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Qin H, Liu C, Li C, Feng C, Bo Huang. Advances in bi-directional relationships for EZH2 and oxidative stress. Exp Cell Res 2024; 434:113876. [PMID: 38070859 DOI: 10.1016/j.yexcr.2023.113876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/14/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
Over the past two decades, polycomb repressive complex 2(PRC2) has emerged as a vital repressive complex in overall cell fate determination. In mammals, enhancer of zeste homolog 2 (EHZ2), which is the core component of PRC2, has also been recognized as an important regulator of inflammatory, redox, tumorigenesis and damage repair signalling networks. To exert these effects, EZH2 must regulate target genes epigenetically or interact directly with other gene expression-regulating factors, such as LncRNAs and microRNAs. Our review provides a comprehensive summary of research advances, discoveries and trends regarding the regulatory mechanisms between EZH2 and reactive oxygen species (ROS). First, we outline novel findings about how EZH2 regulates the generation of ROS at the molecular level. Then, we summarize how oxidative stress controls EHZ2 alteration (upregulation, downregulation, or phosphorylation) via various molecules and signalling pathways. Finally, we address why EZH2 and oxidative stress have an undefined relationship and provide potential future research ideas.
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Affiliation(s)
- Heng Qin
- Department of Pulmonary and Critical Care Medicine, Xinqiao Hospital, Army Medical University, Chongqing, 400037, PR China.
| | - Chang Liu
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing, 400037, PR China.
| | - Changqing Li
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing, 400037, PR China.
| | - Chencheng Feng
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing, 400037, PR China.
| | - Bo Huang
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing, 400037, PR China.
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2
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Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells. Nat Commun 2023; 14:180. [PMID: 36635295 PMCID: PMC9837203 DOI: 10.1038/s41467-023-35859-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
The potential of pluripotent cells to respond to developmental cues and trigger cell differentiation is enhanced during the G1 phase of the cell cycle, but the molecular mechanisms involved are poorly understood. Variations in polycomb activity during interphase progression have been hypothesized to regulate the cell-cycle-phase-dependent transcriptional activation of differentiation genes during lineage transition in pluripotent cells. Here, we show that recruitment of Polycomb Repressive Complex 1 (PRC1) and associated molecular functions, ubiquitination of H2AK119 and three-dimensional chromatin interactions, are enhanced during S and G2 phases compared to the G1 phase. In agreement with the accumulation of PRC1 at target promoters upon G1 phase exit, cells in S and G2 phases show firmer transcriptional repression of developmental regulator genes that is drastically perturbed upon genetic ablation of the PRC1 catalytic subunit RING1B. Importantly, depletion of RING1B during retinoic acid stimulation interferes with the preference of mouse embryonic stem cells (mESCs) to induce the transcriptional activation of differentiation genes in G1 phase. We propose that incremental enrolment of polycomb repressive activity during interphase progression reduces the tendency of cells to respond to developmental cues during S and G2 phases, facilitating activation of cell differentiation in the G1 phase of the pluripotent cell cycle.
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3
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Naqvi AAT, Rizvi SAM, Hassan MI. Pan-cancer analysis of Chromobox (CBX) genes for prognostic significance and cancer classification. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166561. [PMID: 36183965 DOI: 10.1016/j.bbadis.2022.166561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]
Abstract
Polycomb group of proteins play a significant role in chromatin remodelling essential for epigenetic regulation of transcription. Chromobox (CBX) gene family is an important part of canonical polycomb repressive complex 1 (PRC1), belonging to the polycomb group involved in chromatin remodelling. Aberrations in CBX expression are linked to various cancers. To assess their biomarker significance, we performed a pan-cancer analysis of CBX mRNA levels in 18 cancer types. We also performed cancer classification using CBX genes as distinctive features for machine learning model development. Logistic regression (L.R.), support vector machine (SVM), random forest (R.F.), decision tree (D.T.), and XGBoost (XGB) algorithms for model training and classification. The expression of CBX genes was significantly changed in four cancer types, i.e., cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC). The fold change (FC) values suggest that CBX2 was significantly upregulated in CHOL (FC = 1.639), COAD (FC = 1.734), and LUSC (FC = 1.506). On the other hand, CBX7 was found downregulated in COAD (FC = -1.209), LUAD (FC = -1.190), and LUSC (FC = -1.214). The performance of machine learning models for classification was excellent. L.R., R.F., SVM, and XGB obtained a prediction accuracy of 100 % for most cancers. However, D.T. performed comparatively poorly in prediction accuracy. The results suggest that CBX expression is significantly altered in all the cancers studied; therefore, they might be treated as potential biomarkers for therapeutic intervention of these cancers.
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Affiliation(s)
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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4
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Abstract
An ensemble of in vitro cardiac tissue models has been developed over the past several decades to aid our understanding of complex cardiovascular disorders using a reductionist approach. These approaches often rely on recapitulating single or multiple clinically relevant end points in a dish indicative of the cardiac pathophysiology. The possibility to generate disease-relevant and patient-specific human induced pluripotent stem cells has further leveraged the utility of the cardiac models as screening tools at a large scale. To elucidate biological mechanisms in the cardiac models, it is critical to integrate physiological cues in form of biochemical, biophysical, and electromechanical stimuli to achieve desired tissue-like maturity for a robust phenotyping. Here, we review the latest advances in the directed stem cell differentiation approaches to derive a wide gamut of cardiovascular cell types, to allow customization in cardiac model systems, and to study diseased states in multiple cell types. We also highlight the recent progress in the development of several cardiovascular models, such as cardiac organoids, microtissues, engineered heart tissues, and microphysiological systems. We further expand our discussion on defining the context of use for the selection of currently available cardiac tissue models. Last, we discuss the limitations and challenges with the current state-of-the-art cardiac models and highlight future directions.
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Affiliation(s)
- Dilip Thomas
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA (D.T., C.A., J.C.W.).,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA (D.T., C.A., J.C.W.)
| | - Suji Choi
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA (S.C., K.K.P.)
| | - Christina Alamana
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA (D.T., C.A., J.C.W.).,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA (D.T., C.A., J.C.W.)
| | - Kevin Kit Parker
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, MA (S.C., K.K.P.).,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, Wyss Institute for Biologically Inspired Engineering, Boston, MA (K.K.P.)
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA (D.T., C.A., J.C.W.).,Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA (D.T., C.A., J.C.W.).,Greenstone Biosciences, Palo Alto, CA (J.C.W.)
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5
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Angrand PO. Structure and Function of the Polycomb Repressive Complexes PRC1 and PRC2. Int J Mol Sci 2022; 23:ijms23115971. [PMID: 35682651 PMCID: PMC9181254 DOI: 10.3390/ijms23115971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 12/20/2022] Open
Affiliation(s)
- Pierre-Olivier Angrand
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
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6
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Epigenetic Regulation of Chondrocytes and Subchondral Bone in Osteoarthritis. Life (Basel) 2022; 12:life12040582. [PMID: 35455072 PMCID: PMC9030470 DOI: 10.3390/life12040582] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
The aim of this review is to provide an updated review of the epigenetic factors involved in the onset and development of osteoarthritis (OA). OA is a prevalent degenerative joint disease characterized by chronic inflammation, ectopic bone formation within the joint, and physical and proteolytic cartilage degradation which result in chronic pain and loss of mobility. At present, no disease-modifying therapeutics exist for the prevention or treatment of the disease. Research has identified several OA risk factors including mechanical stressors, physical activity, obesity, traumatic joint injury, genetic predisposition, and age. Recently, there has been increased interest in identifying epigenetic factors involved in the pathogenesis of OA. In this review, we detail several of these epigenetic modifications with known functions in the onset and progression of the disease. We also review current therapeutics targeting aberrant epigenetic regulation as potential options for preventive or therapeutic treatment.
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7
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Garipler G, Lu C, Morrissey A, Lopez-Zepeda LS, Pei Y, Vidal SE, Zen Petisco Fiore AP, Aydin B, Stadtfeld M, Ohler U, Mahony S, Sanjana NE, Mazzoni EO. The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes. Cell Rep 2022; 38:110524. [PMID: 35294876 PMCID: PMC8972945 DOI: 10.1016/j.celrep.2022.110524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/21/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
In pluripotent cells, a delicate activation-repression balance maintains pro-differentiation genes ready for rapid activation. The identity of transcription factors (TFs) that specifically repress pro-differentiation genes remains obscure. By targeting ∼1,700 TFs with CRISPR loss-of-function screen, we found that ZBTB11 and ZFP131 are required for embryonic stem cell (ESC) pluripotency. ESCs without ZBTB11 or ZFP131 lose colony morphology, reduce proliferation rate, and upregulate transcription of genes associated with three germ layers. ZBTB11 and ZFP131 bind proximally to pro-differentiation genes. ZBTB11 or ZFP131 loss leads to an increase in H3K4me3, negative elongation factor (NELF) complex release, and concomitant transcription at associated genes. Together, our results suggest that ZBTB11 and ZFP131 maintain pluripotency by preventing premature expression of pro-differentiation genes and present a generalizable framework to maintain cellular potency.
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Affiliation(s)
- Görkem Garipler
- Department of Biology, New York University, New York, NY 10003, USA
| | - Congyi Lu
- Department of Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Alexis Morrissey
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lorena S Lopez-Zepeda
- Department of Biology, Humboldt Universität zu Berlin, Berlin 10117, Germany; Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Yingzhen Pei
- Department of Biology, New York University, New York, NY 10003, USA
| | - Simon E Vidal
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Begüm Aydin
- Department of Biology, New York University, New York, NY 10003, USA
| | - Matthias Stadtfeld
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Uwe Ohler
- Department of Biology, Humboldt Universität zu Berlin, Berlin 10117, Germany; Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA.
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY 10003, USA.
