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Moosavi A, Ardekani AM. Role of Epigenetics in Biology and Human Diseases. IRANIAN BIOMEDICAL JOURNAL 2016; 20:246-58. [PMID: 27377127 PMCID: PMC5075137 DOI: 10.22045/ibj.2016.01] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/22/2016] [Accepted: 03/08/2016] [Indexed: 12/11/2022]
Abstract
For a long time, scientists have tried to describe disorders just by genetic or environmental factors. However, the role of epigenetics in human diseases has been considered from a half of century ago. In the last decade, this subject has attracted many interests, especially in complicated disorders such as behavior plasticity, memory, cancer, autoimmune disease, and addiction as well as neurodegenerative and psychological disorders. This review first explains the history and classification of epigenetic modifications, and then the role of epigenetic in biology and connection between the epigenetics and environment are explained. Furthermore, the role of epigenetics in human diseases is considered by focusing on some diseases with some complicated features, and at the end, we have given the future perspective of this field. The present review article provides concepts with some examples to reveal a broad view of different aspects of epigenetics in biology and human diseases.
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Affiliation(s)
- Azam Moosavi
- Department of Biochemistry, School of Medicine, Alborz University of Medical Sciences, Alborz, Iran
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52
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Chromatin proteins and RNA are associated with DNA during all phases of mitosis. Cell Discov 2016; 2:16038. [PMID: 27807477 PMCID: PMC5078801 DOI: 10.1038/celldisc.2016.38] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/07/2016] [Indexed: 12/11/2022] Open
Abstract
Mitosis brings about major changes to chromosome and nuclear structure. We used recently developed proximity ligation assay-based techniques to investigate the association with DNA of chromatin-associated proteins and RNAs in Drosophila embryos during mitosis. All groups of tested proteins, histone-modifying and chromatin-remodeling proteins and methylated histones remained in close proximity to DNA during all phases of mitosis. We also found that RNA transcripts are associated with DNA during all stages of mitosis. Reduction of H3K27me3 levels or elimination of RNAs had no effect on the association of the components of PcG and TrxG complexes to DNA. Using a combination of proximity ligation assay-based techniques and super-resolution microscopy, we found that the number of protein-DNA and RNA-DNA foci undergoes significant reduction during mitosis, suggesting that mitosis may be accompanied by structural re-arrangement or compaction of specific chromatin domains.
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53
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Festuccia N, Dubois A, Vandormael-Pournin S, Gallego Tejeda E, Mouren A, Bessonnard S, Mueller F, Proux C, Cohen-Tannoudji M, Navarro P. Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network. Nat Cell Biol 2016; 18:1139-1148. [PMID: 27723719 DOI: 10.1038/ncb3418] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 09/07/2016] [Indexed: 12/14/2022]
Abstract
Pluripotent mouse embryonic stem cells maintain their identity throughout virtually infinite cell divisions. This phenomenon, referred to as self-renewal, depends on a network of sequence-specific transcription factors (TFs) and requires daughter cells to accurately reproduce the gene expression pattern of the mother. However, dramatic chromosomal changes take place in mitosis, generally leading to the eviction of TFs from chromatin. Here, we report that Esrrb, a major pluripotency TF, remains bound to key regulatory regions during mitosis. We show that mitotic Esrrb binding is highly dynamic, driven by specific recognition of its DNA-binding motif and is associated with early transcriptional activation of target genes after completion of mitosis. These results indicate that Esrrb may act as a mitotic bookmarking factor, opening another perspective to molecularly understand the role of sequence-specific TFs in the epigenetic control of self-renewal, pluripotency and genome reprogramming.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Developmental &Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France
| | - Agnès Dubois
- Epigenetics of Stem Cells, Department of Developmental &Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France
| | - Sandrine Vandormael-Pournin
- Mouse Functional Genetics, Department of Developmental &Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France
| | - Elena Gallego Tejeda
- Epigenetics of Stem Cells, Department of Developmental &Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France
| | - Adrien Mouren
- Epigenetics of Stem Cells, Department of Developmental &Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France
| | - Sylvain Bessonnard
- Mouse Functional Genetics, Department of Developmental &Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France
| | - Florian Mueller
- Imaging and Modelling, Department of Cell Biology &Infections, Institut Pasteur, CNRS UMR 3691, 25 rue du docteur Roux, Paris 75015, France
| | - Caroline Proux
- Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Michel Cohen-Tannoudji
- Mouse Functional Genetics, Department of Developmental &Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Developmental &Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France
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Aregger M, Kaskar A, Varshney D, Fernandez-Sanchez ME, Inesta-Vaquera FA, Weidlich S, Cowling VH. CDK1-Cyclin B1 Activates RNMT, Coordinating mRNA Cap Methylation with G1 Phase Transcription. Mol Cell 2016; 61:734-746. [PMID: 26942677 PMCID: PMC4781437 DOI: 10.1016/j.molcel.2016.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/11/2015] [Accepted: 02/05/2016] [Indexed: 12/22/2022]
Abstract
The creation of translation-competent mRNA is dependent on RNA polymerase II transcripts being modified by addition of the 7-methylguanosine (m7G) cap. The factors that mediate splicing, nuclear export, and translation initiation are recruited to the transcript via the cap. The cap structure is formed by several activities and completed by RNMT (RNA guanine-7 methyltransferase), which catalyzes N7 methylation of the cap guanosine. We report that CDK1-cyclin B1 phosphorylates the RNMT regulatory domain on T77 during G2/M phase of the cell cycle. RNMT T77 phosphorylation activates the enzyme both directly and indirectly by inhibiting interaction with KPNA2, an RNMT inhibitor. RNMT T77 phosphorylation results in elevated m7G cap methyltransferase activity at the beginning of G1 phase, coordinating mRNA capping with the burst of transcription that occurs following nuclear envelope reformation. RNMT T77 phosphorylation is required for the production of cohort of proteins, and inhibiting T77 phosphorylation reduces the cell proliferation rate.
