Polycomb repressive complex 2 (PRC2) is involved in maintaining transcriptionally silent chromatin states through methylating lysine 27 of histone H3 by the catalytic subunit enhancer of zeste [E(z)]. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. For the first time, we identify the putative ortholog of E(z) in Discoba, a lineage hypothetically proximal to the eukaryotic root, strongly supporting emergence of PRC2 before the diversification of eukaryotes. Analyzing 283 species, we robustly detect a common presence of E(z) and ESC, indicating a conserved functional core. Full-length Su(z)12 orthologs were identified in some lineages and species only, indicating, nonexclusively, high divergence of VEFS-Box-containing Su(z)12-like proteins, functional convergence of sequence-unrelated proteins, or Su(z)12 dispensability. Our results trace E(z) evolution within the SET-domain protein family, proposing a substrate specificity shift during E(z) evolution based on SET-domain and H3 histone interaction prediction.
- Keywords
- tazemetostat, tafasitamab,
- MeSH
- Antigens, CD19 administration & dosage pharmacology drug effects MeSH
- Receptors, Chimeric Antigen drug effects MeSH
- Enhancer of Zeste Homolog 2 Protein pharmacology MeSH
- Lymphoma, Follicular * drug therapy mortality MeSH
- Clinical Trials as Topic MeSH
- Humans MeSH
- Antibodies, Bispecific pharmacology drug effects MeSH
- Drug Approval MeSH
- Check Tag
- Humans MeSH
- Publication type
- Review MeSH
BACKGROUND: Polycomb repressive complexes 1 and 2 play important roles in epigenetic gene regulation by posttranslationally modifying specific histone residues. Polycomb repressive complex 2 is responsible for the trimethylation of lysine 27 on histone H3; Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Both complexes have been thoroughly studied in Arabidopsis, but the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown. RESULTS: Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 (PRC2, PRC1) subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. We identified four main subunits of PRC2 [E(z), Su(z), FIE and MSI] and three main subunits of PRC1 (Pc, Psc and Sce) and determined their chromosomal locations. We found that most of the genes coding for subunit proteins are present as paralogs in bread wheat. Using bread wheat RNA-seq data from different tissues and developmental stages throughout plant ontogenesis revealed variable transcriptional activity for individual paralogs. Phylogenetic analysis showed a high level of protein conservation among temperate cereals. CONCLUSIONS: The identification and chromosomal location of the Polycomb repressive complex 1 and 2 core components in bread wheat may enable a deeper understanding of developmental processes, including vernalization, in commonly grown winter wheat.
- MeSH
- Chromosomes, Plant MeSH
- Phylogeny MeSH
- Chromosome Mapping MeSH
- Evolution, Molecular MeSH
- Computer Simulation MeSH
- Polycomb Repressive Complex 1 genetics MeSH
- Polycomb Repressive Complex 2 genetics MeSH
- Triticum genetics MeSH
- RNA, Plant MeSH
- RNA-Seq MeSH
- Gene Expression Profiling MeSH
- Publication type
- Journal Article MeSH
Hepatocyte nuclear factor 1 beta (HNF1B) is a tissue specific transcription factor, which seems to play an important role in the carcinogenesis of several tumors. In our study we focused on analyzing HNF1B in prostate carcinoma (PC) and adenomyomatous hyperplasia (AH), as well as its possible relation to the upstream gene EZH2 and downstream gene ECI2. The results of our study showed that on an immunohistochemical level, the expression of HNF1B was low in PC, did not differ between PC and AH, and did not correlate with any clinical outcomes. In PC, mutations of HNF1B gene were rare, but the methylation of its promotor was a common finding and was positively correlated with Gleason score and stage. The relationship between HNF1B and EZH2/ECI2 was equivocal, but EZH2 and ECI2 were positively correlated on both mRNA and protein level. The expression of EZH2 was associated with poor prognosis. ECI2 did not correlate with any clinical outcomes. Our results support the oncosuppressive role of HNF1B in PC, which may be silenced by promotor methylation and other mechanisms, but not by gene mutation. The high expression of EZH2 (especially) and ECI2 in PC seems to be a potential therapeutic target.
