1
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Hendricks EL, Liebl FLW. The CHD family chromatin remodeling enzyme, Kismet, promotes both clathrin-mediated and activity-dependent bulk endocytosis. PLoS One 2024; 19:e0300255. [PMID: 38512854 PMCID: PMC10956772 DOI: 10.1371/journal.pone.0300255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/23/2024] [Indexed: 03/23/2024] Open
Abstract
Chromodomain helicase DNA binding domain (CHD) proteins, including CHD7 and CHD8, remodel chromatin to enable transcriptional programs. Both proteins are important for proper neural development as heterozygous mutations in Chd7 and Chd8 are causative for CHARGE syndrome and correlated with autism spectrum disorders, respectively. Their roles in mature neurons are poorly understood despite influencing the expression of genes required for cell adhesion, neurotransmission, and synaptic plasticity. The Drosophila homolog of CHD7 and CHD8, Kismet (Kis), promotes neurotransmission, endocytosis, and larval locomotion. Endocytosis is essential in neurons for replenishing synaptic vesicles, maintaining protein localization, and preserving the size and composition of the presynaptic membrane. Several forms of endocytosis have been identified including clathrin-mediated endocytosis, which is coupled with neural activity and is the most prevalent form of synaptic endocytosis, and activity-dependent bulk endocytosis, which occurs during periods of intense stimulation. Kis modulates the expression of gene products involved in endocytosis including promoting shaggy/GSK3β expression while restricting PI3K92E. kis mutants electrophysiologically phenocopy a liquid facets mutant in response to paradigms that induce clathrin-mediated endocytosis and activity-dependent bulk endocytosis. Further, kis mutants do not show further reductions in endocytosis when activity-dependent bulk endocytosis or clathrin-mediated endocytosis are pharmacologically inhibited. We find that Kis is important in postsynaptic muscle for proper endocytosis but the ATPase domain of Kis is dispensable for endocytosis. Collectively, our data indicate that Kis promotes both clathrin-mediated endocytosis and activity-dependent bulk endocytosis possibly by promoting transcription of several endocytic genes and maintaining the size of the synaptic vesicle pool.
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Affiliation(s)
- Emily L. Hendricks
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois, United States of America
| | - Faith L. W. Liebl
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois, United States of America
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2
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Dreier MR, de la Serna IL. SWI/SNF Chromatin Remodeling Enzymes in Melanoma. EPIGENOMES 2022; 6:epigenomes6010010. [PMID: 35323214 PMCID: PMC8947417 DOI: 10.3390/epigenomes6010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Melanoma is an aggressive malignancy that arises from the transformation of melanocytes on the skin, mucosal membranes, and uvea of the eye. SWI/SNF chromatin remodeling enzymes are multi-subunit complexes that play important roles in the development of the melanocyte lineage and in the response to ultraviolet radiation, a key environmental risk factor for developing cutaneous melanoma. Exome sequencing has revealed frequent loss of function mutations in genes encoding SWI/SNF subunits in melanoma. However, some SWI/SNF subunits have also been demonstrated to have pro-tumorigenic roles in melanoma and to affect sensitivity to therapeutics. This review summarizes studies that have implicated SWI/SNF components in melanomagenesis and have evaluated how SWI/SNF subunits modulate the response to current therapeutics.
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3
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Hsieh FK, Ji F, Damle M, Sadreyev RI, Kingston RE. HERVH-derived lncRNAs negatively regulate chromatin targeting and remodeling mediated by CHD7. Life Sci Alliance 2021; 5:5/1/e202101127. [PMID: 34663690 PMCID: PMC8548210 DOI: 10.26508/lsa.202101127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in CHD7 are diagnostic for human CHARGE syndrome. RNAs expressed from the HERVH repeats modulate CHD7 function providing one mechanism for regulation of differentiation of pluripotent cells. Chd7 encodes an ATP-dependent chromatin remodeler which has been shown to target specific genomic loci and alter local transcription potentially by remodeling chromatin structure. De novo mutations in CHD7 are the major cause of CHARGE syndrome which features multiple developmental defects. We examined whether nuclear RNAs might contribute to its targeting and function and identified a preferential interaction between CHD7 and lncRNAs derived from HERVH loci in pluripotent stem cells. Knockdown of HERVH family lncRNAs using LNAs or knockout of an individual copy of HERVH by CRISPR-Cas9 both resulted in increased binding of CHD7 and increased levels of H3K27ac at a subset of enhancers. Depletion of HERVH family RNAs led to the activation of multiple genes. CHD7 bound HERVH RNA with high affinity but low specificity and this interaction decreased the ability of CHD7 to bind and remodel nucleosomes. We present a model in which HERVH lncRNAs act as a decoy to modulate the dynamics of CHD7 binding to enhancers in pluripotent cells and the activation of numerous genes that might impact the differentiation process.
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Affiliation(s)
- Fu-Kai Hsieh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA .,Department of Genetics, Harvard Medical School, Boston, MA, USA
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4
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Rugowska A, Starosta A, Konieczny P. Epigenetic modifications in muscle regeneration and progression of Duchenne muscular dystrophy. Clin Epigenetics 2021; 13:13. [PMID: 33468200 PMCID: PMC7814631 DOI: 10.1186/s13148-021-01001-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a multisystemic disorder that affects 1:5000 boys. The severity of the phenotype varies dependent on the mutation site in the DMD gene and the resultant dystrophin expression profile. In skeletal muscle, dystrophin loss is associated with the disintegration of myofibers and their ineffective regeneration due to defective expansion and differentiation of the muscle stem cell pool. Some of these phenotypic alterations stem from the dystrophin absence-mediated serine-threonine protein kinase 2 (MARK2) misplacement/downregulation in activated muscle stem (satellite) cells and neuronal nitric oxide synthase loss in cells committed to myogenesis. Here, we trace changes in DNA methylation, histone modifications, and expression of regulatory noncoding RNAs during muscle regeneration, from the stage of satellite cells to myofibers. Furthermore, we describe the abrogation of these epigenetic regulatory processes due to changes in signal transduction in DMD and point to therapeutic treatments increasing the regenerative potential of diseased muscles based on this acquired knowledge.
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Affiliation(s)
- Anna Rugowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Alicja Starosta
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Patryk Konieczny
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland.