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Affiliation(s)
- Michael Aregger
- Centre for Gene Regulation and Expression/MRC Phosphorylation and Ubiquitylation, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Aneesa Kaskar
- Centre for Gene Regulation and Expression/MRC Phosphorylation and Ubiquitylation, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Dhaval Varshney
- Centre for Gene Regulation and Expression/MRC Phosphorylation and Ubiquitylation, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Maria Elena Fernandez-Sanchez
- Centre for Gene Regulation and Expression/MRC Phosphorylation and Ubiquitylation, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Francisco A Inesta-Vaquera
- Centre for Gene Regulation and Expression/MRC Phosphorylation and Ubiquitylation, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Simone Weidlich
- Division of Signal Transduction Therapy, University of Dundee, Dundee DD1 5EH, UK
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression/MRC Phosphorylation and Ubiquitylation, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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55
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Lerner J, Bagattin A, Verdeguer F, Makinistoglu MP, Garbay S, Felix T, Heidet L, Pontoglio M. Human mutations affect the epigenetic/bookmarking function of HNF1B. Nucleic Acids Res 2016; 44:8097-111. [PMID: 27229139 PMCID: PMC5041451 DOI: 10.1093/nar/gkw467] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/13/2016] [Indexed: 12/19/2022] Open
Abstract
Bookmarking factors are transcriptional regulators involved in the mitotic transmission of epigenetic information via their ability to remain associated with mitotic chromatin. The mechanisms through which bookmarking factors bind to mitotic chromatin remain poorly understood. HNF1β is a bookmarking transcription factor that is frequently mutated in patients suffering from renal multicystic dysplasia and diabetes. Here, we show that HNF1β bookmarking activity is impaired by naturally occurring mutations found in patients. Interestingly, this defect in HNF1β mitotic chromatin association is rescued by an abrupt decrease in temperature. The rapid relocalization to mitotic chromatin is reversible and driven by a specific switch in DNA-binding ability of HNF1β mutants. Furthermore, we demonstrate that importin-β is involved in the maintenance of the mitotic retention of HNF1β, suggesting a functional link between the nuclear import system and the mitotic localization/translocation of bookmarking factors. Altogether, our studies have disclosed novel aspects on the mechanisms and the genetic programs that account for the mitotic association of HNF1β, a bookmarking factor that plays crucial roles in the epigenetic transmission of information through the cell cycle.
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Affiliation(s)
- Jonathan Lerner
- Department of Development, Reproduction and Cancer, Institut Cochin, INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Paris 75014, France
| | - Alessia Bagattin
- Department of Development, Reproduction and Cancer, Institut Cochin, INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Paris 75014, France
| | - Francisco Verdeguer
- Department of Development, Reproduction and Cancer, Institut Cochin, INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Paris 75014, France
| | - Munevver P Makinistoglu
- Department of Development, Reproduction and Cancer, Institut Cochin, INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Paris 75014, France
| | - Serge Garbay
- Department of Development, Reproduction and Cancer, Institut Cochin, INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Paris 75014, France
| | - Tristan Felix
- Department of Development, Reproduction and Cancer, Institut Cochin, INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Paris 75014, France
| | - Laurence Heidet
- Department of Pediatric Nephrology, Assistance Publique des Hôpitaux de Paris, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Hospital Necker-Enfants Malades, Paris 75015, France
| | - Marco Pontoglio
- Department of Development, Reproduction and Cancer, Institut Cochin, INSERM U1016/CNRS UMR 8104/Université Paris-Descartes, Paris 75014, France
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56
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Gatchalian J, Gallardo CM, Shinsky SA, Ospina RR, Liendo AM, Krajewski K, Klein BJ, Andrews FH, Strahl BD, M van Wely KH, Kutateladze TG. Chromatin condensation and recruitment of PHD finger proteins to histone H3K4me3 are mutually exclusive. Nucleic Acids Res 2016; 44:6102-12. [PMID: 27016734 PMCID: PMC5291243 DOI: 10.1093/nar/gkw193] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/15/2016] [Indexed: 11/16/2022] Open
Abstract
Histone post-translational modifications, and specific combinations they create, mediate a wide range of nuclear events. However, the mechanistic bases for recognition of these combinations have not been elucidated. Here, we characterize crosstalk between H3T3 and H3T6 phosphorylation, occurring in mitosis, and H3K4me3, a mark associated with active transcription. We detail the molecular mechanisms by which H3T3ph/K4me3/T6ph switches mediate activities of H3K4me3-binding proteins, including those containing plant homeodomain (PHD) and double Tudor reader domains. Our results derived from nuclear magnetic resonance chemical shift perturbation analysis, orthogonal binding assays and cell fluorescence microscopy studies reveal a strong anti-correlation between histone H3T3/T6 phosphorylation and retention of PHD finger proteins in chromatin during mitosis. Together, our findings uncover the mechanistic rules of chromatin engagement for H3K4me3-specific readers during cell division.
