongly affected by the Polycomb and Polycomblike mutations. Polycomb and polyhomeotic proteins are bound to the chromatin at the sites of the repressed w-Adh transgenes.
During development and differentiation, cellular phenotypes are stably propagated through numerous cell divisions. This epigenetic 'cell memory' helps to maintain stable patterns of gene expression. DNA methylation and the propagation of specific chromatin structures may both contribute to cell memory. There are two impediments during the cell cycle that can hinder the inheritance of specific chromatin configurations: first, the pertinent structures must endure the passage of DNA-replication forks in S phase; second, the chromatin state must survive mitosis, when chromatin condenses, transcription is turned off, and almost all double-stranded DNA-binding proteins are displaced. After mitosis, the previous pattern of expressed and silent genes must be restored. This restoration might be governed by mass action, determined by the binding affinities and concentrations of individual components. Alternatively, a subset of factors might remain bound to mitotic chromosomes, providing a molecular bookmark to direct proper chromatin reassembly. Here we analyse DNA at transcription start sites during mitosis in vivo and find that it is conformationally distorted in genes scheduled for reactivation but is undistorted in repressed genes. These protein-dependent conformational perturbations could help to re-establish transcription after mitosis by 'marking' genes for re-expression.
Polycomb response elements (PREs) can establish a silenced state that affects the expression of genes over considerable distances. We have tested the ability of insulator or boundary elements to block the repression of the miniwhite gene by the Ubx PRE. The gypsy element and the scs element interposed between PRE and miniwhite gene protect it against silencing but the scs' is only weakly effective. When the PRE-miniwhite gene construct is insulated from flanking chromosomal sequences by gypsy elements at both ends, it can still establish efficient silencing in some lines but not others. We show that this can be caused by interactions in trans with PREs at other sites. PRE-containing transposons inserted at different sites or even on different chromosomes can interact, resulting in enhanced silencing. These trans interactions are not blocked by the gypsy insulator and reveal the importance of nonhomologous associations between different regions of the genome for both silencing and activation of genes. The similarity between the behavior of PREs and enhancers suggests a model for their long-distance action.
Nature 383, This could be explained by increased stability of silenc
- A Hecht
- S Strahl-Bolsinger
- M Grunstein
Hecht, A., Strahl-Bolsinger, S., and Grunstein, M. (1996). Nature 383, This could be explained by increased stability of silenc-92–96.
For PREs such hypersilenced states
- E F Michelotti
- S Sanford
- D Levens
by cell progeny. For PREs such hypersilenced states Michelotti, E.F., Sanford, S., and Levens, D. (1997). Nature 388, 895–899.
When they Pal-Bhadra
- M Bhadra
- U Birchler
silencing is alleviated by higher temperatures). When they Pal-Bhadra, M., Bhadra, U., and Birchler, J.A. (1997). Cell 90, 479–490.
and chromatin or modify it in a way that persists through Fire
- G Mello
- C C Pettit
- J Wood
- W B Priess
ponents of the PcG complex remain associated with the Seydoux, G., Mello, C.C., Pettit, J., Wood, W.B., Priess, J.R., and chromatin or modify it in a way that persists through Fire, A. (1996). Nature 382, 713–716.
These results suggest that some com
- Of
- A Schumacher
- T Magnuson
els of silencing. These results suggest that some com-Schumacher, A., and Magnuson, T. (1997). Trends Genet. 13, 167–170.
- Busturia