- MeSH
- Dodecenoyl-CoA Isomerase genetics metabolism MeSH
- Enhancer of Zeste Homolog 2 Protein genetics metabolism MeSH
- Hepatocyte Nuclear Factor 1-beta genetics metabolism MeSH
- Prostatic Hyperplasia genetics metabolism pathology MeSH
- Immunohistochemistry methods MeSH
- Cohort Studies MeSH
- Humans MeSH
- RNA, Messenger genetics MeSH
- DNA Methylation MeSH
- Mutation MeSH
- Prostatic Neoplasms genetics metabolism pathology MeSH
- Prognosis MeSH
- Promoter Regions, Genetic MeSH
- Prostate pathology MeSH
- Gene Expression Regulation, Neoplastic MeSH
- Aged MeSH
- Neoplasm Grading MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Aged MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Polycomb repressive complexes maintain transcriptional repression of genes encoding crucial developmental regulators through chromatin modification. Here we investigated the role of Polycomb repressive complex 2 (PRC2) in retinal development by inactivating its key components Eed and Ezh2. Conditional deletion of Ezh2 resulted in a partial loss of PRC2 function and accelerated differentiation of Müller glial cells. In contrast, inactivation of Eed led to the ablation of PRC2 function at early postnatal stage. Cell proliferation was reduced and retinal progenitor cells were significantly decreased in this mutant, which subsequently caused depletion of Müller glia, bipolar, and rod photoreceptor cells, primarily generated from postnatal retinal progenitor cells. Interestingly, the proportion of amacrine cells was dramatically increased at postnatal stages in the Eed-deficient retina. In accordance, multiple transcription factors controlling amacrine cell differentiation were upregulated. Furthermore, ChIP-seq analysis showed that these deregulated genes contained bivalent chromatin (H3K27me3+ H3K4me3+). Our results suggest that PRC2 is required for proliferation in order to maintain the retinal progenitor cells at postnatal stages and for retinal differentiation by controlling amacrine cell generation.
- MeSH
- Cell Differentiation physiology MeSH
- Chromatin metabolism MeSH
- Enhancer of Zeste Homolog 2 Protein metabolism MeSH
- Histones metabolism MeSH
- Stem Cells cytology metabolism MeSH
- Methylation MeSH
- Mice MeSH
- Neurogenesis MeSH
- Neuroglia metabolism MeSH
- Polycomb Repressive Complex 2 metabolism MeSH
- Cell Proliferation MeSH
- Retina metabolism physiology MeSH
- Animals MeSH
- Check Tag
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Developmental exposure to environmental factors has been linked to obesity risk later in life. Nuclear receptors are molecular sensors that play critical roles during development and, as such, are prime candidates to explain the developmental programming of disease risk by environmental chemicals. We have previously characterized the obesogen tributyltin (TBT), which activates the nuclear receptors peroxisome proliferator-activated receptor γ (PPARγ) and retinoid X receptor (RXR) to increase adiposity in mice exposed in utero. Mesenchymal stem cells (MSCs) from these mice are biased toward the adipose lineage at the expense of the osteoblast lineage, and MSCs exposed to TBT in vitro are shunted toward the adipose fate in a PPARγ-dependent fashion. To address where in the adipogenic cascade TBT acts, we developed an in vitro commitment assay that permitted us to distinguish early commitment to the adipose lineage from subsequent differentiation. TBT and RXR activators (rexinoids) had potent effects in committing MSCs to the adipose lineage, whereas the strong PPARγ activator rosiglitazone was inactive. We show that activation of RXR is sufficient for adipogenic commitment and that rexinoids act through RXR to alter the transcriptome in a manner favoring adipogenic commitment. RXR activation alters expression of enhancer of zeste homolog 2 (EZH2) and modifies genome-wide histone 3 lysine 27 trimethylation (H3K27me3) in promoting adipose commitment and programming subsequent differentiation. These data offer insights into the roles of RXR and EZH2 in MSC lineage specification and shed light on how endocrine-disrupting chemicals such as TBT can reprogram stem cell fate.