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Affiliation(s)
- Jovylyn Gatchalian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Carmen Mora Gallardo
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, 28049 Madrid, Spain
| | - Stephen A Shinsky
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ruben Rosas Ospina
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Andrea Mansilla Liendo
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, 28049 Madrid, Spain
| | - Krzysztof Krajewski
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Karel H M van Wely
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, 28049 Madrid, Spain
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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57
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Andrews FH, Gatchalian J, Krajewski K, Strahl BD, Kutateladze TG. Regulation of Methyllysine Readers through Phosphorylation. ACS Chem Biol 2016; 11:547-53. [PMID: 26726824 DOI: 10.1021/acschembio.5b00802] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyllysine post-translational modifications (PTMs) of histones create binding sites for evolutionarily conserved reader domains that link nuclear host proteins and chromatin-modifying complexes to specific genomic regions. In the context of these events, adjacent histone PTMs are capable of altering the binding activity of readers toward their target marks. This provides a mechanism of "combinatorial readout" of PTMs that can enhance, decrease, or eliminate the association of readers with chromatin. In this Perspective, we focus on recent studies describing the impact of dynamic phospho-serine/threonine/tyrosine marks on the interaction of methyllysine readers with histones, summarize mechanistic aspects of the phospho/methyl readout, and highlight the significance of crosstalk between these PTMs. We also demonstrate that in addition to inhibiting binding and serving as a true switch, promoting dissociation of the methyllysine readers from chromatin, the phospho/methyl combination can act together in a cooperative manner--thus adding a new layer of regulatory information that can be encoded in these dual histone PTMs.
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Affiliation(s)
- Forest H. Andrews
- Department
of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Jovylyn Gatchalian
- Department
of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Krzysztof Krajewski
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Brian D. Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Tatiana G. Kutateladze
- Department
of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
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58
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Yu S, Geng Q, Pan Q, Liu Z, Ding S, Xiang Q, Sun F, Wang C, Huang Y, Hong A. MiR-690, a Runx2-targeted miRNA, regulates osteogenic differentiation of C2C12 myogenic progenitor cells by targeting NF-kappaB p65. Cell Biosci 2016; 6:10. [PMID: 26877865 PMCID: PMC4751671 DOI: 10.1186/s13578-016-0073-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 01/24/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The runt-related transcription factor 2 (Runx2) is a cell-fate-determining factor that controls osteoblast differentiation and bone formation. It has been previously demonstrated that microRNAs (miRNAs) play important roles in osteogenesis. However, the Runx2-regulated miRNAs that have been reported thus far are limited. In this study, we pursued to identify these miRNAs in Tet-on stable C2C12 cell line (C2C12/Runx2(Dox) subline). RESULTS Microarray analysis revealed that alterations in miRNA expression occur with 54 miRNAs. Among these miRNAs, miR-690 was identified as a positive regulator of Runx2-induced osteogenic differentiation of C2C12 cells through gain- and loss-of-function assays. Expression of miR-690 is induced by Runx2, which binds directly to the putative promoter of mir-690 (Mirn690). The miR-690 proceeds to inhibit translation of the messenger RNA encoding the nuclear factor kappa B (NF-κB) subunit p65 whose overexpression inhibits Runx2-induced osteogenic differentiation of C2C12 cells. Interleukin-6 (IL-6), a downstream target of NF-κB pathway, is upregulated by p65 overexpression but significantly downregulated during this differentiation process. Furthermore, overexpression of IL-6 impedes the expression of osteocalcin, a defined marker of late osteoblast differentiation. CONCLUSIONS Together, our results suggest that the miR-690 transactivated by Runx2 acts as a positive regulator of Runx2-induced osteogenic differentiation by inactivating the NF-κB pathway via the downregulation of the subunit p65.
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Affiliation(s)
- Shouhe Yu
- Institute of Biomedicine, Jinan University, National Engineering Research Center of Genetic Medicine, Key Lab for Bioengineering Medicine of Guangdong Province, Guangzhou, Guangdong People's Republic of China
| | - Qianqian Geng
- Institute of Biomedicine, Jinan University, National Engineering Research Center of Genetic Medicine, Key Lab for Bioengineering Medicine of Guangdong Province, Guangzhou, Guangdong People's Republic of China
| | - Qiuhui Pan
- Central Laboratory, People's 10th Hospital, Shanghai, People's Republic of China
| | - Zhongyu Liu
- College of Life Science, Yangtze University, Jingzhou, Hubei People's Republic of China
| | - Shan Ding
- Department of Materials Science and Engineering, Jinan University, Engineering Research Center of Artificial Organs and Materials, Ministry of Education, Guangzhou, Guangdong People's Republic of China
| | - Qi Xiang
- Institute of Biomedicine, Jinan University, National Engineering Research Center of Genetic Medicine, Key Lab for Bioengineering Medicine of Guangdong Province, Guangzhou, Guangdong People's Republic of China
| | - Fenyong Sun
- Department of Medical Laboratory, People's 10th Hospital, Shanghai, People's Republic of China
| | - Can Wang
- College of Pharmacy, Jinan University, Guangzhou, Guangdong People's Republic of China
| | - Yadong Huang
- Institute of Biomedicine, Jinan University, National Engineering Research Center of Genetic Medicine, Key Lab for Bioengineering Medicine of Guangdong Province, Guangzhou, Guangdong People's Republic of China
| | - An Hong
- Institute of Biomedicine, Jinan University, National Engineering Research Center of Genetic Medicine, Key Lab for Bioengineering Medicine of Guangdong Province, Guangzhou, Guangdong People's Republic of China
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Abstract
Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle.