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5
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Cui P, Zhang P, Zhang Y, Sun L, Cui G, Guo X, Wang H, Zhang X, Shi Y, Yu Z. HIF-1α/Actl6a/H3K9ac axis is critical for pluripotency and lineage differentiation of human induced pluripotent stem cells. FASEB J 2020; 34:5740-5753. [PMID: 32112486 DOI: 10.1096/fj.201902829rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/02/2020] [Accepted: 02/18/2020] [Indexed: 12/13/2022]
Abstract
Pluripotent stem cells (PSCs) are important models for analyzing cellular metabolism and individual development. As a hypoxia-inducible factor subunit, HIF-1α plays an important role in maintaining the pluripotency of PSCs under hypoxic conditions. However, the mechanisms underlying the self-renewal and pluripotency maintenance of human induced pluripotent stem cells (hiPSCs) via regulating HIF-1α largely remain elusive. In this study, we found that disrupting the expression of HIF-1α reduced self-renewal and pluripotency of hiPSCs. Additionally, HIF-1α-knockdown led to lower mitochondrial membrane potential (ΔΨm ) and higher reactive oxygen species production in hiPSCs. However, HIF-1α-overexpression increased ATP content in hiPSCs, while the role of HIF-1α-knockdown was opposite. The embryoid body (EB) and teratoma formation assays showed that HIF-1α-knockdown promoted endoderm differentiation and development in vitro and in vivo. In terms of the underlying molecular mechanisms, HIF-1α-knockdown inhibited the expression of Actl6a and histone H3K9ac acetylation (H3K9ac). Actl6a knockdown reduced the expression of H3K9ac and the pluripotency of hiPSCs, and also affected endoderm differentiation. These data suggest that hindering HIF-1α expression causes the changes in mitochondrial properties and metabolic disorders in hiPSCs. Furthermore, HIF-1α affects hiPSC pluripotency, and germ layer differentiation via Actl6a and histone acetylation.
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Affiliation(s)
- Peng Cui
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Ping Zhang
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Yanmin Zhang
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Lihua Sun
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Guanghui Cui
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Xin Guo
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - He Wang
- Department of Medical Laboratory, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Xiaowei Zhang
- School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yu Shi
- Department of Research and Teaching, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Zhendong Yu
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
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6
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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7
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Basuroy T, de la Serna IL. SETD7 in cardiomyocyte differentiation and cardiac function. Stem Cell Investig 2019; 6:29. [PMID: 31620476 DOI: 10.21037/sci.2019.08.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 07/30/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Tupa Basuroy
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Ivana L de la Serna
- University of Toledo College of Medicine and Life Sciences, Department of Cancer Biology, Toledo, OH, USA
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8
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Natesan R, Aras S, Effron SS, Asangani IA. Epigenetic Regulation of Chromatin in Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1210:379-407. [PMID: 31900918 DOI: 10.1007/978-3-030-32656-2_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Epigenetics refers to mitotically/meiotically heritable mechanisms that regulate gene transcription without a need for changes in the DNA code. Covalent modifications of DNA, in the form of methylation, and histone post-translational modifications, in the form of acetylation and methylation, constitute the epigenetic code of a cell. Both DNA and histone modifications are highly dynamic and often work in unison to define the epigenetic state of a cell. Most epigenetic mechanisms regulate gene transcription by affecting localized/genome-wide transitions between heterochromatin and euchromatin states, thereby altering the accessibility of the transcriptional machinery and in turn, reduce/increase transcriptional output. Altered chromatin structure is associated with cancer progression, and epigenetic plasticity primarily governs the resistance of cancer cells to therapeutic agents. In this chapter, we specifically focus on regulators of histone methylation and acetylation, the two well-studied chromatin post-translational modifications, in the context of prostate cancer.
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Affiliation(s)
- Ramakrishnan Natesan
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shweta Aras
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel Sander Effron
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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9
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Aras S, Saladi SV, Basuroy T, Marathe HG, Lorès P, de la Serna IL. BAF60A mediates interactions between the microphthalmia-associated transcription factor and the BRG1-containing SWI/SNF complex during melanocyte differentiation. J Cell Physiol 2018; 234:11780-11791. [PMID: 30515787 DOI: 10.1002/jcp.27840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 11/07/2018] [Indexed: 01/10/2023]
Abstract
SWI/SNF chromatin remodeling enzymes are multisubunit complexes that contain one of two catalytic subunits, BRG1 or BRM and 9-11 additional subunits called BRG1 or BRM-associated factors (BAFs). BRG1 interacts with the microphthalmia-associated transcription factor (MITF) and is required for melanocyte development in vitro and in vivo. The subunits of SWI/SNF that mediate interactions between BRG1 and MITF have not been elucidated. Three mutually exclusive isoforms of a 60-kDa subunit (BAF60A, B, or C) often facilitate interactions with transcription factors during lineage specification. We tested the hypothesis that a BAF60 subunit promotes interactions between MITF and the BRG1-containing SWI/SNF complex. We found that MITF can physically interact with BAF60A, BAF60B, and BAF60C. The interaction between MITF and BAF60A required the basic helix-loop-helix domain of MITF. Recombinant BAF60A pulled down recombinant MITF, suggesting that the interaction can occur in the absence of other SWI/SNF subunits and other transcriptional regulators of the melanocyte lineage. Depletion of BAF60A in differentiating melanoblasts inhibited melanin synthesis and expression of MITF target genes. MITF promoted BAF60A recruitment to melanocyte-specific promoters, and BAF60A was required to promote BRG1 recruitment and chromatin remodeling. Thus, BAF60A promotes interactions between MITF and the SWI/SNF complex and is required for melanocyte differentiation.
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Affiliation(s)
- Shweta Aras
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio.,Department of Cancer Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Srinivas Vinod Saladi
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio.,Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Tupa Basuroy
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Himangi G Marathe
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio.,Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York
| | - Patrick Lorès
- INSERM U1016, Institut Cochin/CNRS UMR8104/ Universite Paris Descartes, Faculte de Medecine Cochin, Paris, France
| | - Ivana L de la Serna
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
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10
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An actin-based nucleoskeleton involved in gene regulation and genome organization. Biochem Biophys Res Commun 2018; 506:378-386. [DOI: 10.1016/j.bbrc.2017.11.206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 11/30/2017] [Indexed: 12/21/2022]
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11
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Characterizing the role of SWI/SNF-related chromatin remodeling complexes in planarian regeneration and stem cell function. Stem Cell Res 2018; 32:91-103. [DOI: 10.1016/j.scr.2018.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/18/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022] Open
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12