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8
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Emerging role of G9a in cancer stemness and promises as a therapeutic target. Oncogenesis 2021; 10:76. [PMID: 34775469 PMCID: PMC8590690 DOI: 10.1038/s41389-021-00370-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
The histone methyltransferase G9a is well-documented for its implication in neoplastic growth. However, recent investigations have demonstrated a key involvement of this chromatin writer in maintaining the self-renewal and tumor-initiating capacities of cancer stem cells (CSCs). Direct inhibition of G9a’s catalytic activity was reported as a promising therapeutic target in multiple preclinical studies. Yet, none of the available pharmacological inhibitors of G9a activity have shown success at the early stages of clinical testing. Here, we discuss central findings of oncogenic expression and activation of G9a in CSCs from different origins, as well as the impact of the suppression of G9a histone methyltransferase activity in such contexts. We will explore the challenges posed by direct and systemic inhibition of G9a activity in the perspective of clinical translation of documented small molecules. Finally, we will discuss recent advances in drug discovery as viable strategies to develop context-specific drugs, selectively targeting G9a in CSC populations.
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9
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Raby L, Völkel P, Hasanpour S, Cicero J, Toillon RA, Adriaenssens E, Van Seuningen I, Le Bourhis X, Angrand PO. Loss of Polycomb Repressive Complex 2 Function Alters Digestive Organ Homeostasis and Neuronal Differentiation in Zebrafish. Cells 2021; 10:cells10113142. [PMID: 34831364 PMCID: PMC8620594 DOI: 10.3390/cells10113142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) mediates histone H3K27me3 methylation and the stable transcriptional repression of a number of gene expression programs involved in the control of cellular identity during development and differentiation. Here, we report on the generation and on the characterization of a zebrafish line harboring a null allele of eed, a gene coding for an essential component of the PRC2. Homozygous eed-deficient mutants present a normal body plan development but display strong defects at the level of the digestive organs, such as reduced size of the pancreas, hepatic steatosis, and a loss of the intestinal structures, to die finally at around 10-12 days post fertilization. In addition, we found that PRC2 loss of function impairs neuronal differentiation in very specific and discrete areas of the brain and increases larval activity in locomotor assays. Our work highlights that zebrafish is a suited model to study human pathologies associated with PRC2 loss of function and H3K27me3 decrease.
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Affiliation(s)
- Ludivine Raby
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Pamela Völkel
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Shaghayegh Hasanpour
- Department of Fisheries and Animal Sciences, Faculty of Natural Resources, University of Tehran, Karaj 31587-77871, Iran;
| | - Julien Cicero
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
- Univ. Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), F-62300 Lens, France
| | - Robert-Alain Toillon
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Eric Adriaenssens
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Isabelle Van Seuningen
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Xuefen Le Bourhis
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
| | - Pierre-Olivier Angrand
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR 9020-U 1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France; (L.R.); (P.V.); (J.C.); (R.-A.T.); (E.A.); (I.V.S.); (X.L.B.)
- Correspondence: ; Tel.: +33-3-2033-6222
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10
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Yi SA, Nam KH, Lee MG, Oh H, Noh JS, Jeong JK, Kwak S, Jeon YJ, Kwon SH, Lee J, Han JW. Transcriptomics-Based Repositioning of Natural Compound, Eudesmin, as a PRC2 Modulator. Molecules 2021; 26:molecules26185665. [PMID: 34577136 PMCID: PMC8465685 DOI: 10.3390/molecules26185665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
Extensive epigenetic remodeling occurs during the cell fate determination of stem cells. Previously, we discovered that eudesmin regulates lineage commitment of mesenchymal stem cells through the inhibition of signaling molecules. However, the epigenetic modulations upon eudesmin treatment in genomewide level have not been analyzed. Here, we present a transcriptome profiling data showing the enrichment in PRC2 target genes by eudesmin treatment. Furthermore, gene ontology analysis showed that PRC2 target genes downregulated by eudesmin are closely related to Wnt signaling and pluripotency. We selected DKK1 as an eudesmin-dependent potential top hub gene in the Wnt signaling and pluripotency. Through the ChIP-qPCR and RT-qPCR, we found that eudesmin treatment increased the occupancy of PRC2 components, EZH2 and SUZ12, and H3K27me3 level on the promoter region of DKK1, downregulating its transcription level. According to the analysis of GEO profiles, DEGs by depletion of Oct4 showed an opposite pattern to DEGs by eudesmin treatment. Indeed, the expression of pluripotency markers, Oct4, Sox2, and Nanog, was upregulated upon eudesmin treatment. This finding demonstrates that pharmacological modulation of PRC2 dynamics by eudesmin might control Wnt signaling and maintain pluripotency of stem cells.
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Affiliation(s)
- Sang Ah Yi
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
| | - Ki Hong Nam
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
| | - Min Gyu Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
| | - Hwamok Oh
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
| | - Jae Sung Noh
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
| | - Jae Kyun Jeong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
| | - Sangwoo Kwak
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
| | - Ye Ji Jeon
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, International Campus, Yonsei University, Incheon 21983, Korea;
| | - Jaecheol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Korea
- Biomedical Institute for Convergence at SKKU (BICS), Natural Sciences Campus, Sungkyunkwan University, Suwon 16419, Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (S.A.Y.); (K.H.N.); (M.G.L.); (H.O.); (J.S.N.); (J.K.J.); (S.K.); (Y.J.J.); (J.L.)
- Correspondence: ; Tel.: +82-31-290-7716
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11
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Zhao Y, Wang T, Zhang Y, Shi L, Zhang C, Zhang J, Yao J, Chen Q, Zhong X, Wei Y, Shan Y, Pan G. Coordination of EZH2 and SOX2 specifies human neural fate decision. CELL REGENERATION 2021; 10:30. [PMID: 34487238 PMCID: PMC8421500 DOI: 10.1186/s13619-021-00092-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022]
Abstract
Polycomb repressive complexes (PRCs) are essential in mouse gastrulation and specify neural ectoderm in human embryonic stem cells (hESCs), but the underlying molecular basis remains unclear. Here in this study, by employing an array of different approaches, such as gene knock-out, RNA-seq, ChIP-seq, et al., we uncover that EZH2, an important PRC factor, specifies the normal neural fate decision through repressing the competing meso/endoderm program. EZH2−/− hESCs show an aberrant re-activation of meso/endoderm genes during neural induction. At the molecular level, EZH2 represses meso/endoderm genes while SOX2 activates the neural genes to coordinately specify the normal neural fate. Moreover, EZH2 also supports the proliferation of human neural progenitor cells (NPCs) through repressing the aberrant expression of meso/endoderm program during culture. Together, our findings uncover the coordination of epigenetic regulators such as EZH2 and lineage factors like SOX2 in normal neural fate decision.
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Affiliation(s)
- Yuan Zhao
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Shi
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, Shandong, China
| | - Cong Zhang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingyuan Zhang
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiao Yao
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Qianyu Chen
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaofen Zhong
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yanxing Wei
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China. .,Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Hong Kong, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China. .,Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, Shandong, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
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12
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Zoroddu S, Marchesi I, Bagella L. PRC2: an epigenetic multiprotein complex with a key role in the development of rhabdomyosarcoma carcinogenesis. Clin Epigenetics 2021; 13:156. [PMID: 34372908 PMCID: PMC8351429 DOI: 10.1186/s13148-021-01147-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/02/2021] [Indexed: 02/02/2023] Open
Abstract
Skeletal muscle formation represents a complex of highly organized and specialized systems that are still not fully understood. Epigenetic systems underline embryonic development, maintenance of stemness, and progression of differentiation. Polycomb group proteins play the role of gene silencing of stemness markers that regulate muscle differentiation. Enhancer of Zeste EZH2 is the catalytic subunit of the complex that is able to trimethylate lysine 27 of histone H3 and induce silencing of the involved genes. In embryonal Rhabdomyosarcoma and several other tumors, EZH2 is often deregulated and, in some cases, is associated with tumor malignancy. This review explores the molecular processes underlying the failure of muscle differentiation with a focus on the PRC2 complex. These considerations could open new studies aimed at the development of new cutting-edge therapeutic strategies in the onset of Rhabdomyosarcoma.
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Affiliation(s)
- Stefano Zoroddu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100, Sassari, Italy
| | - Irene Marchesi
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100, Sassari, Italy
- Kitos Biotech Srls, Tramariglio, Alghero, SS, Italy
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100, Sassari, Italy.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
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13
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Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis. Blood 2021; 137:1327-1339. [PMID: 33512425 DOI: 10.1182/blood.2020005780] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/05/2020] [Indexed: 11/20/2022] Open
Abstract
While constitutive CCCTC-binding factor (CTCF)-binding sites are needed to maintain relatively invariant chromatin structures, such as topologically associating domains, the precise roles of CTCF to control cell-type-specific transcriptional regulation remain poorly explored. We examined CTCF occupancy in different types of primary blood cells derived from the same donor to elucidate a new role for CTCF in gene regulation during blood cell development. We identified dynamic, cell-type-specific binding sites for CTCF that colocalize with lineage-specific transcription factors. These dynamic sites are enriched for single-nucleotide polymorphisms that are associated with blood cell traits in different linages, and they coincide with the key regulatory elements governing hematopoiesis. CRISPR-Cas9-based perturbation experiments demonstrated that these dynamic CTCF-binding sites play a critical role in red blood cell development. Furthermore, precise deletion of CTCF-binding motifs in dynamic sites abolished interactions of erythroid genes, such as RBM38, with their associated enhancers and led to abnormal erythropoiesis. These results suggest a novel, cell-type-specific function for CTCF in which it may serve to facilitate interaction of distal regulatory emblements with target promoters. Our study of the dynamic, cell-type-specific binding and function of CTCF provides new insights into transcriptional regulation during hematopoiesis.
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14
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Vodnala M, Choi EB, Fong YW. Low complexity domains, condensates, and stem cell pluripotency. World J Stem Cells 2021; 13:416-438. [PMID: 34136073 PMCID: PMC8176841 DOI: 10.4252/wjsc.v13.i5.416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Biological reactions require self-assembly of factors in the complex cellular milieu. Recent evidence indicates that intrinsically disordered, low-complexity sequence domains (LCDs) found in regulatory factors mediate diverse cellular processes from gene expression to DNA repair to signal transduction, by enriching specific biomolecules in membraneless compartments or hubs that may undergo liquid-liquid phase separation (LLPS). In this review, we discuss how embryonic stem cells take advantage of LCD-driven interactions to promote cell-specific transcription, DNA damage response, and DNA repair. We propose that LCD-mediated interactions play key roles in stem cell maintenance and safeguarding genome integrity.