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Affiliation(s)
- Klara Weipoltshammer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
| | - Christian Schöfer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
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60
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Zheng Y, Murphy LC. Regulation of steroid hormone receptors and coregulators during the cell cycle highlights potential novel function in addition to roles as transcription factors. NUCLEAR RECEPTOR SIGNALING 2016; 14:e001. [PMID: 26778927 PMCID: PMC4714463 DOI: 10.1621/nrs.14001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/01/2015] [Indexed: 01/15/2023]
Abstract
Cell cycle progression is tightly controlled by several kinase families including Cyclin-Dependent Kinases, Polo-Like Kinases, and Aurora Kinases. A large amount of data show that steroid hormone receptors and various components of the cell cycle, including cell cycle regulated kinases, interact, and this often results in altered transcriptional activity of the receptor. Furthermore, steroid hormones, through their receptors, can also regulate the transcriptional expression of genes that are required for cell cycle regulation. However, emerging data suggest that steroid hormone receptors may have roles in cell cycle progression independent of their transcriptional activity. The following is a review of how steroid receptors and their coregulators can regulate or be regulated by the cell cycle machinery, with a particular focus on roles independent of transcription in G2/M.
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Affiliation(s)
- Yingfeng Zheng
- Department of Biochemistry and Medical Genetics (YZ, LCM), University of Manitoba; Manitoba Institute of Cell Biology (YZ, LCM), CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Leigh C Murphy
- Department of Biochemistry and Medical Genetics (YZ, LCM), University of Manitoba; Manitoba Institute of Cell Biology (YZ, LCM), CancerCare Manitoba, Winnipeg, Manitoba, Canada
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61
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Fritz A, Barutcu AR, Martin-Buley L, vanWijnen AJ, Zaidi SK, Imbalzano AN, Lian JB, Stein JL, Stein GS. Chromosomes at Work: Organization of Chromosome Territories in the Interphase Nucleus. J Cell Biochem 2016; 117:9-19. [PMID: 26192137 PMCID: PMC4715719 DOI: 10.1002/jcb.25280] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 07/17/2015] [Indexed: 12/26/2022]
Abstract
The organization of interphase chromosomes in chromosome territories (CTs) was first proposed more than one hundred years ago. The introduction of increasingly sophisticated microscopic and molecular techniques, now provide complementary strategies for studying CTs in greater depth than ever before. Here we provide an overview of these strategies and how they are being used to elucidate CT interactions and the role of these dynamically regulated, nuclear-structure building blocks in directly supporting nuclear function in a physiologically responsive manner.
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Affiliation(s)
- Andrew Fritz
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - A. Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Lori Martin-Buley
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - André J. vanWijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Sayyed K. Zaidi
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jane B. Lian
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L. Stein
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Gary S. Stein
- University of Vermont Cancer Center, Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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62
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Montecino M, Stein G, Stein J, Zaidi K, Aguilar R. Multiple levels of epigenetic control for bone biology and pathology. Bone 2015; 81:733-738. [PMID: 25865577 PMCID: PMC4600412 DOI: 10.1016/j.bone.2015.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 12/12/2022]
Abstract
Multiple dimensions of epigenetic control contribute to regulation of gene expression that governs bone biology and pathology. Once confined to DNA methylation and a limited number of post-translational modifications of histone proteins, the definition of epigenetic mechanisms is expanding to include contributions of non-coding RNAs and mitotic bookmarking, a mechanism for retaining phenotype identity during cell proliferation. Together these different levels of epigenetic control of physiological processes and their perturbations that are associated with compromised gene expression during the onset and progression of disease, have contributed to an unprecedented understanding of the activities (operation) of the genomic landscape. Here, we address general concepts that explain the contribution of epigenetic control to the dynamic regulation of gene expression during eukaryotic transcription. This article is part of a Special Issue entitled Epigenetics and Bone.
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Affiliation(s)
- Martin Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile.
| | - Gary Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA.
| | - Janet Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Kaleem Zaidi
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Rodrigo Aguilar
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile
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63
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Kuzmich AI, Tyulkina DV, Vinogradova TV, Sverdlov ED. Pioneer transcription factors in normal development and carcinogenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 41:636-43. [DOI: 10.1134/s1068162015060084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Scott RE, Ghule PN, Stein JL, Stein GS. Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. J Cell Physiol 2015; 230:2533-42. [PMID: 25808367 PMCID: PMC4481160 DOI: 10.1002/jcp.24990] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/18/2015] [Indexed: 12/13/2022]
Abstract
The early stages of carcinogenesis are linked to defects in the cell cycle. A series of cell cycle checkpoints are involved in this process. The G1/S checkpoint that serves to integrate the control of cell proliferation and differentiation is linked to carcinogenesis and the mitotic spindle checkpoint is associated with the development of chromosomal instability. This paper presents the outcome of systems biology studies designed to evaluate if networks of covariate cell cycle gene transcripts exist in proliferative mammalian tissues including mice, rats, and humans. The GeneNetwork website that contains numerous gene expression datasets from different species, sexes, and tissues represents the foundational resource for these studies (www.genenetwork.org). In addition, WebGestalt, a gene ontology tool, facilitated the identification of expression networks of genes that co-vary with key cell cycle targets, especially Cdc20 and Plk1 (www.bioinfo.vanderbilt.edu/webgestalt). Cell cycle expression networks of such covariate mRNAs exist in multiple proliferative tissues including liver, lung, pituitary, adipose, and lymphoid tissues among others but not in brain or retina that have low proliferative potential. Sixty-three covariate cell cycle gene transcripts (mRNAs) compose the average cell cycle network with P = e(-13) to e(-36) . Cell cycle expression networks show species, sex and tissue variability, and they are enriched in mRNA transcripts associated with mitosis, many of which are associated with chromosomal instability.