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Zhang Y, Cui P, Li Y, Feng G, Tong M, Guo L, Li T, Liu L, Li W, Zhou Q. Mitochondrially produced ATP affects stem cell pluripotency via Actl6a-mediated histone acetylation. FASEB J 2018; 32:1891-1902. [PMID: 29222327 DOI: 10.1096/fj.201700626rr] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ATP is mainly generated by glycolysis in pluripotent stem cells (PSCs) and is consumed to maintain cell viability. Differences in mitochondrial activity among induced (i)PSCs with different degrees of pluripotency are poorly understood. In this study, by comparing gene expression and mitochondrial activity among iPSCs with different degrees of pluripotency, we found that mitochondrial complex I gene expression, complex I activity, and cellular ATP levels were much higher in fully pluripotent stem cell lines than in partially pluripotent stem cell lines. Actin-like protein 6a (Actl6a), a component of ATP-dependent chromatin remodeling and histone acetylation complexes, was more highly expressed in fully pluripotent stem cell lines. ATP promoted Actl6a expression and histone acetylation. Actl6a knockdown reduced the pluripotency of embryonic stem cells (ESCs), and this reduction could not be rescued by the addition of ATP. Furthermore, inhibiting ATP formation by treatment with rotenone reduced the pluripotency of ESCs. These data suggest that the abundance of mitochondrially produced ATP affects stem cell pluripotency via Actl6a-mediated histone acetylation.-Zhang, Y., Cui, P., Li, Y., Feng, G., Tong, M., Guo, L., Li, T., Liu, L., Li, W., Zhou, Q. Mitochondrially produced ATP affects stem cell pluripotency via Actl6a-mediated histone acetylation.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Peng Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhuan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Man Tong
- Key Laboratory of Genetic Network Biology, Collaborative Center for Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lu Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tianda Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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13
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Marathe HG, Watkins-Chow DE, Weider M, Hoffmann A, Mehta G, Trivedi A, Aras S, Basuroy T, Mehrotra A, Bennett DC, Wegner M, Pavan WJ, de la Serna IL. BRG1 interacts with SOX10 to establish the melanocyte lineage and to promote differentiation. Nucleic Acids Res 2017; 45:6442-6458. [PMID: 28431046 PMCID: PMC5499657 DOI: 10.1093/nar/gkx259] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/04/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in SOX10 cause neurocristopathies which display varying degrees of hypopigmentation. Using a sensitized mutagenesis screen, we identified Smarca4 as a modifier gene that exacerbates the phenotypic severity of Sox10 haplo-insufficient mice. Conditional deletion of Smarca4 in SOX10 expressing cells resulted in reduced numbers of cranial and ventral trunk melanoblasts. To define the requirement for the Smarca4 -encoded BRG1 subunit of the SWI/SNF chromatin remodeling complex, we employed in vitro models of melanocyte differentiation in which induction of melanocyte-specific gene expression is closely linked to chromatin alterations. We found that BRG1 was required for expression of Dct, Tyrp1 and Tyr, genes that are regulated by SOX10 and MITF and for chromatin remodeling at distal and proximal regulatory sites. SOX10 was found to physically interact with BRG1 in differentiating melanocytes and binding of SOX10 to the Tyrp1 distal enhancer temporally coincided with recruitment of BRG1. Our data show that SOX10 cooperates with MITF to facilitate BRG1 binding to distal enhancers of melanocyte-specific genes. Thus, BRG1 is a SOX10 co-activator, required to establish the melanocyte lineage and promote expression of genes important for melanocyte function.
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Affiliation(s)
- Himangi G Marathe
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Dawn E Watkins-Chow
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4472, USA
| | - Matthias Weider
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Alana Hoffmann
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Gaurav Mehta
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Archit Trivedi
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Shweta Aras
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Tupa Basuroy
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Aanchal Mehrotra
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
| | - Dorothy C Bennett
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - William J Pavan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4472, USA
| | - Ivana L de la Serna
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614, USA
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14
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Zhao H, Han Z, Liu X, Gu J, Tang F, Wei G, Jin Y. The chromatin remodeler Chd4 maintains embryonic stem cell identity by controlling pluripotency- and differentiation-associated genes. J Biol Chem 2017; 292:8507-8519. [PMID: 28298436 DOI: 10.1074/jbc.m116.770248] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/13/2017] [Indexed: 12/23/2022] Open
Abstract
The unique properties of embryonic stem cells (ESCs), including unlimited self-renewal and pluripotent differentiation potential, are sustained by integrated genetic and epigenetic networks composed of transcriptional factors and epigenetic modulators. However, the molecular mechanisms underlying the function of these regulators are not fully elucidated. Chromodomain helicase DNA-binding protein 4 (Chd4), an ATPase subunit of the nucleosome remodeling and deacetylase (NuRD) complex, is highly expressed in ESCs. However, its function in ESC regulation remains elusive. Here we report that Chd4 is required for the maintenance of ESC self-renewal. RNAi-mediated silencing of Chd4 disrupted self-renewal and up-regulated lineage commitment-associated genes under self-renewal culture conditions. During ESC differentiation in embryoid body formation, we observed significantly stronger induction of differentiation-associated genes in Chd4-deficient cells. The phenotype was different from that caused by the deletion of Mbd3, another subunit of the NuRD complex. Transcriptomic analyses revealed that Chd4 secured ESC identity by controlling the expression of subsets of pluripotency- and differentiation-associated genes. Importantly, Chd4 repressed the transcription of T box protein 3 (Tbx3), a transcription factor with important functions in ESC fate determination. Tbx3 knockdown partially rescued aberrant activation of differentiation-associated genes, especially of endoderm-associated genes, induced by Chd4 depletion. Moreover, we identified an interaction of Chd4 with the histone variant H2A.Z. This variant stabilized Chd4 by inhibiting Chd4 protein degradation through the ubiquitin-proteasome pathway. Collectively, this study identifies the Chd4-Tbx3 axis in controlling ESC fate and a role of H2A.Z in maintaining the stability of Chd4 proteins.
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Affiliation(s)
- Haixin Zhao
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China; University of the Chinese Academy of Sciences
| | - Zhijun Han
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyuan Liu
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China
| | - Junjie Gu
- Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Fan Tang
- Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Gang Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ying Jin
- Key Laboratory of Stem Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, 320 Yueyang Road, Shanghai 200031, China; Laboratory of Molecular Developmental Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China.
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15
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Identification of CHD1L as an Important Regulator for Spermatogonial Stem Cell Survival and Self-Renewal. Stem Cells Int 2016; 2016:4069543. [PMID: 28003832 PMCID: PMC5149700 DOI: 10.1155/2016/4069543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/27/2016] [Indexed: 12/22/2022] Open
Abstract
Chromodomain helicase/ATPase DNA binding protein 1-like gene (Chd1l) participates in chromatin-dependent processes, including transcriptional activation and DNA repair. In this study, we have found for the first time that Chd1l is mainly expressed in the testicular tissues of prepubertal and adult mice and colocalized with PLZF, OCT4, and GFRα1 in the neonatal mouse testis and THY1+ undifferentiated spermatogonia or spermatogonial stem cells (SSCs). Knockdown of endogenous Chd1l in cultured mouse undifferentiated SSCs inhibited the expression levels of Oct4, Plzf, Gfrα1, and Pcna genes, suppressed SSC colony formation, and reduced BrdU incorporation, while increasing SSC apoptosis. Moreover, the Chd1l gene expression is activated by GDNF in the cultured mouse SSCs, and the GDNF signaling pathway was modulated by endogenous levels of Chd1l; as demonstrated by the gene expression levels of GDNF, inducible transcripts Etv5, Bcl6b, Pou3f, and Lhx1, but not that of GDNF-independent gene, Taf4b, were significantly downregulated by Chd1l knockdown in mouse SSCs. Taken together, this study provides the first evidence to support the notion that Chd1l is an intrinsic and novel regulator for SSC survival and self-renewal, and it exerts such regulation at least partially through a GDNF signaling pathway.