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Affiliation(s)
- Munender Vodnala
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Eun-Bee Choi
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Yick W Fong
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
- Harvard Stem Cell Institute, Cambridge, MA 02138, United States.
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15
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Roy U, Raghavan SC. Deleterious point mutations in T-cell acute lymphoblastic leukemia: Mechanistic insights into leukemogenesis. Int J Cancer 2021; 149:1210-1220. [PMID: 33634864 DOI: 10.1002/ijc.33527] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/11/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is characterized by the leukemogenic transformation of immature T cells, which accumulate an array of genetic and epigenetic lesions, leading to a sustained proliferation of abnormal T cells. Genetic alterations in the DNA repair genes, protooncogenes, transcription factors, and epigenetic modifiers have been studied in the past decade using next-generation sequencing and high-resolution copy number arrays. While other genomic lesions like chromosomal rearrangements, inversions, insertions, and gene fusions have been well studied at functional level, the mechanism of generation of driver mutations in T-ALL is the subject of current investigation. Novel oncogenic mutations in the TP53, BRCA2, PTEN, IL7R, RAS, NOTCH1, ETV6, BCL11B, WT1, DNMT3A, PRC2, PHF6, USP7, KDM6A and an array of other genes disrupt the genetic and epigenetic homeostasis in T-ALL. In this review, we have summarized the mechanistic role of deleterious driver mutations in T-ALL initiation and progression. We speculate that the formation of non-B DNA structures could be one of the primary reasons for the occurrence of different genomic lesions seen in T-ALL, which warrants further investigation. Understanding the mechanism behind the genesis of oncogenic mutations will pave the way to develop targeted therapies that can improve the overall survival and treatment outcome.
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Affiliation(s)
- Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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16
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The Role of Polycomb Group Protein BMI1 in DNA Repair and Genomic Stability. Int J Mol Sci 2021; 22:ijms22062976. [PMID: 33804165 PMCID: PMC7998361 DOI: 10.3390/ijms22062976] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 12/31/2022] Open
Abstract
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.
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17
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Zhao X, Rastogi A, Deton Cabanillas AF, Ait Mohamed O, Cantrel C, Lombard B, Murik O, Genovesio A, Bowler C, Bouyer D, Loew D, Lin X, Veluchamy A, Vieira FRJ, Tirichine L. Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2021; 229:3208-3220. [PMID: 33533496 DOI: 10.1111/nph.17129] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/24/2020] [Indexed: 05/28/2023]
Abstract
In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated.
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Affiliation(s)
- Xue Zhao
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
- CNRS UMR6286, UFIP UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière 44322, Nantes Cedex 03, France
| | - Achal Rastogi
- Corteva AgriscienceTM, Ascendas IT Park, 12th floor, Atria, V, Madhapur, Telangana, 500081, India
| | - Anne Flore Deton Cabanillas
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Ouardia Ait Mohamed
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Catherine Cantrel
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Berangère Lombard
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, PSL Research University, 26 rue d'Ulm, Cedex 05 Paris, 75248, France
| | - Omer Murik
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Auguste Genovesio
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Daniel Bouyer
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, PSL Research University, 26 rue d'Ulm, Cedex 05 Paris, 75248, France
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, Centre de Recherche, College of Ocean Camp; Earth Sciences,, Xiamen University, Xiamen, 361102, China
| | - Alaguraj Veluchamy
- Laboratory of Chromatin Biochemistry, 4700 King Abdullah University of Science and Technology (KAUST), BESE Division Building 2, Level 3, Office B2-3327, Thuwal, 23955-6900, Saudi Arabia
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Leila Tirichine
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
- CNRS UMR6286, UFIP UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière 44322, Nantes Cedex 03, France
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18
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Cheon YP, Choi D, Lee SH, Kim CG. YY1 and CP2c in Unidirectional Spermatogenesis and Stemness. Dev Reprod 2021; 24:249-262. [PMID: 33537512 PMCID: PMC7837418 DOI: 10.12717/dr.2020.24.4.249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/21/2020] [Accepted: 12/29/2020] [Indexed: 11/17/2022]
Abstract
Spermatogonial stem cells (SSCs) have stemness characteristics, including germ cell-specific imprints that allow them to form gametes. Spermatogenesis involves changes in gene expression such as a transition from expression of somatic to germ cell-specific genes, global repression of gene expression, meiotic sex chromosome inactivation, highly condensed packing of the nucleus with protamines, and morphogenesis. These step-by-step processes finally generate spermatozoa that are fertilization competent. Dynamic epigenetic modifications also confer totipotency to germ cells after fertilization. Primordial germ cells (PGCs) in embryos do not enter meiosis, remain in the proliferative stage, and are referred to as gonocytes, before entering quiescence. Gonocytes develop into SSCs at about 6 days after birth in rodents. Although chromatin structural modification by Polycomb is essential for gene silencing in mammals, and epigenetic changes are critical in spermatogenesis, a comprehensive understanding of transcriptional regulation is lacking. Recently, we evaluated the expression profiles of Yin Yang 1 (YY1) and CP2c in the gonads of E14.5 and 12-week-old mice. YY1 localizes at the nucleus and/or cytoplasm at specific stages of spermatogenesis, possibly by interaction with CP2c and YY1-interacting transcription factor. In the present article, we discuss the possible roles of YY1 and CP2c in spermatogenesis and stemness based on our results and a review of the relevant literature.
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Affiliation(s)
- Yong-Pil Cheon
- Division of Developmental Biology and Physiology, Institute for Basic Sciences, Sungshin University, Seoul 02844, Korea
| | - Donchan Choi
- Department of Life Science, College of Environmental Sciences, Yong-In University, Yongin 17092, Korea
| | - Sung-Ho Lee
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
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19
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Youmans DT, Gooding AR, Dowell RD, Cech TR. Competition between PRC2.1 and 2.2 subcomplexes regulates PRC2 chromatin occupancy in human stem cells. Mol Cell 2021; 81:488-501.e9. [PMID: 33338397 PMCID: PMC7867654 DOI: 10.1016/j.molcel.2020.11.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/05/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) silences expression of developmental transcription factors in pluripotent stem cells by methylating lysine 27 on histone H3. Two mutually exclusive subcomplexes, PRC2.1 and PRC2.2, are defined by the set of accessory proteins bound to the core PRC2 subunits. Here we introduce separation-of-function mutations into the SUZ12 subunit of PRC2 to drive it into a PRC2.1 or 2.2 subcomplex in human induced pluripotent stem cells (iPSCs). We find that PRC2.2 occupies polycomb target genes at low levels and that homeobox transcription factors are upregulated when this complex is exclusively present. In contrast with previous studies, we find that chromatin occupancy of PRC2 increases drastically when it is forced to form PRC2.1. Additionally, several cancer-associated mutations also coerce formation of PRC2.1. We suggest that PRC2 chromatin occupancy can be altered in the context of disease or development by tuning the ratio of PRC2.1 to PRC2.2.
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Affiliation(s)
- Daniel T Youmans
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; Medical Scientist Training Program, University of Colorado School of Medicine, Aurora, CO 80045, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Anne R Gooding
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Thomas R Cech
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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20
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Wang S, Xu X, Liu Y, Jin J, Zhu F, Bai W, Guo Y, Zhang J, Zuo H, Xu Z, Zuo B. RIP-Seq of EZH2 Identifies TCONS-00036665 as a Regulator of Myogenesis in Pigs. Front Cell Dev Biol 2021; 8:618617. [PMID: 33511127 PMCID: PMC7835406 DOI: 10.3389/fcell.2020.618617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 and contains a SET domain that catalyzes histone H3 trimethylation on lysine 27 (H3K27me3) to generate an epigenetic silencing mark. EZH2 interacts with transcription factors or RNA transcripts to perform its function. In this study, we applied RNA immunoprecipitation sequencing and long intergenic non-coding RNA (lincRNA) sequencing methods to identify EZH2-binding lincRNAs. A total of 356 novel EZH2-binding lincRNAs were identified by bioinformatics analysis and an EZH2-binding lincRNA TCONS-00036665 was characterized. TCONS-00036665 promoted pig skeletal satellite cell proliferation but inhibited cell differentiation, and this function was conserved between pigs and mice. Further mechanistic studies indicated that TCONS-00036665 can bind to EZH2 and recruits EZH2 to the promoters of the target genes p21, MyoG, and Myh4, which leads to the enrichment of H3K27me3 and the repression of target gene expression and pig myogenesis. In conclusion, the lincRNA TCONS-00036665 regulates pig myogenesis through its interaction with EZH2.
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Affiliation(s)
- Shanshan Wang
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xuewen Xu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yan Liu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jianjun Jin
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Feng Zhu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Wei Bai
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yubo Guo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jiali Zhang
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hao Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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21
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Muñoa-Hoyos I, Halsall JA, Araolaza M, Ward C, Garcia I, Urizar-Arenaza I, Gianzo M, Garcia P, Turner B, Subirán N. Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs. Clin Epigenetics 2020; 12:170. [PMID: 33168052 PMCID: PMC7654014 DOI: 10.1186/s13148-020-00955-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Environmentally induced epigenetic changes can lead to health problems or disease, but the mechanisms involved remain unclear. Morphine can pass through the placental barrier leading to abnormal embryo development. However, the mechanism by which morphine causes these effects and how they sometimes persist into adulthood is not well known. To unravel the morphine-induced chromatin alterations involved in aberrant embryo development, we explored the role of the H3K27me3/PRC2 repressive complex in gene expression and its transmission across cellular generations in response to morphine. Results Using mouse embryonic stem cells as a model system, we found that chronic morphine treatment induces a global downregulation of the histone modification H3K27me3. Conversely, ChIP-Seq showed a remarkable increase in H3K27me3 levels at specific genomic sites, particularly promoters, disrupting selective target genes related to embryo development, cell cycle and metabolism. Through a self-regulatory mechanism, morphine downregulated the transcription of PRC2 components responsible for H3K27me3 by enriching high H3K27me3 levels at the promoter region. Downregulation of PRC2 components persisted for at least 48 h (4 cell cycles) following morphine removal, though promoter H3K27me3 levels returned to control levels.