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Affiliation(s)
- RE Scott
- Varigenix, Inc., Memphis, Tennessee
| | - PN Ghule
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont, USA
| | - JL Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont, USA
| | - GS Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont, USA
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Wu TF, Yao YL, Lai IL, Lai CC, Lin PL, Yang WM. Loading of PAX3 to Mitotic Chromosomes Is Mediated by Arginine Methylation and Associated with Waardenburg Syndrome. J Biol Chem 2015; 290:20556-64. [PMID: 26149688 DOI: 10.1074/jbc.m114.607713] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Indexed: 11/06/2022] Open
Abstract
PAX3 is a transcription factor critical to gene regulation in mammalian development. Mutations in PAX3 are associated with Waardenburg syndrome (WS), but the mechanism of how mutant PAX3 proteins cause WS remains unclear. Here, we found that PAX3 loads on mitotic chromosomes using its homeodomain. PAX3 WS mutants with mutations in homeodomain lose the ability to bind mitotic chromosomes. Moreover, loading of PAX3 on mitotic chromosomes requires arginine methylation, which is regulated by methyltransferase PRMT5 and demethylase JMJD6. Mutant PAX3 proteins that lose mitotic chromosome localization block cell proliferation and normal development of zebrafish. These results reveal the molecular mechanism of PAX3s loading on mitotic chromosomes and the importance of this localization pattern in normal development. Our findings suggest that PAX3 WS mutants interfere with the normal functions of PAX3 in a dominant negative manner, which is important to the understanding of the pathogenesis of Waardenburg syndrome.
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Affiliation(s)
- Tsu-Fang Wu
- From the Department of Life Sciences, Department of Biotechnology, Hung Kuang University, Taichung 43302, Taiwan
| | - Ya-Li Yao
- Department of Biotechnology, Asia University, Taichung 41354, Taiwan, and
| | - I-Lu Lai
- the Institute of Molecular Biology, and
| | | | - Pei-Lun Lin
- Bachelor Program of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
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66
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Wu T, Donohoe ME. The converging roles of BRD4 and gene transcription in pluripotency and oncogenesis. RNA & DISEASE 2015; 2:e894. [PMID: 26405693 PMCID: PMC4578175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Affiliation(s)
- Tao Wu
- Burke Medical Research Institute, White Plains, NY 10605, U.S.A, Department of Neuroscience Brain Mind Research Institute, Department of Cell & Development, Weill Cornell Medical College, New York, NY 10065, U.S.A
| | - Mary E Donohoe
- Burke Medical Research Institute, White Plains, NY 10605, U.S.A, Department of Neuroscience Brain Mind Research Institute, Department of Cell & Development, Weill Cornell Medical College, New York, NY 10065, U.S.A
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67
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Meyer MB, Benkusky NA, Pike JW. Selective Distal Enhancer Control of the Mmp13 Gene Identified through Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Genomic Deletions. J Biol Chem 2015; 290:11093-107. [PMID: 25773540 DOI: 10.1074/jbc.m115.648394] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Indexed: 12/29/2022] Open
Abstract
Matrix metalloproteinase 13 (Mmp13, collagenase-3) plays an essential role in bone metabolism and mineral homeostasis. It is regulated by numerous factors, including BMP-2, parathyroid hormone, and 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3), through transcription factors such as Runt-related transcription factor 2 (RUNX2), CCAAT/enhancer-binding protein β (C/EBPβ), OSX, and vitamin D receptor (VDR). During osteoblast maturation, the basal expression of Mmp13 and its sensitivity to 1,25(OH)2D3 are strikingly increased. In this report, ChIP-sequencing analysis in mouse preosteoblasts revealed that the Mmp13 gene was probably regulated by three major enhancers located -10, -20, and -30 kb upstream of the gene promoter, occupied by activated VDR and prebound C/EBPβ and RUNX2, respectively. Initially, bacterial artificial chromosome clone recombineering and traditional mutagenesis defined binding sites for VDR and RUNX2. We then employed a CRISPR/Cas9 gene editing approach to delete the -10 and -30 kb Mmp13 enhancers, a region proximal to the promoter, and VDR or RUNX2. VDR-mediated up-regulation of Mmp13 transcription was completely abrogated upon removal of the -10 kb enhancer, resulting in a 1,25(OH)2D3-directed repression of Mmp13. Deletion of either the -30 kb enhancer or RUNX2 resulted in a complete loss of basal transcript activity and a ChIP-identified destabilization of the chromatin enhancer environment and factor binding. Whereas enhancer deletions only affected Mmp13 expression, the RUNX2 deletion led to changes in gene expression, a reduction in cellular proliferation, and an inability to differentiate. We conclude that the Mmp13 gene is regulated via at least three specific distal enhancers that display independent activities yet are able to integrate response from multiple signaling pathways in a model of activation and suppression.
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Affiliation(s)
- Mark B Meyer
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Nancy A Benkusky
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - J Wesley Pike
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
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68
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Abstract
Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. This review by Iwafuchi-Doi and Zaret focuses on the most recent studies of pioneer factors in cell programming and reprogramming, how pioneer factors have special chromatin-binding properties, and facilitators and impediments to chromatin binding. A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in “closed” chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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69
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Bianchi A, Lanzuolo C. Into the chromatin world: Role of nuclear architecture in epigenome regulation. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Arcidiacono T, Mingione A, Macrina L, Pivari F, Soldati L, Vezzoli G. Idiopathic calcium nephrolithiasis: a review of pathogenic mechanisms in the light of genetic studies. Am J Nephrol 2014; 40:499-506. [PMID: 25504362 DOI: 10.1159/000369833] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Calcium nephrolithiasis is a multifactorial disease with a polygenic milieu. Association studies identified genetic polymorphisms potentially implicated in the pathogenesis of calcium nephrolithiasis. The present article reviews the mechanisms of calcium stone formation and the potential contribution of gene polymorphisms to lithogenic mechanisms. SUMMARY Endoscopy observations suggested that precipitation of calcium-oxalate on the Randall's plaque at the papilla surface may cause idiopathic calcium-oxalate stones. The Randall's plaque is a hydroxyapatite deposit in the interstitium of the kidney medulla, which resembles a soft tissue calcification. Conversely, calcium-phosphate stones may develop from crystalline deposits located at the tip of the Bellini duct. Polymorphisms of eleven genes have been associated with stones in genome-wide association studies and replicated candidate-gene association studies: VDR, SLC34A1, SLC34A4, CLDN14, and CaSR genes coding for proteins regulating tubular phosphate and calcium reabsorption; CaSR, MGP, OPN, PLAU, and UMOD genes coding for proteins preventing calcium salt precipitation; AQP1 gene coding for a water channel in the proximal tubule. The renal activity of the last gene, DGKH, is unknown. Polymorphisms in these genes may predispose to calcium-oxalate and -phosphate stones by increasing the risk of calcium-phosphate precipitation in the tubular fluid. Key Messages: Genetic findings suggest that tubular fluid supersaturation with respect to calcium and phosphate predisposes to calcium-oxalate stones by triggering cellular mechanisms that lead to the Randall's plaque formation.