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16
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Toto PC, Puri PL, Albini S. SWI/SNF-directed stem cell lineage specification: dynamic composition regulates specific stages of skeletal myogenesis. Cell Mol Life Sci 2016; 73:3887-96. [PMID: 27207468 PMCID: PMC5158306 DOI: 10.1007/s00018-016-2273-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/06/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022]
Abstract
SWI/SNF chromatin-remodeling complexes are key regulators of the epigenetic modifications that determine whether stem cells maintain pluripotency or commit toward specific lineages through development and during postnatal life. Dynamic combinatorial assembly of multiple variants of SWI/SNF subunits is emerging as the major determinant of the functional versatility of SWI/SNF. Here, we summarize the current knowledge on the structural and functional properties of the alternative SWI/SNF complexes that direct stem cell fate toward skeletal muscle lineage and control distinct stages of skeletal myogenesis. In particular, we will refer to recent evidence pointing to the essential role of two SWI/SNF components not expressed in embryonic stem cells-the catalytic subunit BRM and the structural component BAF60C-whose induction in muscle progenitors coincides with the expansion of their transcriptional repertoire.
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Affiliation(s)
- Paula Coutinho Toto
- Sanford Burnham Prebys Medical Discovery Institute, 10905 Road to the Cure, San Diego, CA, 92121, USA
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, 10905 Road to the Cure, San Diego, CA, 92121, USA.
- IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143, Rome, Italy.
| | - Sonia Albini
- Sanford Burnham Prebys Medical Discovery Institute, 10905 Road to the Cure, San Diego, CA, 92121, USA.
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17
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Mellai M, Cattaneo M, Storaci AM, Annovazzi L, Cassoni P, Melcarne A, De Blasio P, Schiffer D, Biunno I. SEL1L SNP rs12435998, a predictor of glioblastoma survival and response to radio-chemotherapy. Oncotarget 2016; 6:12452-67. [PMID: 25948789 PMCID: PMC4494950 DOI: 10.18632/oncotarget.3611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/14/2015] [Indexed: 12/18/2022] Open
Abstract
The suppressor of Lin-12-like (C. elegans) (SEL1L) is involved in the endoplasmic reticulum (ER)-associated degradation pathway, malignant transformation and stem cells. In 412 formalin-fixed and paraffin-embedded brain tumors and 39 Glioblastoma multiforme (GBM) cell lines, we determined the frequency of five SEL1L single nucleotide genetic variants with regulatory and coding functions by a SNaPShot™ assay. We tested their possible association with brain tumor risk, prognosis and therapy. We studied the in vitro cytotoxicity of valproic acid (VPA), temozolomide (TMZ), doxorubicin (DOX) and paclitaxel (PTX), alone or in combination, on 11 GBM cell lines, with respect to the SNP rs12435998 genotype. The SNP rs12435998 was prevalent in anaplastic and malignant gliomas, and in meningiomas of all histologic grades, but unrelated to brain tumor risks. In GBM patients, the SNP rs12435998 was associated with prolonged overall survival (OS) and better response to TMZ-based radio-chemotherapy. GBM stem cells with this SNP showed lower levels of SEL1L expression and enhanced sensitivity to VPA.
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Affiliation(s)
- Marta Mellai
- Neuro-Bio-Oncology Center/Policlinico di Monza Foundation, Vercelli 13100, Italy
| | - Monica Cattaneo
- Institute for Genetic and Biomedical Research, National Research Council, Milan 20138, Italy
| | | | - Laura Annovazzi
- Neuro-Bio-Oncology Center/Policlinico di Monza Foundation, Vercelli 13100, Italy
| | - Paola Cassoni
- Department of Medical Sciences, University of Turin/Città della Salute e della Scienza, Turin 10126, Italy
| | - Antonio Melcarne
- Department of Neurosurgery, CTO Hospital/Città della Salute e della Scienza, Turin 10126, Italy
| | | | - Davide Schiffer
- Neuro-Bio-Oncology Center/Policlinico di Monza Foundation, Vercelli 13100, Italy
| | - Ida Biunno
- Institute for Genetic and Biomedical Research, National Research Council, Milan 20138, Italy.,IRCCS-Multimedica, Milan 20138, Italy
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18
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Bozkaya OG, Ataman E, Randa C, Cura DO, Gürsoy S, Aksel O, Ulgenalp A. Three novel mutations of CHD7 gene in two turkish patients with charge syndrome; A double point mutation and an insertion. Balkan J Med Genet 2016; 18:65-70. [PMID: 26929907 PMCID: PMC4768827 DOI: 10.1515/bjmg-2015-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The CHARGE (coloboma, heart defects, atresia, retardation, genital, ear) syndrome is a genetic disease characterized by ocular coloboma, choanal atresia or stenosis and semicircular canal abnormalities. Most of the patients clinically diagnosed with CHARGE syndrome have mutations in chromodomain helicase DNA-binding protein 7 (CHD7) gene. The CHD7 gene is located on chromosome 8q12.1, and up to now, there are more than 500 pathogenic mutations identified in the literature. We report two patients diagnosed with CHARGE syndrome with two novel mutations in the CHD7 gene: the first patient has double consecutive novel mutations in three adjacent codons, and the other has a novel insertion.
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Affiliation(s)
- O Giray Bozkaya
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - E Ataman
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - C Randa
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - D Onur Cura
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - S Gürsoy
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - O Aksel
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
| | - A Ulgenalp
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir 35340, Turkey
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19
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Paranjpe SS, Veenstra GJC. Establishing pluripotency in early development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:626-36. [PMID: 25857441 DOI: 10.1016/j.bbagrm.2015.03.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 01/23/2023]
Abstract
The earliest steps of embryonic development involve important changes in chromatin and transcription factor networks, which are orchestrated to establish pluripotent cells that will form the embryo. DNA methylation, histone modifications, the pluripotency regulatory network of transcription factors, maternal factors and newly translated proteins all contribute to these transitions in dynamic ways. Moreover, these dynamics are linked to the onset of zygotic transcription. We will review recent progress in our understanding of chromatin state and regulation of gene expression in the context of embryonic development in vertebrates, in particular mouse, Xenopus and zebrafish. We include work on mouse embryonic stem cells and highlight work that illustrates how early embryonic dynamics establish gene regulatory networks and the state of pluripotency.
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Affiliation(s)
- Sarita S Paranjpe
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
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20
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Mehrotra A, Mehta G, Aras S, Trivedi A, de la Serna IL. SWI/SNF chromatin remodeling enzymes in melanocyte differentiation and melanoma. Crit Rev Eukaryot Gene Expr 2015; 24:151-61. [PMID: 24940768 DOI: 10.1615/critreveukaryotgeneexpr.2014007882] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epidermal melanocytes are pigment-producing cells derived from the neural crest that protects skin from the damaging effects of solar radiation. Malignant melanoma, a highly aggressive cancer, arises from melanocytes. SWI/SNF enzymes are multiprotein complexes that remodel chromatin structure and have extensive roles in cellular differentiation. Components of the complex have been found to be mutated or lost in several human cancers. This review focuses on studies that implicate SWI/SNF enzymes in melanocyte differentiation and in melanoma.