- MeSH
- Adipogenesis drug effects genetics physiology MeSH
- Cell Differentiation drug effects genetics MeSH
- Chromatin drug effects physiology MeSH
- Endocrine Disruptors pharmacology MeSH
- Epigenesis, Genetic drug effects MeSH
- Gene Expression drug effects MeSH
- Enhancer of Zeste Homolog 2 Protein genetics MeSH
- Gene Knockdown Techniques veterinary MeSH
- Mesenchymal Stem Cells cytology MeSH
- Mice, Inbred C57BL MeSH
- Mice MeSH
- Obesity etiology MeSH
- PPAR gamma physiology MeSH
- Retinoid X Receptors drug effects physiology MeSH
- Sequence Analysis, RNA veterinary MeSH
- Trialkyltin Compounds pharmacology MeSH
- Adipocytes cytology MeSH
- Animals MeSH
- Check Tag
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Downregulation of miR26A1 has been reported in various B-cell malignancies; however, the mechanism behind its deregulation remains largely unknown. We investigated miR26A1 methylation and expression levels in a well-characterized series of chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). From 450K methylation arrays, we first observed miR26A1 (cg26054057) as uniformly hypermethylated in MCL (n = 24) (all >75%), while CLL (n = 18) showed differential methylation between prognostic subgroups. Extended analysis using pyrosequencing confirmed our findings and real-time quantitative PCR verified low miR26A1 expression in both CLL (n = 70) and MCL (n = 38) compared to normal B-cells. Notably, the level of miR26A1 methylation predicted outcome in CLL, with higher levels seen in poor-prognostic, IGHV-unmutated CLL. Since EZH2 was recently reported as a target for miR26A1, we analyzed the expression levels of both miR26A1 and EZH2 in primary CLL samples and observed an inverse correlation. By overexpression of miR26A1 in CLL and MCL cell lines, reduced EZH2 protein levels were observed using both Western blot and flow cytometry. In contrast, methyl-inhibitor treatment led to upregulated miR26A1 expression with a parallel decrease of EZH2 expression. Finally, increased levels of apoptosis were observed in miR26A1-overexpressing cell lines, further underscoring the functional relevance of miR26A1. In summary, we propose that epigenetic silencing of miR26A1 is required for the maintenance of increased levels of EZH2, which in turn translate into a worse outcome, as shown in CLL, highlighting miR26A1 as a tumor suppressor miRNA.
- MeSH
- Apoptosis genetics MeSH
- Leukemia, Lymphocytic, Chronic, B-Cell genetics pathology MeSH
- Epigenesis, Genetic MeSH
- Enhancer of Zeste Homolog 2 Protein biosynthesis genetics MeSH
- Humans MeSH
- Lymphoma, Mantle-Cell genetics pathology MeSH
- DNA Methylation genetics MeSH
- MicroRNAs biosynthesis genetics MeSH
- Cell Line, Tumor MeSH
- Promoter Regions, Genetic MeSH
- Gene Expression Regulation, Neoplastic MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
In mammals, the noncoding Xist RNA triggers transcriptional silencing of one of the two X chromosomes in female cells. Here, we report a genetic screen for silencing factors in X chromosome inactivation using haploid mouse embryonic stem cells (ESCs) that carry an engineered selectable reporter system. This system was able to identify several candidate factors that are genetically required for chromosomal repression by Xist. Among the list of candidates, we identify the RNA-binding protein Spen, the homolog of split ends. Independent validation through gene deletion in ESCs confirms that Spen is required for gene repression by Xist. However, Spen is not required for Xist RNA localization and the recruitment of chromatin modifications, including Polycomb protein Ezh2. The identification of Spen opens avenues for further investigation into the gene-silencing pathway of Xist and shows the usefulness of haploid ESCs for genetic screening of epigenetic pathways.
- MeSH
- Embryonic Stem Cells metabolism MeSH
- Haploidy MeSH
- Nuclear Proteins genetics metabolism MeSH
- Cells, Cultured MeSH
- Mice MeSH
- Polycomb Repressive Complex 2 genetics metabolism MeSH
- RNA, Long Noncoding genetics MeSH
- Gene Silencing * MeSH
- Animals MeSH
- Check Tag
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