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Affiliation(s)
- Teresa Arcidiacono
- Nephrology and Dialysis Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
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71
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Lopez-Camacho C, van Wijnen AJ, Lian JB, Stein JL, Stein GS. CBFβ and the leukemogenic fusion protein CBFβ-SMMHC associate with mitotic chromosomes to epigenetically regulate ribosomal genes. J Cell Biochem 2014; 115:2155-64. [PMID: 25079347 PMCID: PMC4199869 DOI: 10.1002/jcb.24892] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 07/25/2014] [Indexed: 01/01/2023]
Abstract
Mitotic bookmarking is an epigenetic control mechanism that sustains gene expression in progeny cells; it is often found in genes related to the maintenance of cellular phenotype and growth control. RUNX transcription factors regulate a broad spectrum of RNA Polymerase (Pol II) transcribed genes important for lineage commitment but also regulate RNA Polymerase I (Pol I) driven ribosomal gene expression, thus coordinating control of cellular identity and proliferation. In this study, using fluorescence microscopy and biochemical approaches we show that the principal RUNX co-factor, CBFβ, associates with nucleolar organizing regions (NORs) during mitosis to negatively regulate RUNX-dependent ribosomal gene expression. Of clinical relevance, we establish for the first time that the leukemogenic fusion protein CBFβ-SMMHC (smooth muscle myosin heavy chain) also associates with ribosomal genes in interphase chromatin and mitotic chromosomes to promote and epigenetically sustain regulation of ribosomal genes through RUNX factor interactions. Our results demonstrate that CBFβ contributes to the transcriptional regulation of ribosomal gene expression and provide further understanding of the epigenetic role of CBFβ-SMMHC in proliferation and maintenance of the leukemic phenotype.
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Affiliation(s)
- Cesar Lopez-Camacho
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT 05405 USA
| | - Andre J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT 05405 USA
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT 05405 USA
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT 05405 USA
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72
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Dekker J. Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture. Epigenetics Chromatin 2014; 7:25. [PMID: 25435919 PMCID: PMC4247682 DOI: 10.1186/1756-8935-7-25] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/15/2014] [Indexed: 01/19/2023] Open
Abstract
Genetic and epigenetic inheritance through mitosis is critical for dividing cells to maintain their state. This process occurs in the context of large-scale re-organization of chromosome conformation during prophase leading to the formation of mitotic chromosomes, and during the reformation of the interphase nucleus during telophase and early G1. This review highlights how recent studies over the last 5 years employing chromosome conformation capture combined with classical models of chromosome organization based on decades of microscopic observations, are providing new insights into the three-dimensional organization of chromatin inside the interphase nucleus and within mitotic chromosomes. One striking observation is that interphase genome organization displays cell type-specific features that are related to cell type-specific gene expression, whereas mitotic chromosome folding appears universal and tissue invariant. This raises the question of whether or not there is a need for an epigenetic memory for genome folding. Herein, the two different folding states of mammalian genomes are reviewed and then models are discussed wherein instructions for cell type-specific genome folding are locally encoded in the linear genome and transmitted through mitosis, e.g., as open chromatin sites with or without continuous binding of transcription factors. In the next cell cycle these instructions are used to re-assemble protein complexes on regulatory elements which then drive three-dimensional folding of the genome from the bottom up through local action and self-assembly into higher order levels of cell type-specific organization. In this model, no explicit epigenetic memory for cell type-specific chromosome folding is required.
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Affiliation(s)
- Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103 USA
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73
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Lopez-Camacho C, van Wijnen AJ, Lian JB, Stein JL, Stein GS. Core binding factor β (CBFβ) is retained in the midbody during cytokinesis. J Cell Physiol 2014; 229:1466-74. [PMID: 24648201 DOI: 10.1002/jcp.24588] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/18/2014] [Indexed: 01/09/2023]
Abstract
Core Binding Factor β (CBFβ) is complexed with the RUNX family of transcription factors in the nucleus to support activation or repression of genes related to bone (RUNX2), hematopoiesis (RUNX1) and gastrointestinal (RUNX3) development. Furthermore, RUNX proteins contribute to the onset and progression of different types of cancer. Although CBFβ localizes to cytoskeletal architecture, its biological role in the cytoplasmic compartment remains to be established. Additionally, the function and localization of CBFβ during the cell cycle are important questions relevant to its biological role. Here we show that CBFβ dynamically distributes in different stages of cell division and importantly is present during telophase at the midbody, a temporal structure important for successful cytokinesis. A functional role for CBFβ localization at the midbody is supported by striking defects in cytokinesis that include polyploidy and abscission failure following siRNA-mediated downregulation of endogenous CBFβ or overexpression of the inv(16) fusion protein CBFβ-SMMHC. Our results suggest that CBFβ retention in the midbody during cytokinesis reflects a novel function that contributes to epigenetic control.