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Affiliation(s)
- A Mehrotra
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
| | - G Mehta
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
| | - S Aras
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
| | - A Trivedi
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
| | - I L de la Serna
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
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21
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Shukla S, Meeran SM. Epigenetics of cancer stem cells: Pathways and therapeutics. Biochim Biophys Acta Gen Subj 2014; 1840:3494-3502. [PMID: 25240776 DOI: 10.1016/j.bbagen.2014.09.017] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 12/30/2022]
Abstract
BACKGROUND Epigenetic alterations including DNA methylation and histone modifications are the key factors in the differentiation of stem cells into different tissue subtypes. The generation of cancer stem cells (CSCs) in the process of carcinogenesis may also involve similar kind of epigenetic reprogramming where, in contrast, it leads to the loss of expression of genes specific to the differentiated state and regaining of stem cell-specific characteristics. The most important predicament with treatment of cancers includes the non-responsive quiescent CSC. SCOPE OF REVIEW The distinctive capabilities of the CSCs make cancer treatment even more difficult as this population of cells tends to remain quiescent for longer intervals and then gets reactivated leading to tumor relapse. Therefore, the current review is aimed to focus on recent advances in understanding the relation of epigenetic reprogramming to the generation, self-renewal and proliferation of CSCs. MAJOR CONCLUSION CSC-targeted therapeutic approaches would improve the chances of patient survival by reducing the frequency of tumor relapse. Differentiation therapy is an emerging therapeutic approach in which the CSCs are induced to differentiate from their quiescent state to a mature differentiated form, through activation of differentiation-related signalling pathways, miRNA-mediated alteration and epigenetic differentiation therapy. Thus, understanding the origin of CSC and their epigenetic regulation is crucial to develop treatment strategy against not only for the heterogeneous population of cancer cells but also to CSCs. GENERAL SIGNIFICANCE Characterizing the epigenetic marks of CSCs and the associated signalling cascades might help in developing therapeutic strategies against chemo-resistant cancers.
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Affiliation(s)
- Samriddhi Shukla
- Laboratory of Cancer Epigenetics, Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Syed Musthapa Meeran
- Laboratory of Cancer Epigenetics, Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India.
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22
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Kelly RDW, Sumer H, McKenzie M, Facucho-Oliveira J, Trounce IA, Verma PJ, St John JC. The effects of nuclear reprogramming on mitochondrial DNA replication. Stem Cell Rev Rep 2013; 9:1-15. [PMID: 21994000 DOI: 10.1007/s12015-011-9318-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Undifferentiated mouse embryonic stem cells (ESCs) possess low numbers of mitochondrial DNA (mtDNA), which encodes key subunits associated with the generation of ATP through oxidative phosphorylation (OXPHOS). As ESCs differentiate, mtDNA copy number is regulated by the nuclear-encoded mtDNA replication factors, which initiate a major replication event on Day 6 of differentiation. Here, we examined mtDNA replication events in somatic cells reprogrammed to pluripotency, namely somatic cell-ES (SC-ES), somatic cell nuclear transfer ES (NT-ES) and induced pluripotent stem (iPS) cells, all at low-passage. MtDNA copy number in undifferentiated iPS cells was similar to ESCs whilst SC-ES and NT-ES cells had significantly increased levels, which correlated positively and negatively with Nanog and Sox2 expression, respectively. During pluripotency and differentiation, the expression of the mtDNA-specific replication factors, PolgA and Peo1, were differentially expressed in iPS and SC-ES cells when compared to ESCs. Throughout differentiation, reprogrammed somatic cells were unable to accumulate mtDNA copy number, characteristic of ESCs, especially on Day 6. In addition, iPS and SC-ES cells were also unable to regulate ATP content in a manner similar to differentiating ESCs prior to Day 14. The treatment of reprogrammed somatic cells with an inhibitor of de novo DNA methylation, 5-Azacytidine, prior to differentiation enabled iPS cells, but not SC-ES and NT-ES cells, to accumulate mtDNA copies per cell in a manner similar to ESCs. These data demonstrate that the reprogramming process disrupts the regulation of mtDNA replication during pluripotency but this can be re-established through the use of epigenetic modifiers.
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Affiliation(s)
- Richard D W Kelly
- Centre for Reproduction and Development, Monash Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, Victoria, 3168, Australia
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23
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Seffer I, Nemeth Z, Hoffmann G, Matics R, Seffer AG, Koller A. Unexplored potentials of epigenetic mechanisms of plants and animals-theoretical considerations. GENETICS & EPIGENETICS 2013; 5:23-41. [PMID: 25512705 PMCID: PMC4222336 DOI: 10.4137/geg.s11752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Morphological and functional changes of cells are important for adapting to environmental changes and associated with continuous regulation of gene expressions. Genes are regulated–in part–by epigenetic mechanisms resulting in alternating patterns of gene expressions throughout life. Epigenetic changes responding to the environmental and intercellular signals can turn on/off specific genes, but do not modify the DNA sequence. Most epigenetic mechanisms are evolutionary conserved in eukaryotic organisms, and several homologs of epigenetic factors are present in plants and animals. Moreover, in vitro studies suggest that the plant cytoplasm is able to induce a nuclear reassembly of the animal cell, whereas others suggest that the ooplasm is able to induce condensation of plant chromatin. Here, we provide an overview of the main epigenetic mechanisms regulating gene expression and discuss fundamental epigenetic mechanisms and factors functioning in both plants and animals. Finally, we hypothesize that animal genome can be reprogrammed by epigenetic factors from the plant protoplast.
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Affiliation(s)
| | - Zoltan Nemeth
- Seffer-Renner Medical Clinic, Budapest, Hungary. ; Department of Pathophysiology and Gerontology, Medical School, and Szentagothai Res Centre, University of Pecs, Pecs, Hungary
| | - Gyula Hoffmann
- Institute of Biology, Faculty of Sciences, University of Pecs, Pecs, Hungary
| | - Robert Matics
- Department of Pathophysiology and Gerontology, Medical School, and Szentagothai Res Centre, University of Pecs, Pecs, Hungary
| | - A Gergely Seffer
- Surgery Clinic, Medical School, University of Pecs, Pecs, Hungary
| | - Akos Koller
- Department of Pathophysiology and Gerontology, Medical School, and Szentagothai Res Centre, University of Pecs, Pecs, Hungary. ; Department of Physiology, New York Medical College, Valhalla NY, USA
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24
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Anand M, Prasad BV. The computational analysis of human testis transcriptome reveals closer ties to pluripotency. J Hum Reprod Sci 2013; 5:266-73. [PMID: 23531778 PMCID: PMC3604834 DOI: 10.4103/0974-1208.106339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/25/2012] [Accepted: 07/28/2012] [Indexed: 11/04/2022] Open
Abstract
AIMS The purpose of this study was to identify the differentially expressed genes (DEG) in human testis and also evaluate the relationship between human testis, human Embryonic Stem Cells (hESC), mouse testis and mouse ESCs (mESC). SETTINGS AND DESIGN It is a prospective analysis designed computationally. METHODS AND MATERIAL The microarray data for human testis, hESCs, mouse testis and mESCs were obtained from NCBI-GEO and analyzed for identification of DEGs. The results were then compared with mouse testis and extended to ESCs. STATISTICAL ANALYSIS USED Data was analyzed in R using various Bioconductor packages. To identify DEGs, 2-fold cut-off and a False Discovery Rate (FDR) below 0.01 criterions was used. RESULTS A total 2868 transcripts (DEGs) were found to be significantly up-regulated and 2011 transcripts significantly down-regulated in human testis compared to other normal tissues. Of the up-regulated transcripts, 232 transcripts were grouped as unclassified i.e. had unknown annotations at the time of analysis. Gene Ontology (GO) based functional annotation of testis specific DEGs indicate that most of the DEGs (~80%) are involved in various metabolic processes. Pathway analysis shows over-representation of Ubiquitin-mediated proteolysis pathway. A core group of 67 transcripts were found to be common among human testis, mouse testis, hESCs and mESCs. CONCLUSIONS Testis seems to be metabolically very active relative to other normal tissues as indicated by functional annotation. The comparison of human and mouse testis shows conserved functions and pathways involved in both species. Large numbers of genes were found conserved between testis and ESCs suggesting very close expression level relationship between reproductive organs and complex phenomenon such as dedifferentiation and reprogramming.