Conclusions Morphine induces targeting of the PRC2 complex to selected promoters, including those of PRC2 components, leading to characteristic changes in gene expression and a global reduction in H3K27me3. Following morphine removal, enhanced promoter H3K27me3 levels revert to normal sooner than global H3K27me3 or PRC2 component transcript levels. We suggest that H3K27me3 is involved in initiating morphine-induced changes in gene expression, but not in their maintenance. Graphic abstract Model of Polycomb repressive complex 2 (PRC2) and H3K27me3 alterations induced by chronic morphine exposure. Morphine induces H3K27me3 enrichment at promoters of genes encoding core members of the PRC2 complex and is associated with their transcriptional downregulation.![]()
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Affiliation(s)
- Iraia Muñoa-Hoyos
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.,Innovation in Assisted Reproduction Group, Bizkaia Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - John A Halsall
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Manu Araolaza
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain
| | - Carl Ward
- Stem Cell Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Idoia Garcia
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.,Biodonostia Health Research Institute, 2009 San Sebastian, Gipuzkoa, Spain
| | - Itziar Urizar-Arenaza
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain.,Innovation in Assisted Reproduction Group, Bizkaia Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Marta Gianzo
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain
| | - Paloma Garcia
- Stem Cell Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Bryan Turner
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Nerea Subirán
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940, Leioa, Bizkaia, Spain. .,Innovation in Assisted Reproduction Group, Bizkaia Health Research Institute, 48903 Barakaldo, Bizkaia, Spain.
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22
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Bai M, Ye D, Guo X, Xi J, Liu N, Wu Y, Jia W, Wang G, Chen W, Li G, Jiapaer Z, Kang J. Critical regulation of a NDIME/MEF2C axis in embryonic stem cell neural differentiation and autism. EMBO Rep 2020; 21:e50283. [PMID: 33016573 DOI: 10.15252/embr.202050283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/28/2020] [Accepted: 09/04/2020] [Indexed: 12/27/2022] Open
Abstract
A microdeletion within human chromosome 5q14.3 has been associated with the occurrence of neurodevelopmental disorders, such as autism and intellectual disability, and MEF2C haploinsufficiency was identified as main cause. Here, we report that a brain-enriched long non-coding RNA, NDIME, is located near the MEF2C locus and is required for normal neural differentiation of mouse embryonic stem cells (mESCs). NDIME interacts with EZH2, the major component of polycomb repressive complex 2 (PRC2), and blocks EZH2-mediated trimethylation of histone H3 lysine 27 (H3K27me3) at the Mef2c promoter, promoting MEF2C transcription. Moreover, the expression levels of both NDIME and MEF2C were strongly downregulated in the hippocampus of a mouse model of autism, and the adeno-associated virus (AAV)-mediated expression of NDIME in the hippocampus of these mice significantly increased MEF2C expression and ameliorated autism-like behaviors. The results of this study reveal an epigenetic mechanism by which NDIME regulates MEF2C transcription and neural differentiation and suggest potential effects and therapeutic approaches of the NDIME/MEF2C axis in autism.
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Affiliation(s)
- Mingliang Bai
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Dan Ye
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Institute for Advanced Study, Tongji University, Shanghai, China
| | - Jiajie Xi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Nana Liu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenwen Jia
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Institute of Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guiying Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wen Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guoping Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zeyidan Jiapaer
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Xinjiang Key Laboratory of Biology Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Tsingtao Advanced Research Institute, Tongji University, Qingdao, China
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23
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Abstract
The interaction between polycomb-repressive complexes 1/2 (PRC1/2) and long non-coding RNA (lncRNA), such as the X inactive specific transcript Xist and the HOX transcript antisense RNA (HOTAIR), has been the subject of intense debate. While cross-linking, immuno-precipitation and super-resolution microscopy argue against direct interaction of Polycomb with some lncRNAs, there is increasing evidence supporting the ability of both PRC1 and PRC2 to functionally associate with RNA. Recent data indicate that these interactions are in most cases spurious, but nonetheless crucial for a number of cellular activities. In this review, we suggest that while PRC1/2 recruitment by HOTAIR might be direct, in the case of Xist, it might occur indirectly and, at least in part, through the process of liquid-liquid phase separation. We present recent models of lncRNA-mediated PRC1/2 recruitment to their targets and describe potential RNA-mediated roles in the three-dimensional organization of the nucleus.
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Affiliation(s)
- Andrea Cerase
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain.,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy.,Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163, Genoa, Italy
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24
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Dong C, Nakagawa R, Oyama K, Yamamoto Y, Zhang W, Dong A, Li Y, Yoshimura Y, Kamiya H, Nakayama JI, Ueda J, Min J. Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19. eLife 2020; 9:58675. [PMID: 32869745 PMCID: PMC7492083 DOI: 10.7554/elife.58675] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/29/2020] [Indexed: 12/30/2022] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is a multicomponent histone H3K27 methyltransferase complex, best known for silencing the Hox genes during embryonic development. The Polycomb-like proteins PHF1, MTF2, and PHF19 are critical components of PRC2 by stimulating its catalytic activity in embryonic stem cells. The Tudor domains of PHF1/19 have been previously shown to be readers of H3K36me3 in vitro. However, some other studies suggest that PHF1 and PHF19 co-localize with the H3K27me3 mark but not H3K36me3 in cells. Here, we provide further evidence that PHF1 co-localizes with H3t in testis and its Tudor domain preferentially binds to H3tK27me3 over canonical H3K27me3 in vitro. Our complex structures of the Tudor domains of PHF1 and PHF19 with H3tK27me3 shed light on the molecular basis for preferential recognition of H3tK27me3 by PHF1 and PHF19 over canonical H3K27me3, implicating that H3tK27me3 might be a physiological ligand of PHF1/19.
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Affiliation(s)
- Cheng Dong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Reiko Nakagawa
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Kyohei Oyama
- Department of Cardiac Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Yusuke Yamamoto
- Department of Cardiac Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Weilian Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan
| | - Hiroyuki Kamiya
- Department of Cardiac Surgery, Asahikawa Medical University, Asahikawa, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Jun Ueda
- Centre for Advanced Research and Education, Asahikawa Medical University, Asahikawa, Japan
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Canada.,Department of Physiology, University of Toronto, Toronto, Canada
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25
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Kralemann LEM, Liu S, Trejo-Arellano MS, Muñoz-Viana R, Köhler C, Hennig L. Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis. Genome Biol 2020; 21:144. [PMID: 32546254 PMCID: PMC7296913 DOI: 10.1186/s13059-020-02062-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and subsequent trimethylation of lysine 27 of histone 3 (H3K27me3). Previous work proposed that H2Aub1 removal by the ubiquitin-specific proteases 12 and 13 (UBP12 and UBP13) is part of the repressive PRC1&2 system, but its functional role remains elusive. RESULTS We show that UBP12 and UBP13 work together with PRC1, PRC2, and EMF1 to repress genes involved in stimulus response. We find that PRC1-mediated H2Aub1 is associated with gene responsiveness, and its repressive function requires PRC2 recruitment. We further show that the requirement of PRC1 for PRC2 recruitment depends on the initial expression status of genes. Lastly, we demonstrate that removal of H2Aub1 by UBP12/13 prevents loss of H3K27me3, consistent with our finding that the H3K27me3 demethylase REF6 is positively associated with H2Aub1. CONCLUSIONS Our data allow us to propose a model in which deposition of H2Aub1 permits genes to switch between repression and activation by H3K27me3 deposition and removal. Removal of H2Aub1 by UBP12/13 is required to achieve stable PRC2-mediated repression.
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Affiliation(s)
- Lejon E. M. Kralemann
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| | - Shujing Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| | - Minerva S. Trejo-Arellano
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| | - Rafael Muñoz-Viana
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, 03550 Sant Joan d’Alacant, Spain
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, SE-75007 Uppsala, Sweden
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26
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MMTR/Dmap1 Sets the Stage for Early Lineage Commitment of Embryonic Stem Cells by Crosstalk with PcG Proteins. Cells 2020; 9:cells9051190. [PMID: 32403252 PMCID: PMC7290897 DOI: 10.3390/cells9051190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/05/2020] [Accepted: 05/08/2020] [Indexed: 01/13/2023] Open
Abstract
Chromatin remodeling, including histone modification, chromatin (un)folding, and nucleosome remodeling, is a significant transcriptional regulation mechanism. By these epigenetic modifications, transcription factors and their regulators are recruited to the promoters of target genes, and thus gene expression is controlled through either transcriptional activation or repression. The Mat1-mediated transcriptional repressor (MMTR)/DNA methyltransferase 1 (DNMT1)-associated protein (Dmap1) is a transcription corepressor involved in chromatin remodeling, cell cycle regulation, DNA double-strand break repair, and tumor suppression. The Tip60-p400 complex proteins, including MMTR/Dmap1, interact with the oncogene Myc in embryonic stem cells (ESCs). These proteins interplay with the stem cell-related proteome networks and regulate gene expressions. However, the detailed mechanisms of their functions are unknown. Here, we show that MMTR/Dmap1, along with other Tip60-p400 complex proteins, bind the promoters of differentiation commitment genes in mouse ESCs. Hence, MMTR/Dmap1 controls gene expression alterations during differentiation. Furthermore, we propose a novel mechanism of MMTR/Dmap1 function in early stage lineage commitment of mouse ESCs by crosstalk with the polycomb group (PcG) proteins. The complex controls histone mark bivalency and transcriptional poising of commitment genes. Taken together, our comprehensive findings will help better understand the MMTR/Dmap1-mediated transcriptional regulation in ESCs and other cell types.