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Affiliation(s)
- Cesar Lopez-Camacho
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
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74
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Barutcu AR, Tai PWL, Wu H, Gordon JAR, Whitfield TW, Dobson JR, Imbalzano AN, Lian JB, van Wijnen AJ, Stein JL, Stein GS. The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter. Nucleic Acids Res 2014; 42:10360-72. [PMID: 25120271 PMCID: PMC4176362 DOI: 10.1093/nar/gku712] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/04/2014] [Accepted: 07/22/2014] [Indexed: 12/25/2022] Open
Abstract
Three-dimensional organization of chromatin is fundamental for transcriptional regulation. Tissue-specific transcriptional programs are orchestrated by transcription factors and epigenetic regulators. The RUNX2 transcription factor is required for differentiation of precursor cells into mature osteoblasts. Although organization and control of the bone-specific Runx2-P1 promoter have been studied extensively, long-range regulation has not been explored. In this study, we investigated higher-order organization of the Runx2-P1 promoter during osteoblast differentiation. Mining the ENCODE database revealed interactions between Runx2-P1 and Supt3h promoters in several non-mesenchymal human cell lines. Supt3h is a ubiquitously expressed gene located within the first intron of Runx2. These two genes show shared synteny across species from humans to sponges. Chromosome conformation capture analysis in the murine pre-osteoblastic MC3T3-E1 cell line revealed increased contact frequency between Runx2-P1 and Supt3h promoters during differentiation. This increase was accompanied by enhanced DNaseI hypersensitivity along with RUNX2 and CTCF binding at the Supt3h promoter. Furthermore, interplasmid-3C and luciferase reporter assays showed that the Supt3h promoter can modulate Runx2-P1 activity via direct association. Taken together, our data demonstrate physical proximity between Runx2-P1 and Supt3h promoters, consistent with their syntenic nature. Importantly, we identify the Supt3h promoter as a potential regulator of the bone-specific Runx2-P1 promoter.
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Affiliation(s)
- A Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Phillip W L Tai
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Hai Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Jonathan A R Gordon
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Troy W Whitfield
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jason R Dobson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jane B Lian
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - André J van Wijnen
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Janet L Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Gary S Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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75
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Wong MM, Byun JS, Sacta M, Jin Q, Baek S, Gardner K. Promoter-bound p300 complexes facilitate post-mitotic transmission of transcriptional memory. PLoS One 2014; 9:e99989. [PMID: 24945803 PMCID: PMC4063784 DOI: 10.1371/journal.pone.0099989] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 05/21/2014] [Indexed: 11/18/2022] Open
Abstract
A central hallmark of epigenetic inheritance is the parental transmission of changes in patterns of gene expression to progeny without modification of DNA sequence. Although, the trans-generational conveyance of this molecular memory has been traditionally linked to covalent modification of histone and/or DNA, recent studies suggest a role for proteins that persist or remain bound within chromatin to "bookmark" specific loci for enhanced or potentiated responses in daughter cells immediately following cell division. In this report we describe a role for p300 in enabling gene bookmarking by pre-initiation complexes (PICs) containing RNA polymerase II (pol II), Mediator and TBP. Once formed these complexes require p300 to enable reacquisition of protein complex assemblies, chromatin modifications and long range chromatin interactions that facilitate post-mitotic transmission of transcriptional memory of prior environmental stimuli.
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Affiliation(s)
- Madeline M. Wong
- Genetics Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jung S. Byun
- Genetics Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Maria Sacta
- Genetics Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Qihuang Jin
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, United States of America
| | - SongJoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Kevin Gardner
- Genetics Branch, National Cancer Institute, Bethesda, Maryland, United States of America
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76
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Meyer MB, Benkusky NA, Pike JW. The RUNX2 cistrome in osteoblasts: characterization, down-regulation following differentiation, and relationship to gene expression. J Biol Chem 2014; 289:16016-31. [PMID: 24764292 PMCID: PMC4047377 DOI: 10.1074/jbc.m114.552216] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/23/2014] [Indexed: 01/09/2023] Open
Abstract
RUNX2 is a transcription factor that is first expressed in early osteoblast-lineage cells and represents a primary determinant of osteoblastogenesis. While numerous target genes are regulated by RUNX2, little is known of sites on the genome occupied by RUNX2 or of the gene networks that are controlled by these sites. To explore this, we conducted a genome-wide analysis of the RUNX2 cistrome in both pre-osteoblastic MC3T3-E1 cells (POB) and their mature osteoblast progeny (OB), characterized the two cistromes and assessed their relationship to changes in gene expression. We found that although RUNX2 was widely bound to the genome in POB cells, this binding profile was reduced upon differentiation to OBs. Numerous sites were lost upon differentiation, new sites were also gained; many sites remained common to both cell states. Additional features were identified as well including location relative to potential target genes, abundance with respect to single genes, the frequent presence of a consensus TGTGGT RUNX2 binding motif, co-occupancy by C/EBPβ and the presence of a typical epigenetic histone enhancer signature. This signature was changed quantitatively following differentiation. While RUNX2 binding sites were associated extensively with adjacent genes, the distal nature of the majority of these sites prevented assessment of whether they represented direct targets of RUNX2 action. Changes in gene expression, however, revealed an abundance of genes that contained RUNX2 binding sites and were regulated in concert. These studies establish a basis for further analysis of the role of RUNX2 activity and its function during osteoblast lineage maturation.