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Affiliation(s)
- Mt Anand
- IGNOU-/²/T Center of Excellence for Advanced Education and Research, Pune, Maharashtra, India
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25
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Nicetto D, Hahn M, Jung J, Schneider TD, Straub T, David R, Schotta G, Rupp RAW. Suv4-20h histone methyltransferases promote neuroectodermal differentiation by silencing the pluripotency-associated Oct-25 gene. PLoS Genet 2013; 9:e1003188. [PMID: 23382689 PMCID: PMC3561085 DOI: 10.1371/journal.pgen.1003188] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 11/07/2012] [Indexed: 01/31/2023] Open
Abstract
Post-translational modifications (PTMs) of histones exert fundamental roles in regulating gene expression. During development, groups of PTMs are constrained by unknown mechanisms into combinatorial patterns, which facilitate transitions from uncommitted embryonic cells into differentiated somatic cell lineages. Repressive histone modifications such as H3K9me3 or H3K27me3 have been investigated in detail, but the role of H4K20me3 in development is currently unknown. Here we show that Xenopus laevis Suv4-20h1 and h2 histone methyltransferases (HMTases) are essential for induction and differentiation of the neuroectoderm. Morpholino-mediated knockdown of the two HMTases leads to a selective and specific downregulation of genes controlling neural induction, thereby effectively blocking differentiation of the neuroectoderm. Global transcriptome analysis supports the notion that these effects arise from the transcriptional deregulation of specific genes rather than widespread, pleiotropic effects. Interestingly, morphant embryos fail to repress the Oct4-related Xenopus gene Oct-25. We validate Oct-25 as a direct target of xSu4-20h enzyme mediated gene repression, showing by chromatin immunoprecipitaton that it is decorated with the H4K20me3 mark downstream of the promoter in normal, but not in double-morphant, embryos. Since knockdown of Oct-25 protein significantly rescues the neural differentiation defect in xSuv4-20h double-morphant embryos, we conclude that the epistatic relationship between Suv4-20h enzymes and Oct-25 controls the transit from pluripotent to differentiation-competent neural cells. Consistent with these results in Xenopus, murine Suv4-20h1/h2 double-knockout embryonic stem (DKO ES) cells exhibit increased Oct4 protein levels before and during EB formation, and reveal a compromised and biased capacity for in vitro differentiation, when compared to normal ES cells. Together, these results suggest a regulatory mechanism, conserved between amphibians and mammals, in which H4K20me3-dependent restriction of specific POU-V genes directs cell fate decisions, when embryonic cells exit the pluripotent state. The quest of modern developmental biology is a detailed molecular description of the process that leads from the fertilized egg to the complex and highly differentiated adult organism. This process is controlled largely on the level of gene expression. While early embryonic cells are pluripotent and capable of transcribing most of their genome, older cells have become committed to the germ layer and differentiation programs during gastrulation. They express then a subset of genes compatible with their future physiological function. Young, pluripotent cells and post-gastrula, committed cells express different networks of transcription factors and contain chromatin of different structure and composition. How these two regulatory layers are interconnected during development is incompletely understood. We describe a novel and unexpected link between the pluripotency-associated POU-V gene Oct-25 and xSuv4-20h histone methyltransferases. XSuv4-20h enzymes are required to repress the Oct-25 gene, a homolog of mammalian Oct4, in the neuroectoderm of frog embryos as a prerequisite for neural differentiation. Consistently, murine Suv4-20h double-null ES cells show increased Oct4 protein levels before and during in vitro differentiation and display compromised differentiation in comparison to wild-type ES cells. Thus, Suv4-20h enzymes control specific POU-V genes and are involved in germ-layer specific differentiation.
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Affiliation(s)
- Dario Nicetto
- Adolf Butenandt Institut, Institut für Molekularbiologie, Ludwig Maximilians-Universität, München, Germany
| | - Matthias Hahn
- Center for Integrated Protein Science (Munich) at the Institut für Molekularbiologie, Adolf-Butenandt-Institut, LMU, München, Germany
| | - Julia Jung
- Medizinische Klinik I am Klinikum der Universität München (LMU), München, Germany
| | - Tobias D. Schneider
- Adolf Butenandt Institut, Institut für Molekularbiologie, Ludwig Maximilians-Universität, München, Germany
| | - Tobias Straub
- Adolf Butenandt Institut, Institut für Molekularbiologie, Ludwig Maximilians-Universität, München, Germany
| | - Robert David
- Medizinische Klinik I am Klinikum der Universität München (LMU), München, Germany
| | - Gunnar Schotta
- Center for Integrated Protein Science (Munich) at the Institut für Molekularbiologie, Adolf-Butenandt-Institut, LMU, München, Germany
| | - Ralph A. W. Rupp
- Adolf Butenandt Institut, Institut für Molekularbiologie, Ludwig Maximilians-Universität, München, Germany
- * E-mail:
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26
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Abstract
SIGNIFICANCE Derived from the inner cell mass of the preimplantation embryo, embryonic stem cells are prototype pluripotent stem (PS) cells that have the ability of self-renewal and differentiation into almost all cell types. Exploration of the mechanisms governing this pluripotency is important for understanding reprogramming mechanisms and stem cell behavior of PS cells and can lead to enhancing reprogramming efficiency and other applications. RECENT ADVANCES Induced pluripotent stem cells are recently discovered PS cells that can be derived from somatic cells by overexpression of pluripotency-related transcription factors. Recent studies have shown that transcription factors and their epigenetic regulation play important roles in the generating, maintaining, and differentiating these PS cells. Recent advances in sequencing technologies allow detailed analysis of target epigenomes and microRNAs (miRs), and have revealed unique epigenetic marks and miRs for PS cells. CRITICAL ISSUES Epigenetic modifications of genes include histone modifications, DNA methylation, and chromatin remodeling. Working closely with epigenetic modifiers, miRs play an important role in inducing and maintaining pluripotency. FUTURE DIRECTIONS The dynamic changes in epigenetic marks during reprogramming and their role in cell fate changes are being uncovered. This review focuses on these new advances in the epigenetics of PS cells.