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27
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Raby L, Völkel P, Le Bourhis X, Angrand PO. The Polycomb Orthologues in Teleost Fishes and Their Expression in the Zebrafish Model. Genes (Basel) 2020; 11:genes11040362. [PMID: 32230868 PMCID: PMC7230241 DOI: 10.3390/genes11040362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 01/25/2023] Open
Abstract
The Polycomb Repressive Complex 1 (PRC1) is a chromatin-associated protein complex involved in transcriptional repression of hundreds of genes controlling development and differentiation processes, but also involved in cancer and stem cell biology. Within the canonical PRC1, members of Pc/CBX protein family are responsible for the targeting of the complex to specific gene loci. In mammals, the Pc/CBX protein family is composed of five members generating, through mutual exclusion, different PRC1 complexes with potentially distinct cellular functions. Here, we performed a global analysis of the cbx gene family in 68 teleost species and traced the distribution of the cbx genes through teleost evolution in six fish super-orders. We showed that after the teleost-specific whole genome duplication, cbx4, cbx7 and cbx8 are retained as pairs of ohnologues. In contrast, cbx2 and cbx6 are present as pairs of ohnologues in the genome of several teleost clades but as singletons in others. Furthermore, since zebrafish is a widely used vertebrate model for studying development, we report on the expression of the cbx family members during zebrafish development and in adult tissues. We showed that all cbx genes are ubiquitously expressed with some variations during early development.
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28
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Marcho C, Oluwayiose OA, Pilsner JR. The preconception environment and sperm epigenetics. Andrology 2020; 8:924-942. [PMID: 31901222 DOI: 10.1111/andr.12753] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/12/2019] [Accepted: 12/31/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Infertility is a common reproductive disorder, with male factor infertility accounting for approximately half of all cases. Taking a paternal perceptive, recent research has shown that sperm epigenetics, such as changes in DNA methylation, histone modification, chromatin structure, and noncoding RNA expression, can impact reproductive and offspring health. Importantly, environmental conditions during the preconception period has been demonstrated to shape sperm epigenetics. OBJECTIVES To provide an overview on epigenetic modifications that regulate normal gene expression and epigenetic remodeling that occurs during spermatogenesis, and to discuss the epigenetic alterations that may occur to the paternal germline as a consequence of preconception environmental conditions and exposures. MATERIALS AND METHODS We examined published literature available on databases (PubMed, Google Scholar, ScienceDirect) focusing on adult male preconception environmental exposures and sperm epigenetics in epidemiologic studies and animal models. RESULTS The preconception period is a sensitive developmental window in which a variety of exposures such as toxicants, nutrition, drugs, stress, and exercise, affects sperm epigenetics. DISCUSSION AND CONCLUSION Understanding the environmental legacy of the sperm epigenome during spermatogenesis will enhance our understanding of reproductive health and improve reproductive success and offspring well-being.
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Affiliation(s)
- Chelsea Marcho
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Oladele A Oluwayiose
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts
| | - J Richard Pilsner
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts
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29
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Shan Y, Zhang Y, Zhao Y, Wang T, Zhang J, Yao J, Ma N, Liang Z, Huang W, Huang K, Zhang T, Su Z, Chen Q, Zhu Y, Wu C, Zhou T, Sun W, Wei Y, Zhang C, Li C, Su S, Liao B, Zhong M, Zhong X, Nie J, Pei D, Pan G. JMJD3 and UTX determine fidelity and lineage specification of human neural progenitor cells. Nat Commun 2020; 11:382. [PMID: 31959746 PMCID: PMC6971254 DOI: 10.1038/s41467-019-14028-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/13/2019] [Indexed: 02/08/2023] Open
Abstract
Neurogenesis, a highly orchestrated process, entails the transition from a pluripotent to neural state and involves neural progenitor cells (NPCs) and neuronal/glial subtypes. However, the precise epigenetic mechanisms underlying fate decision remain poorly understood. Here, we delete KDM6s (JMJD3 and/or UTX), the H3K27me3 demethylases, in human embryonic stem cells (hESCs) and show that their deletion does not impede NPC generation from hESCs. However, KDM6-deficient NPCs exhibit poor proliferation and a failure to differentiate into neurons and glia. Mechanistically, both JMJD3 and UTX are found to be enriched in gene loci essential for neural development in hNPCs, and KDM6 impairment leads to H3K27me3 accumulation and blockade of DNA accessibility at these genes. Interestingly, forced expression of neuron-specific chromatin remodelling BAF (nBAF) rescues the neuron/glia defect in KDM6-deficient NPCs despite H3K27me3 accumulation. Our findings uncover the differential requirement of KDM6s in specifying NPCs and neurons/glia and highlight the contribution of individual epigenetic regulators in fate decisions in a human development model. Neurogenesis is an ordered transition from pluriptotent cells to neural precursor cells (NPCs) to neurons. Here the authors show that loss of the lysine demethylases JMJD3 and UTX leads reduced DNA accessibility at neurogenesis loci in human NPCs, and that the chromatin remodeller BAF can rescue differentiation defects.
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Affiliation(s)
- Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yuan Zhao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jingyuan Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jiao Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Ning Ma
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Zechuan Liang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Wenhao Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Ke Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tian Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Zhenghui Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Qianyu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanling Zhu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Chuman Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tiancheng Zhou
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Wei Sun
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanxing Wei
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Cong Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Chenxu Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Shuquan Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Baojian Liao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Mei Zhong
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaofen Zhong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jinfu Nie
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China. .,Shandong Medicinal Biotechnology Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250012, China. .,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, China.
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30
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Naskou J, Beiter Y, van Rensburg R, Honisch E, Rudelius M, Schlensog M, Gottstein J, Walter L, Braicu EI, Sehouli J, Darb-Esfahani S, Staebler A, Hartkopf AD, Brucker S, Wallwiener D, Beyer I, Niederacher D, Fehm T, Templin MF, Neubauer H. EZH2 Loss Drives Resistance to Carboplatin and Paclitaxel in Serous Ovarian Cancers Expressing ATM. Mol Cancer Res 2019; 18:278-286. [DOI: 10.1158/1541-7786.mcr-19-0141] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/28/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022]
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31
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Wang CY, Brand H, Shaw ND, Talkowski ME, Lee JT. Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans. Genetics 2019; 213:685-703. [PMID: 31420322 PMCID: PMC6781896 DOI: 10.1534/genetics.119.302600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an architectural factor critical for X-chromosome inactivation (XCI) and the repression of select autosomal gene clusters. In mice, homozygous nonsense mutations in Smchd1 cause female-specific embryonic lethality due to an XCI defect. However, although human mutations in SMCHD1 are associated with congenital arhinia and facioscapulohumeral muscular dystrophy type 2 (FSHD2), the diseases do not show a sex-specific bias, despite the essential nature of XCI in humans. To investigate whether there is a dosage imbalance for the sex chromosomes, we here analyze transcriptomic data from arhinia and FSHD2 patient blood and muscle cells. We find that X-linked dosage compensation is maintained in these patients. In mice, SMCHD1 controls not only protocadherin (Pcdh) gene clusters, but also Hox genes critical for craniofacial development. Ablating Smchd1 results in aberrant expression of these genes, coinciding with altered chromatin states and three-dimensional (3D) topological organization. In a subset of FSHD2 and arhinia patients, we also found dysregulation of clustered PCDH, but not HOX genes. Overall, our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters.
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Affiliation(s)
- Chen-Yu Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Natalie D Shaw
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael E Talkowski
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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32
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Abstract
Transcriptional co-activator Prdm16 controls brown fat development and white fat browning, but how this thermogenic function is modulated post-translationally is poorly understood. Here, we report that Cbx4, a Polycomb group protein, is a SUMO E3 ligase for Prdm16 and that Cbx4-mediated sumoylation of Prdm16 is required for thermogenic gene expression. Cbx4 expression is enriched in brown fat and is induced in adipose tissue by acute cold exposure. Sumoylation of Prdm16 at lysine 917 by Cbx4 blocks its ubiquitination-mediated degradation, thereby augmenting its stability and thermogenic function. Moreover, this sumoylation event primes Prdm16 to be further stabilized by methyltransferase Ehmt1. Heterozygous Cbx4-knockout mice develop metabolic phenotypes resembling those of Prdm16-knockout mice. Furthermore, fat-specific Cbx4 knockdown and overexpression produce remarkable, opposite effects on white fat remodeling. Our results identify a modifying enzyme for Prdm16, and they demonstrate a central role of Cbx4 in the control of Prdm16 stability and white fat browning.
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Affiliation(s)
- Qingbo Chen
- Department of Molecular, Cell and Cancer Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lei Huang
- Department of Molecular, Cell and Cancer Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dongning Pan
- Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Lihua J Zhu
- Department of Molecular, Cell and Cancer Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yong-Xu Wang
- Department of Molecular, Cell and Cancer Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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33
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Guo X, Wang Z, Lu C, Hong W, Wang G, Xu Y, Liu Z, Kang J. LincRNA-1614 coordinates Sox2/PRC2-mediated repression of developmental genes in pluripotency maintenance. J Mol Cell Biol 2019; 10:118-129. [PMID: 28992244 PMCID: PMC5951109 DOI: 10.1093/jmcb/mjx041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 09/12/2017] [Indexed: 11/14/2022] Open
Abstract
Large-intergenic noncoding RNAs (lincRNAs) cooperate with core transcription factors to coordinate the pluripotency network of embryonic stem cells. The mechanisms by which lincRNAs affect chromatin structure and gene transcription remain mostly unknown. Here, we identified that a lincRNA (linc1614), occupied by pluripotency factors at its promoter, was indispensable for both maintenance and acquisition of pluripotency. Linc1614 served as a specific partner of core factor Sox2 in maintaining pluripotency, primarily by mediating the function of Sox2 in the repression of developmental genes. Moreover, Ezh2, an essential subunit of polycomb repressive complex 2 (PRC2), physically interacted with linc1614 and contributed to lincRNA-mediated transcriptional silencing. Thus, we propose that the interplay of linc1614 with Sox2 implicates this lincRNA as a recruitment platform that mediates transcriptional silencing by guiding the PRC2 complex to the loci of developmental genes.
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Affiliation(s)
- Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai 200092, China.,Institute of Regenerative Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Zikang Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Chenqi Lu
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Wujun Hong
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Guiying Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yanxin Xu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Zhongmin Liu
- Institute of Regenerative Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Health Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Science and Technology, Tongji University, Shanghai 200092, China
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34
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Descamps B, Saif J, Benest AV, Biglino G, Bates DO, Chamorro-Jorganes A, Emanueli C. BDNF (Brain-Derived Neurotrophic Factor) Promotes Embryonic Stem Cells Differentiation to Endothelial Cells Via a Molecular Pathway, Including MicroRNA-214, EZH2 (Enhancer of Zeste Homolog 2), and eNOS (Endothelial Nitric Oxide Synthase). Arterioscler Thromb Vasc Biol 2019; 38:2117-2125. [PMID: 30354255 DOI: 10.1161/atvbaha.118.311400] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Objective- The NTs (neurotrophins), BDNF (brain-derived neurotrophic factor) and NT-3 promote vascular development and angiogenesis. This study investigated the contribution of endogenous NTs in embryonic stem cell (ESC) vascular differentiation and the potential of exogenous BDNF to improve the process of ESC differentiation to endothelial cells (ECs). Approach and Results- Mouse ESCs were differentiated into vascular cells using a 2-dimensional embryoid body (EB) model. Supplementation of either BDNF or NT-3 increased EC progenitors' abundance at day 7 and enlarged the peripheral vascular plexus with ECs and SM22α+ (smooth muscle 22 alpha-positive) smooth muscle cells by day 13. Conversely, inhibition of either BDNF or NT-3 receptor signaling reduced ECs, without affecting smooth muscle cells spread. This suggests that during vascular development, endogenous NTs are especially relevant for endothelial differentiation. At mechanistic level, we have identified that BDNF-driven ESC-endothelial differentiation is mediated by a pathway encompassing the transcriptional repressor EZH2 (enhancer of zeste homolog 2), microRNA-214 (miR-214), and eNOS (endothelial nitric oxide synthase). It was known that eNOS, which is needed for endothelial differentiation, can be transcriptionally repressed by EZH2. In turn, miR-214 targets EZH2 for inhibition. We newly found that in ESC-ECs, BDNF increases miR-214 expression, reduces EZH2 occupancy of the eNOS promoter, and increases eNOS expression. Moreover, we found that NRP-1 (neuropilin 1), KDR (kinase insert domain receptor), and pCas130 (p130 Crk-associated substrate kinase), which reportedly induce definitive endothelial differentiation of pluripotent cells, were increased in BDNF-conditioned ESC-EC. Mechanistically, miR-214 mediated the BDNF-induced expressional changes, contributing to BDNF-driven endothelial differentiation. Finally, BDNF-conditioned ESC-ECs promoted angiogenesis in vitro and in vivo. Conclusions- BDNF promotes ESC-endothelial differentiation acting via miR-214.
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Affiliation(s)
- Betty Descamps
- From the Bristol Heart Institute, School of Clinical Sciences, University of Bristol, United Kingdom (B.D., J.S., G.B., C.E.)
| | - Jaimy Saif
- From the Bristol Heart Institute, School of Clinical Sciences, University of Bristol, United Kingdom (B.D., J.S., G.B., C.E.)
| | - Andrew V Benest
- Tumour and Vascular Biology Laboratories, Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, United Kingdom (A.V.B., D.O.B.)
| | - Giovanni Biglino
- From the Bristol Heart Institute, School of Clinical Sciences, University of Bristol, United Kingdom (B.D., J.S., G.B., C.E.)
| | - David O Bates
- Tumour and Vascular Biology Laboratories, Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, United Kingdom (A.V.B., D.O.B.)
| | | | - Costanza Emanueli
- From the Bristol Heart Institute, School of Clinical Sciences, University of Bristol, United Kingdom (B.D., J.S., G.B., C.E.)
- National Heart and Lung Institute, Imperial College London, United Kingdom (A.C.-J., C.E.)
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35
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Ezh1 arises from Ezh2 gene duplication but its function is not required for zebrafish development. Sci Rep 2019; 9:4319. [PMID: 30867490 PMCID: PMC6416316 DOI: 10.1038/s41598-019-40738-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/18/2019] [Indexed: 02/07/2023] Open
Abstract
Trimethylation on H3K27 mediated by Polycomb Repressive Complex 2 (PRC2) is required to control gene repression programs involved in development, regulation of tissue homeostasis or maintenance and lineage specification of stem cells. In Drosophila, the PRC2 catalytic subunit is the single protein E(z), while in mammals this function is fulfilled by two proteins, Ezh1 and Ezh2. Based on database searches, we propose that Ezh1 arose from an Ezh2 gene duplication that has occurred in the common ancestor to elasmobranchs and bony vertebrates. Expression studies in zebrafish using in situ hybridization and RT-PCR followed by the sequencing of the amplicon revealed that ezh1 mRNAs are maternally deposited. Then, ezh1 transcripts are ubiquitously distributed in the entire embryo at 24 hpf and become more restricted to anterior part of the embryo at later developmental stages. To unveil the function of ezh1 in zebrafish, a mutant line was generated using the TALEN technology. Ezh1-deficient mutant fish are viable and fertile, but the loss of ezh1 function is responsible for the earlier death of ezh2 mutant larvae indicating that ezh1 contributes to zebrafish development in absence of zygotic ezh2 gene function. Furthermore, we show that presence of ezh1 transcripts from the maternal origin accounts for the delayed lethality of ezh2-deficient larvae.
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36
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Yang L, Zha Y, Ding J, Ye B, Liu M, Yan C, Dong Z, Cui H, Ding HF. Histone demethylase KDM6B has an anti-tumorigenic function in neuroblastoma by promoting differentiation. Oncogenesis 2019; 8:3. [PMID: 30631055 PMCID: PMC6328563 DOI: 10.1038/s41389-018-0112-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/19/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023] Open
Abstract
Induction of differentiation is a therapeutic strategy in high-risk neuroblastoma, a childhood cancer of the sympathetic nervous system. Neuroblastoma differentiation requires transcriptional upregulation of neuronal genes. How this process is regulated at epigenetic levels is not well understood. Here we report that the histone H3 lysine 27 demethylase KDM6B is an epigenetic activator of neuroblastoma cell differentiation. KDM6B mRNA expression is downregulated in poorly differentiated high-risk neuroblastomas and upregulated in differentiated tumors, and high KDM6B expression is prognostic for better survival in neuroblastoma patients. In neuroblastoma cell lines, KDM6B depletion promotes cell proliferation, whereas KDM6B overexpression induces neuronal differentiation and inhibits cell proliferation and tumorgenicity. Mechanistically, KDM6B epigenetically activates the transcription of neuronal genes by removing the repressive chromatin marker histone H3 lysine 27 trimethylation. In addition, we show that KDM6B functions downstream of the retinoic acid-HOXC9 axis in inducing neuroblastoma cell differentiation: KDM6B expression is upregulated by retinoic acid via HOXC9, and KDM6B is required for HOXC9-induced neuroblastoma cell differentiation. Finally, we present evidence that KDM6B interacts with HOXC9 to target neuronal genes for epigenetic activation. These findings identify a KDM6B-dependent epigenetic mechanism in the control of neuroblastoma cell differentiation, providing a rationale for reducing histone H3 lysine 27 trimethylation as a strategy for enhancing differentiation-based therapy in high-risk neuroblastoma.
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Affiliation(s)
- Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Yunhong Zha
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Jane Ding
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Bingwei Ye
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Mengling Liu
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA.,Department of Biochemistry and Molecular, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Zheng Dong
- Department of Cell Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Charlie Norwood VA Medical Center, Augusta, GA, 30904, USA
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China.
| | - Han-Fei Ding
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA. .,Department of Biochemistry and Molecular, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA. .,Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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37
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Abstract
Gametogenesis represents the most dramatic cellular differentiation pathways in both female and male flies. At the genome level, meiosis ensures that diploid germ cells become haploid gametes. At the epigenome level, extensive changes are required to turn on and shut off gene expression in a precise spatiotemporally controlled manner. Research applying conventional molecular genetics and cell biology, in combination with rapidly advancing genomic tools have helped us to investigate (1) how germ cells maintain lineage specificity throughout their adult reproductive lifetime; (2) what molecular mechanisms ensure proper oogenesis and spermatogenesis, as well as protect genome integrity of the germline; (3) how signaling pathways contribute to germline-soma communication; and (4) if such communication is important. In this chapter, we highlight recent discoveries that have improved our understanding of these questions. On the other hand, restarting a new life cycle upon fertilization is a unique challenge faced by gametes, raising questions that involve intergenerational and transgenerational epigenetic inheritance. Therefore, we also discuss new developments that link changes during gametogenesis to early embryonic development-a rapidly growing field that promises to bring more understanding to some fundamental questions regarding metazoan development.
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38
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Ganapathi M, Boles NC, Charniga C, Lotz S, Campbell M, Temple S, Morse RH. Effect of Bmi1 over-expression on gene expression in adult and embryonic murine neural stem cells. Sci Rep 2018; 8:7464. [PMID: 29749381 PMCID: PMC5945652 DOI: 10.1038/s41598-018-25921-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 04/30/2018] [Indexed: 11/13/2022] Open
Abstract
The ability of isolated neural stem cells (NSCs) to proliferate as neurospheres is indicative of their competence as stem cells, and depends critically on the polycomb group (PcG) member Bmi1: knockdown of Bmi1 results in defective proliferation and self-renewal of isolated NSCs, whereas overexpression of Bmi1 enhances these properties. Here we report genome-wide changes in gene expression in embryonic and adult NSCs (eNSCs and aNSCs) caused by overexpression of Bmi1. We find that genes whose expression is altered by perturbations in Bmi1 levels in NSCs are mostly distinct from those affected in other multipotent stem/progenitor cells, such as those from liver and lung, aside from a small core of common targets that is enriched for genes associated with cell migration and mobility. We also show that genes differing in expression between prospectively isolated quiescent and activated NSCs are not affected by Bmi1 overexpression. In contrast, a comparison of genes showing altered expression upon Bmi1 overexpression in eNSCs and in aNSCs reveals considerable overlap, in spite of their different provenances in the brain and their differing developmental programs.