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Affiliation(s)
- Ji Woong Han
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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27
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He L, Liu H, Tang L. SWI/SNF chromatin remodeling complex: a new cofactor in reprogramming. Stem Cell Rev Rep 2012; 8:128-36. [PMID: 21655945 DOI: 10.1007/s12015-011-9285-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Induced pluripotent stem (iPS) cells can be derived from somatic cells. Four key factors are required in this process including Oct4, Sox2, Klf4 and c-Myc. Ectopic expression of these four factors in somatic cells leads to reprogramming. Recent studies show that the SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling complex plays critical roles in reprogramming of somatic cells and maintaining the pluripotency of stem cells. The possible mechanism is that SWI/SNF enhances the binding activity of reprogramming factors to pluripotent gene promoters and thus increases the reprogramming efficiency. Here, we review these recent advances and discuss how SWI/SNF plays a role in reprogramming. Understanding this mechanism will be helpful to find out the detail of reprogramming, which may provide a new therapy in medical science by generating patient-specific pluripotent stem cells.
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Affiliation(s)
- Ling He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
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28
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Vessoni AT, Muotri AR, Okamoto OK. Autophagy in stem cell maintenance and differentiation. Stem Cells Dev 2012; 21:513-20. [PMID: 22066548 DOI: 10.1089/scd.2011.0526] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Autophagy is a lysosome-dependent degradation pathway that allows cells to recycle damaged or superfluous cytoplasmic content, such as proteins, organelles, and lipids. As a consequence of autophagy, the cells generate metabolic precursors for macromolecular biosynthesis or ATP generation. Deficiencies in this pathway were associated to several pathological conditions, such as neurodegenerative and cardiac diseases, cancer, and aging. The aim of this review is to summarize recent discoveries showing that autophagy also plays a critical role in stem cell maintenance and in a variety of cell differentiation processes. We also discuss a possible role for autophagy during cellular reprogramming and induced pluripotent stem (iPS) cell generation by taking advantage of ATP generation for chromatin remodeling enzyme activity and mitophagy. Finally, the significance of autophagy modulation is discussed in terms of augmenting efficiency of iPS cell generation and differentiation processes.
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Affiliation(s)
- Alexandre Teixeira Vessoni
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Vallaster M, Vallaster CD, Wu SM. Epigenetic mechanisms in cardiac development and disease. Acta Biochim Biophys Sin (Shanghai) 2012; 44:92-102. [PMID: 22194017 DOI: 10.1093/abbs/gmr090] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
During mammalian development, cardiac specification and ultimately lineage commitment to a specific cardiac cell type is accomplished by the action of specific transcription factors (TFs) and their meticulous control on an epigenetic level. In this review, we detail how cardiac-specific TFs function in concert with nucleosome remodeling and histone-modifying enzymes to regulate a diverse network of genes required for processes such as cell growth and proliferation, or epithelial to mesenchymal transition (EMT), for instance. We provide examples of how several cardiac TFs, such as Nkx2.5, WHSC1, Tbx5, and Tbx1, which are associated with developmental and congenital heart defects, are required for the recruitment of histone modifiers, such as Jarid2, p300, and Ash2l, and components of ATP-dependent remodeling enzymes like Brg1, Baf60c, and Baf180. Binding of these TFs to their respective sites at cardiac genes coincides with a distinct pattern of histone marks, indicating that the precise regulation of cardiac gene networks is orchestrated by interactions between TFs and epigenetic modifiers. Furthermore, we speculate that an epigenetic signature, comprised of TF occupancy, histone modifications, and overall chromatin organization, is an underlying mechanism that governs cardiac morphogenesis and disease.
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Affiliation(s)
- Marcus Vallaster
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, 02114, USA
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Delgado-Olguín P, Recillas-Targa F. Chromatin structure of pluripotent stem cells and induced pluripotent stem cells. Brief Funct Genomics 2011; 10:37-49. [PMID: 21325400 DOI: 10.1093/bfgp/elq038] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pluripotent embryonic stem (ES) cells are specialized cells with a dynamic chromatin structure, which is intimately connected with their pluripotency and physiology. In recent years somatic cells have been reprogrammed to a pluripotent state through over-expression of a defined set of transcription factors. These cells, known as induced pluripotent stem (iPS) cells, recapitulate ES cell properties and can be differentiated to apparently all cell lineages, making iPS cells a suitable replacement for ES cells in future regenerative medicine. Chromatin modifiers play a key function in establishing and maintaining pluripotency, therefore, elucidating the mechanisms controlling chromatin structure in both ES and iPS cells is of utmost importance to understanding their properties and harnessing their therapeutic potential. In this review, we discuss recent studies that provide a genome-wide view of the chromatin structure signature in ES cells and iPS cells and that highlight the central role of histone modifiers and chromatin remodelers in pluripotency maintenance and induction.
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Affiliation(s)
- Paul Delgado-Olguín
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, 1650 Owens street, San Francisco, CA 94158, USA.
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Chatterjee TK, Idelman G, Blanco V, Blomkalns AL, Piegore MG, Weintraub DS, Kumar S, Rajsheker S, Manka D, Rudich SM, Tang Y, Hui DY, Bassel-Duby R, Olson EN, Lingrel JB, Ho SM, Weintraub NL. Histone deacetylase 9 is a negative regulator of adipogenic differentiation. J Biol Chem 2011; 286:27836-47. [PMID: 21680747 DOI: 10.1074/jbc.m111.262964] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Differentiation of preadipocytes into mature adipocytes capable of efficiently storing lipids is an important regulatory mechanism in obesity. Here, we examined the involvement of histone deacetylases (HDACs) and histone acetyltransferases (HATs) in the regulation of adipogenesis. We find that among the various members of the HDAC and HAT families, only HDAC9 exhibited dramatic down-regulation preceding adipogenic differentiation. Preadipocytes from HDAC9 gene knock-out mice exhibited accelerated adipogenic differentiation, whereas HDAC9 overexpression in 3T3-L1 preadipocytes suppressed adipogenic differentiation, demonstrating its direct role as a negative regulator of adipogenesis. HDAC9 expression was higher in visceral as compared with subcutaneous preadipocytes, negatively correlating with their potential to undergo adipogenic differentiation in vitro. HDAC9 localized in the nucleus, and its negative regulation of adipogenesis segregates with the N-terminal nuclear targeting domain, whereas the C-terminal deacetylase domain is dispensable for this function. HDAC9 co-precipitates with USF1 and is recruited with USF1 at the E-box region of the C/EBPα gene promoter in preadipocytes. Upon induction of adipogenic differentiation, HDAC9 is down-regulated, leading to its dissociation from the USF1 complex, whereas p300 HAT is up-regulated to allow its association with USF1 and accumulation at the E-box site of the C/EBPα promoter in differentiated adipocytes. This reciprocal regulation of HDAC9 and p300 HAT in the USF1 complex is associated with increased C/EBPα expression, a master regulator of adipogenic differentiation. These findings provide new insights into mechanisms of adipogenic differentiation and document a critical regulatory role for HDAC9 in adipogenic differentiation through a deacetylase-independent mechanism.