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Affiliation(s)
- Mythily Ganapathi
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Dept. of Health, Albany, NY, USA
| | | | | | - Steven Lotz
- Neural Stem Cell Institute, Rensselaer, NY, USA
| | | | | | - Randall H Morse
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Dept. of Health, Albany, NY, USA. .,Department of Biomedical Science, University at Albany School of Public Health, Albany, NY, USA.
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39
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Zayed H, Petersen I. Stem cell transcription factor SOX2 in synovial sarcoma and other soft tissue tumors. Pathol Res Pract 2018; 214:1000-1007. [PMID: 29773426 DOI: 10.1016/j.prp.2018.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND SOX2 has gained considerable interest as a pluripotency inducing gene. Co-transfection of SOX2 together with NANOG, KLF4 and c-MYC into adult fibroblasts was able to generate pluripotent stem cells. SOX2 has been reported to be expressed in synovial sarcoma, a tumor being characterized by the SS18-SSX gene fusion forming part of the SWI/SNF chromatin remodeling complex that affects histone methylation. The role of SOX2 in this tumor type as well as other soft tissue tumor entities however is still poorly characterized. We analyzed SOX2 protein expression in soft tissue tumors. Alongside we tested Histone H3 expression (H3K27me3) in SOX2 positive cases to investigate this epigenetic mark and its correlation with the SOX2 status and clinicopathological parameters. METHODOLOGY In total, 60 samples of synovial sarcomas from the reference center for soft tissue tumors at the institute of pathology of the Jena University hospital were included into the study along with 343 other tissue tumors. Protein analysis was done by immunohistochemistry of tissue microarrays. All synovial sarcoma cases were confirmed by molecular testing using SS18 FISH break apart probes. RESULTS SOX2 reactivity was detectable in 35 synovial sarcoma cases (58.3%) while 25 (41.7%) were negative. Only 13 cases of the other 343 soft tissue tumors, varying from nodular fasciitis to undifferentiated pleomorphic sarcoma, revealed a SOX2 expression, 12 out of these were undifferentiated high grade sarcoma. There was no obvious correlation with the clinicopathological data. H3K27me3 immunohistochemistry of the synovial sarcoma cases revealed a high statistically significant correlation between SOX2 and H3K27me3 expression (p < 0,0005, Chi square test). Similar to SOX2, there was no correlation between H3K27me3 expression and tumor grade. Six SOX2 positive synovial sarcoma cases were analyzed by FISH using a SOX2/CEN3 dual color FISH probe. None of these cases revealed an amplification of the SOX2 gene. CONCLUSION The data confirms previous studies reporting SOX2 and H3K27me3 expression in synovial sarcoma and reveals that both biomarkers are related to each other. It strengthens the notion that the tumor type is driven by epigenetic processes similar to those that are operating in pluripotent stem cells. The relevance of these parameters in the pathway pathology of synovial sarcoma, i.e. the timing and dosing of SOX2 and H3K27me3 expression initiated by the SS18-SSX driver mutation together with the interplay of these events with other signaling pathways, cellular mechanisms and additional mutations in tumor progression, will require further studies.
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Affiliation(s)
- Heba Zayed
- Institute of Pathology, Jena University Hospital, Germany; National Cancer Institute, Cairo University, Egypt
| | - Iver Petersen
- Institute of Pathology, Jena University Hospital, Germany.
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40
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Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat Cell Biol 2018; 20:620-631. [DOI: 10.1038/s41556-018-0093-4] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 03/21/2018] [Indexed: 12/24/2022]
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41
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Marasca F, Bodega B, Orlando V. How Polycomb-Mediated Cell Memory Deals With a Changing Environment. Bioessays 2018. [DOI: 10.1002/bies.201700137] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Federica Marasca
- Istituto Nazionale di Genetica Molecolare (INGM) “Romeo and Enrica Invernizzi”; Milan 20122 Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare (INGM) “Romeo and Enrica Invernizzi”; Milan 20122 Italy
| | - Valerio Orlando
- King Abdullah University of Science and Technology (KAUST); Environmental Epigenetics Research Program; Biological and Environmental Sciences and Engineering Division; Thuwal 23955-6900 Saudi Arabia
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42
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From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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43
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Choi R, Goldstein BJ. Olfactory epithelium: Cells, clinical disorders, and insights from an adult stem cell niche. Laryngoscope Investig Otolaryngol 2018; 3:35-42. [PMID: 29492466 PMCID: PMC5824112 DOI: 10.1002/lio2.135] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/11/2017] [Accepted: 12/24/2017] [Indexed: 12/18/2022] Open
Abstract
Disorders causing a loss of the sense of smell remain a therapeutic challenge. Basic research has, however, greatly expanded our knowledge of the organization and function of the olfactory system. This review describes advances in our understanding of the cellular components of the peripheral olfactory system, specifically the olfactory epithelium in the nose. The article discusses recent findings regarding the mechanisms involved in regeneration and cellular renewal from basal stem cells in the adult olfactory epithelium, considering the strategies involved in embryonic olfactory development and insights from research on other stem cell niches. In the context of clinical conditions causing anosmia, the current view of adult olfactory neurogenesis, tissue homeostasis, and failures in these processes is considered, along with current and future treatment strategies. Level of Evidence NA.
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Affiliation(s)
- Rhea Choi
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of MedicineMiamiFloridaU.S.A
- Program in Neurosciences, University of Miami Miller School of MedicineMiamiFloridaU.S.A
- Medical Scientist Training Program, University of Miami Miller School of MedicineMiamiFloridaU.S.A
| | - Bradley J. Goldstein
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of MedicineMiamiFloridaU.S.A
- Program in Neurosciences, University of Miami Miller School of MedicineMiamiFloridaU.S.A
- Department of OtolaryngologyUniversity of Miami Miller School of MedicineMiamiFloridaU.S.A
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Hernandez-Muñoz I, Figuerola E, Sanchez-Molina S, Rodriguez E, Fernández-Mariño AI, Pardo-Pastor C, Bahamonde MI, Fernández-Fernández JM, García-Domínguez DJ, Hontecillas-Prieto L, Lavarino C, Carcaboso AM, de Torres C, Tirado OM, de Alava E, Mora J. RING1B contributes to Ewing sarcoma development by repressing the NaV1.6 sodium channel and the NF-κB pathway, independently of the fusion oncoprotein. Oncotarget 2018; 7:46283-46300. [PMID: 27317769 PMCID: PMC5216798 DOI: 10.18632/oncotarget.10092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/28/2016] [Indexed: 11/25/2022] Open
Abstract
Ewing sarcoma (ES) is an aggressive tumor defined by EWSR1 gene fusions that behave as an oncogene. Here we demonstrate that RING1B is highly expressed in primary ES tumors, and its expression is independent of the fusion oncogene. RING1B-depleted ES cells display an expression profile enriched in genes functionally involved in hematological development but RING1B depletion does not induce cellular differentiation. In ES cells, RING1B directly binds the SCN8A sodium channel promoter and its depletion results in enhanced Nav1.6 expression and function. The signaling pathway most significantly modulated by RING1B is NF-κB. RING1B depletion results in enhanced p105/p50 expression, which sensitizes ES cells to apoptosis by FGFR/SHP2/STAT3 blockade. Reduced NaV1.6 function protects ES cells from apoptotic cell death by maintaining low NF-κB levels. Our findings identify RING1B as a trait of the cell-of-origin and provide a potential targetable vulnerability.
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Affiliation(s)
| | - Elisabeth Figuerola
- Developmental Tumor Biology Laboratory, Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950-Barcelona, Spain
| | - Sara Sanchez-Molina
- Developmental Tumor Biology Laboratory, Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950-Barcelona, Spain
| | - Eva Rodriguez
- Developmental Tumor Biology Laboratory, Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950-Barcelona, Spain
| | - Ana Isabel Fernández-Mariño
- Laboratori de Fisiologia Molecular, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003-Barcelona, Spain.,Present Affiliation: Department of Neuroscience and Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison-53705, USA
| | - Carlos Pardo-Pastor
- Laboratori de Fisiologia Molecular, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003-Barcelona, Spain
| | - María Isabel Bahamonde
- Laboratori de Fisiologia Molecular, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003-Barcelona, Spain
| | - José M Fernández-Fernández
- Laboratori de Fisiologia Molecular, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003-Barcelona, Spain
| | - Daniel J García-Domínguez
- Department of Pediatric Hematology and Oncology, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, 41013-Seville, Spain
| | - Lourdes Hontecillas-Prieto
- Department of Pediatric Hematology and Oncology, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, 41013-Seville, Spain
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950-Barcelona, Spain
| | - Angel M Carcaboso
- Developmental Tumor Biology Laboratory, Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950-Barcelona, Spain
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950-Barcelona, Spain
| | - Oscar M Tirado
- Sarcoma Research Group, Laboratori d'Oncología Molecular, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, 08908-Barcelona, Spain
| | - Enrique de Alava
- Department of Pediatric Hematology and Oncology, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, 41013-Seville, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950-Barcelona, Spain
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Possible effect of SNAIL family transcriptional repressor 1 polymorphisms in non-syndromic cleft lip with or without cleft palate. Clin Oral Investig 2018; 22:2535-2541. [PMID: 29374328 DOI: 10.1007/s00784-018-2350-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/17/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Orofacial development is a complex process subjected to failure impairing. Indeed, the cleft of the lip and/or of the palate is among the most frequent inborn malformations. The JARID2 gene has been suggested to be involved in non-syndromic cleft lip with or without cleft palate (nsCL/P) etiology. JARID2 interacts with the polycomb repressive complex 2 (PRC2) in regulating the expression patterns of developmental genes by modifying the chromatin state. MATERIALS AND METHODS Genes coding for the PRC2 components, as well as other genes active in cell differentiation and embryonic development, were selected for a family-based association study to verify their involvement in nsCL/P. A total of 632 families from Italy and Asia participated to the study. RESULTS Evidence of allelic association was found with polymorphisms of SNAI1; in particular, the rs16995010-G allele was undertransmitted to the nsCL/P cases [P = 0.004, odds ratio = 0.69 (95% C.I. 0.54-0.89)]. However, the adjusted significance value corrected for all the performed tests was P = 0.051. CONCLUSIONS The findings emerging by the present study suggest for the first time an involvement of SNAI1 in the nsCL/P onset. CLINICAL RELEVANCE Interestingly, SNAI1 is known to promote epithelial to mesenchymal transition by repressing E-cadherin expression, but it needs an intact PRC2 to act this function. Alterations of this process could contribute to the complex etiology of nsCL/P.