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Affiliation(s)
- Tapan K Chatterjee
- Department of Internal Medicine, Division of Cardiovascular Diseases, University of Cincinnati, Cincinnati, Ohio 45267, USA.
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Reiland S, Salekdeh GH, Krijgsveld J. Defining pluripotent stem cells through quantitative proteomic analysis. Expert Rev Proteomics 2011; 8:29-42. [PMID: 21329426 DOI: 10.1586/epr.10.100] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Embryonic stem cells (ESCs) are at the center stage of intense research, inspired by their potential to give rise to all cell types of the adult individual. This property makes ESCs suitable candidates for generating specialized cells to replace damaged tissue lost after injury or disease. However, such clinical applications require a detailed insight of the molecular mechanisms underlying the self-renewal, expansion and differentiation of stem cells. This has gained further relevance since the introduction of induced pluripotent stem cells (iPSCs), which are functionally very similar to ESCs. The key property that iPSCs can be derived from somatic cells lifts some of the major ethical issues related to the need for embryos to generate ESCs. Yet, this has only increased the need to define the similarity of iPSCs and ESCs at the molecular level, both before and after they are induced to differentiate. In this article, we describe the proteomic approaches that have been used to characterize ESCs with regard to self-renewal and differentiation, with an emphasis on signaling cascades and histone modifications. We take this as a lead to discuss how quantitative proteomics can be deployed to study reprogramming and iPSC identity. In addition, we discuss how emerging proteomic technologies can become a useful tool to monitor the (de)differentiation status of ESCs and iPSCs.
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Affiliation(s)
- Sonja Reiland
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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Faralli H, Martin E, Coré N, Liu QC, Filippi P, Dilworth FJ, Caubit X, Fasano L. Teashirt-3, a novel regulator of muscle differentiation, associates with BRG1-associated factor 57 (BAF57) to inhibit myogenin gene expression. J Biol Chem 2011; 286:23498-510. [PMID: 21543328 DOI: 10.1074/jbc.m110.206003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In adult muscles and under normal physiological conditions, satellite cells are found in a quiescent state but can be induced to enter the cell cycle by signals resulting from exercise, injury-induced muscle regeneration, or specific disease states. Once activated, satellite cells proliferate, self-renew, and differentiate to form myofibers. In the present study, we found that the zinc finger-containing factor Teashirt-3 (TSHZ3) was expressed in quiescent satellite cells of adult mouse skeletal muscles. We showed that following treatment with cardiotoxin TSHZ3 was strongly expressed in satellite cells of regenerating muscles. Moreover, immunohistochemical analysis indicated that TSHZ3 was expressed in both quiescent and activated satellite cells on intact myofibers in culture. TSHZ3 expression was maintained in myoblasts but disappeared with myotube formation. In C2C12 myoblasts, we showed that overexpression of Tshz3 impaired myogenic differentiation and promoted the down-regulation of myogenin (Myog) and up-regulation of paired-box factor 7 (Pax7). Moreover, knockdown experiments revealed a selective effect of Tshz3 on Myog regulation, and transcriptional reporter experiments indicated that TSHZ3 repressed Myog promoter. We identified the BRG1-associated factor 57 (BAF57), a subunit of the SWI/SNF complex, as a partner of TSHZ3. We showed that TSHZ3 cooperated with BAF57 to repress MYOD-dependent Myog expression. These results suggest a novel mechanism for transcriptional repression by TSHZ3 in which TSHZ3 and BAF57 cooperate to modulate MyoD activity on the Myog promoter to regulate skeletal muscle differentiation.
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Affiliation(s)
- Hervé Faralli
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216, CNRS-Université de la Méditerranée, Campus de Luminy, Case 907, 13288 Marseille Cedex 09, France
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Saladi SV, Keenen B, Marathe HG, Qi H, Chin KV, de la Serna IL. Modulation of extracellular matrix/adhesion molecule expression by BRG1 is associated with increased melanoma invasiveness. Mol Cancer 2010; 9:280. [PMID: 20969766 PMCID: PMC3098014 DOI: 10.1186/1476-4598-9-280] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 10/22/2010] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Metastatic melanoma is an aggressive malignancy that is resistant to therapy and has a poor prognosis. The progression of primary melanoma to metastatic disease is a multi-step process that requires dynamic regulation of gene expression through currently uncharacterized epigenetic mechanisms. Epigenetic regulation of gene expression often involves changes in chromatin structure that are catalyzed by chromatin remodeling enzymes. Understanding the mechanisms involved in the regulation of gene expression during metastasis is important for developing an effective strategy to treat metastatic melanoma. SWI/SNF enzymes are multisubunit complexes that contain either BRG1 or BRM as the catalytic subunit. We previously demonstrated that heterogeneous SWI/SNF complexes containing either BRG1 or BRM are epigenetic modulators that regulate important aspects of the melanoma phenotype and are required for melanoma tumorigenicity in vitro. RESULTS To characterize BRG1 expression during melanoma progression, we assayed expression of BRG1 in patient derived normal skin and in melanoma specimen. BRG1 mRNA levels were significantly higher in stage IV melanomas compared to stage III tumors and to normal skin. To determine the role of BRG1 in regulating the expression of genes involved in melanoma metastasis, we expressed BRG1 in a melanoma cell line that lacks BRG1 expression and examined changes in extracellular matrix and adhesion molecule expression. We found that BRG1 modulated the expression of a subset of extracellular matrix remodeling enzymes and adhesion proteins. Furthermore, BRG1 altered melanoma adhesion to different extracellular matrix components. Expression of BRG1 in melanoma cells that lack BRG1 increased invasive ability while down-regulation of BRG1 inhibited invasive ability in vitro. Activation of metalloproteinase (MMP) 2 expression greatly contributed to the BRG1 induced increase in melanoma invasiveness. We found that BRG1 is recruited to the MMP2 promoter and directly activates expression of this metastasis associated gene. CONCLUSIONS We provide evidence that BRG1 expression increases during melanoma progression. Our study has identified BRG1 target genes that play an important role in melanoma metastasis and we show that BRG1 promotes melanoma invasive ability in vitro. These results suggest that increased BRG1 levels promote the epigenetic changes in gene expression required for melanoma metastasis to proceed.
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Affiliation(s)
- Srinivas Vinod Saladi
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Bridget Keenen
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Himangi G Marathe
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Huiling Qi
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Khew-Voon Chin
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
- Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH 43614, USA
- Center for Diabetes and Endocrine Research, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH 43614, USA
| | - Ivana L de la Serna
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine, Toledo, OH 43614, USA
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