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A Role for Monomethylation of Histone H3-K27 in Gene Activity in Drosophila. Genetics 2017; 208:1023-1036. [PMID: 29242288 DOI: 10.1534/genetics.117.300585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/07/2017] [Indexed: 01/09/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a conserved chromatin-modifying enzyme that methylates histone H3 on lysine-27 (K27). PRC2 can add one, two, or three methyl groups and the fully methylated product, H3-K27me3, is a hallmark of Polycomb-silenced chromatin. Less is known about functions of K27me1 and K27me2 and the dynamics of flux through these states. These modifications could serve mainly as intermediates to produce K27me3 or they could each convey distinct epigenetic information. To investigate this, we engineered a variant of Drosophila melanogaster PRC2 which is converted into a monomethyltransferase. A single substitution, F738Y, in the lysine-substrate binding pocket of the catalytic subunit, E(Z), creates an enzyme that retains robust K27 monomethylation but dramatically reduced di- and trimethylation. Overexpression of E(Z)-F738Y in fly cells triggers desilencing of Polycomb target genes significantly more than comparable overexpression of catalytically deficient E(Z), suggesting that H3-K27me1 contributes positively to gene activity. Consistent with this, normal genomic distribution of H3-K27me1 is enriched on actively transcribed Drosophila genes, with localization overlapping the active H3-K36me2/3 chromatin marks. Thus, distinct K27 methylation states link to either repression or activation depending upon the number of added methyl groups. If so, then H3-K27me1 deposition may involve alternative methyltransferases beyond PRC2, which is primarily repressive. Indeed, assays on fly embryos with PRC2 genetically inactivated, and on fly cells with PRC2 chemically inhibited, show that substantial H3-K27me1 accumulates independently of PRC2. These findings imply distinct roles for K27me1 vs. K27me3 in transcriptional control and an expanded machinery for methylating H3-K27.
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47
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PRC1 Prevents Replication Stress during Chondrogenic Transit Amplification. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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48
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Collinson A, Collier AJ, Morgan NP, Sienerth AR, Chandra T, Andrews S, Rugg-Gunn PJ. Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells. Cell Rep 2017; 17:2700-2714. [PMID: 27926872 PMCID: PMC5177603 DOI: 10.1016/j.celrep.2016.11.032] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/11/2016] [Accepted: 11/09/2016] [Indexed: 12/11/2022] Open
Abstract
Through the histone methyltransferase EZH2, the Polycomb complex PRC2 mediates H3K27me3 and is associated with transcriptional repression. PRC2 regulates cell-fate decisions in model organisms; however, its role in regulating cell differentiation during human embryogenesis is unknown. Here, we report the characterization of EZH2-deficient human embryonic stem cells (hESCs). H3K27me3 was lost upon EZH2 deletion, identifying an essential requirement for EZH2 in methylating H3K27 in hESCs, in contrast to its non-essential role in mouse ESCs. Developmental regulators were derepressed in EZH2-deficient hESCs, and single-cell analysis revealed an unexpected acquisition of lineage-restricted transcriptional programs. EZH2-deficient hESCs show strongly reduced self-renewal and proliferation, thereby identifying a more severe phenotype compared to mouse ESCs. EZH2-deficient hESCs can initiate differentiation toward developmental lineages; however, they cannot fully differentiate into mature specialized tissues. Thus, EZH2 is required for stable ESC self-renewal, regulation of transcriptional programs, and for late-stage differentiation in this model of early human development. Comprehensive examination of EZH2 function in human ESC regulation EZH2 deficiency causes lineage-restricted derepression of developmental regulators More severe self-renewal and growth defects in EZH2-deficient hESCs than in mESCs EZH2-deficient hESCs can differentiate to early lineages but cannot form mature tissues
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Affiliation(s)
- Adam Collinson
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Amanda J Collier
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Natasha P Morgan
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Arnold R Sienerth
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Tamir Chandra
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.
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49
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Pistoni M, Helsen N, Vanhove J, Boon R, Xu Z, Ordovas L, Verfaillie CM. Dynamic regulation of EZH2 from HPSc to hepatocyte-like cell fate. PLoS One 2017; 12:e0186884. [PMID: 29091973 PMCID: PMC5665677 DOI: 10.1371/journal.pone.0186884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 10/09/2017] [Indexed: 11/18/2022] Open
Abstract
Currently, drug metabolization and toxicity studies rely on the use of primary human hepatocytes and hepatoma cell lines, which both have conceivable limitations. Human pluripotent stem cell (hPSC)-derived hepatocyte-like cells (HLCs) are an alternative and valuable source of hepatocytes that can overcome these limitations. EZH2 (enhancer of zeste homolog 2), a transcriptional repressor of the polycomb repressive complex 2 (PRC2), may play an important role in hepatocyte development, but its role during in vitro hPSC-HLC differentiation has not yet been assessed. We here demonstrate dynamic regulation of EZH2 during hepatic differentiation of hPSC. To enhance EZH2 expression, we inducibly overexpressed EZH2 between d0 and d8, demonstrating a significant improvement in definitive endoderm formation, and improved generation of HLCs. Despite induction of EZH2 overexpression until d8, EZH2 transcript and protein levels decreased from d4 onwards, which might be caused by expression of microRNAs predicted to inhibit EZH2 expression. In conclusion, our studies demonstrate that EZH2 plays a role in endoderm formation and hepatocyte differentiation, but its expression is tightly post-transcriptionally regulated during this process.
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Affiliation(s)
- Mariaelena Pistoni
- KU Leuven—Department Development and Regeneration, Stem Cell Institute (SCIL), Leuven, Belgium
- * E-mail:
| | - Nicky Helsen
- KU Leuven—Department Development and Regeneration, Stem Cell Institute (SCIL), Leuven, Belgium
| | - Jolien Vanhove
- KU Leuven—Department Development and Regeneration, Stem Cell Institute (SCIL), Leuven, Belgium
| | - Ruben Boon
- KU Leuven—Department Development and Regeneration, Stem Cell Institute (SCIL), Leuven, Belgium
| | - Zhuofei Xu
- KU Leuven—Department Development and Regeneration, Stem Cell Institute (SCIL), Leuven, Belgium
| | - Laura Ordovas
- KU Leuven—Department Development and Regeneration, Stem Cell Institute (SCIL), Leuven, Belgium
| | - Catherine M. Verfaillie
- KU Leuven—Department Development and Regeneration, Stem Cell Institute (SCIL), Leuven, Belgium
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50
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Pursani V, Pethe P, Bashir M, Sampath P, Tanavde V, Bhartiya D. Genetic and Epigenetic Profiling Reveals EZH2-mediated Down Regulation of OCT-4 Involves NR2F2 during Cardiac Differentiation of Human Embryonic Stem Cells. Sci Rep 2017; 7:13051. [PMID: 29026152 PMCID: PMC5638931 DOI: 10.1038/s41598-017-13442-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023] Open
Abstract
Human embryonic (hES) stem cells are widely used as an in vitro model to understand global genetic and epigenetic changes that occur during early embryonic development. In-house derived hES cells (KIND1) were subjected to directed differentiation into cardiovascular progenitors (D12) and beating cardiomyocytes (D20). Transcriptome profiling of undifferentiated (D0) and differentiated (D12 and 20) cells was undertaken by microarray analysis. ChIP and sequential ChIP were employed to study role of transcription factor NR2F2 during hES cells differentiation. Microarray profiling showed that an alteration of about 1400 and 1900 transcripts occurred on D12 and D20 respectively compared to D0 whereas only 19 genes were altered between D12 and D20. This was found associated with corresponding expression pattern of chromatin remodelers, histone modifiers, miRNAs and lncRNAs marking the formation of progenitors and cardiomyocytes on D12 and D20 respectively. ChIP sequencing and sequential ChIP revealed the binding of NR2F2 with polycomb group member EZH2 and pluripotent factor OCT4 indicating its crucial involvement in cardiac differentiation. The study provides a detailed insight into genetic and epigenetic changes associated with hES cells differentiation into cardiac cells and a role for NR2F2 is deciphered for the first time to down-regulate OCT-4 via EZH2 during cardiac differentiation.
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Affiliation(s)
- Varsha Pursani
- Stem Cell Biology Department, ICMR- National Institute for Research in Reproductive Health, Mumbai, 400012, India
| | - Prasad Pethe
- Stem Cell Biology Department, ICMR- National Institute for Research in Reproductive Health, Mumbai, 400012, India
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS University, Mumbai, 400056, India
| | - Mohsin Bashir
- Institute of Medical Biology, Agency for Science Technology & Research (A*STAR), Singapore, 138648, Singapore
| | - Prabha Sampath
- Institute of Medical Biology, Agency for Science Technology & Research (A*STAR), Singapore, 138648, Singapore
| | - Vivek Tanavde
- Bioinformatics Institute, Agency for Science Technology & Research (A*STAR), Singapore, 138671, Singapore
- Division of Biological & Life Sciences, School of Arts & Sciences, Ahmedabad University, Ahmedabad, 380009, India
| | - Deepa Bhartiya
- Stem Cell Biology Department, ICMR- National Institute for Research in Reproductive Health, Mumbai, 400012, India.
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