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Affiliation(s)
- Mark B Meyer
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Nancy A Benkusky
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - J Wesley Pike
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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77
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Tai PWL, Zaidi SK, Wu H, Grandy RA, Montecino MM, van Wijnen AJ, Lian JB, Stein GS, Stein JL. The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. J Cell Physiol 2014; 229:711-27. [PMID: 24242872 PMCID: PMC3996806 DOI: 10.1002/jcp.24508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 12/31/2022]
Abstract
Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology.
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Affiliation(s)
- Phillip W. L. Tai
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Sayyed K. Zaidi
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Hai Wu
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Rodrigo A. Grandy
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Martin M. Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
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78
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Lodhi N, Kossenkov AV, Tulin AV. Bookmarking promoters in mitotic chromatin: poly(ADP-ribose)polymerase-1 as an epigenetic mark. Nucleic Acids Res 2014; 42:7028-38. [PMID: 24861619 PMCID: PMC4066802 DOI: 10.1093/nar/gku415] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. After mitosis, it is thought that bookmarking transcription factors remain at promoters, regulating which genes become active and which remain silent. Herein, we demonstrate that poly(ADP-ribose)polymerase-1 (PARP-1) is a genome-wide epigenetic memory mark in mitotic chromatin, and we further show that the presence of PARP-1 is absolutely crucial for reactivation of transcription after mitosis. Based on these findings, a novel molecular model of epigenetic memory transmission through the cell cycle is proposed.
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Affiliation(s)
- Niraj Lodhi
- Fox Chase Cancer Center, Philadelphia, PA, 19111 USA
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Siriwardana NS, Meyer R, Havasi A, Dominguez I, Panchenko MV. Cell cycle-dependent chromatin shuttling of HBO1-JADE1 histone acetyl transferase (HAT) complex. Cell Cycle 2014; 13:1885-901. [PMID: 24739512 PMCID: PMC4111752 DOI: 10.4161/cc.28759] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
HAT HBO1 interacts with 2 isoforms of JADE1: JADE1S and JADE1L. JADE1 promotes acetylation of nucleosomal histones by HBO1. HBO1–JADE1 complex facilitates cell proliferation by unclear mechanisms. Here we report intracellular chromatin shuttling of HBO1–JADE1 complex during mitosis coupled to phosphorylation of JADE1. In interphase of dividing cells JADE1S was localized to the nucleus and associated with chromatin. As cells approached mitosis, specifically prophase, JADE1S dissociated from chromatin and associated with cytoplasm. JADE1S chromatin re-association began in telophase and paralleled nuclear envelope membrane reassembly. By early G1, JADE1S was re-associated with chromatin and localized to the nucleus. Importantly, cytoplasmic but not chromatin-associated JADE1 protein was phosphorylated. Mass-Spectrometric analysis of JADE1S protein isolated from G2/M-arrested cells identified 6 phosphorylated amino acid residues: S89, T92, S102, S121, S392, and T468, including 3 novel sites. Temporally, JADE1S phosphorylation and dephosphorylation during mitosis correlated with JADE1S chromatin dissociation and recruitment. JADE1S chromatin recruitment was accompanied by the global histone H4 acetylation. Pharmacological inhibitor of Aurora A kinase prevented JADE1S protein band shift and chromatin dissociation, suggesting regulatory function for phosphorylation. In vivo experiments supported our in vitro results. In mouse kidneys, JADE1S transiently accumulated in the cytoplasm of tubular epithelial cells during kidney regeneration. The transient increase in the number of cells with cytoplasmic JADE1S directly correlated with activation of tubular cell proliferation and inversely correlated with the number of cells with nuclear JADE1S staining, supporting biological role of HBO1–JADE1 shuttling during organ regeneration.
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Affiliation(s)
| | - Rosana Meyer
- Department of Pathology; Boston University School of Medicine; Boston, MA USA
| | - Andrea Havasi
- Renal Section; Department of Medicine; Boston Medical Center; Boston, MA USA
| | - Isabel Dominguez
- Hematology-Oncology Section; Department of Medicine; Boston University School of Medicine; Boston, MA USA
| | - Maria V Panchenko
- Department of Pathology; Boston University School of Medicine; Boston, MA USA
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80
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Wu H, Whitfield TW, Gordon JAR, Dobson JR, Tai PWL, van Wijnen AJ, Stein JL, Stein GS, Lian JB. Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis. Genome Biol 2014; 15:R52. [PMID: 24655370 PMCID: PMC4056528 DOI: 10.1186/gb-2014-15-3-r52] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 03/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Osteogenesis is a highly regulated developmental process and continues during the turnover and repair of mature bone. Runx2, the master regulator of osteoblastogenesis, directs a transcriptional program essential for bone formation through genetic and epigenetic mechanisms. While individual Runx2 gene targets have been identified, further insights into the broad spectrum of Runx2 functions required for osteogenesis are needed. RESULTS By performing genome-wide characterization of Runx2 binding at the three major stages of osteoblast differentiation--proliferation, matrix deposition and mineralization--we identify Runx2-dependent regulatory networks driving bone formation. Using chromatin immunoprecipitation followed by high-throughput sequencing over the course of these stages, we identify approximately 80,000 significantly enriched regions of Runx2 binding throughout the mouse genome. These binding events exhibit distinct patterns during osteogenesis, and are associated with proximal promoters and also non-promoter regions: upstream, introns, exons, transcription termination site regions, and intergenic regions. These peaks were partitioned into clusters that are associated with genes in complex biological processes that support bone formation. Using Affymetrix expression profiling of differentiating osteoblasts depleted of Runx2, we identify novel Runx2 targets including Ezh2, a critical epigenetic regulator; Crabp2, a retinoic acid signaling component; Adamts4 and Tnfrsf19, two remodelers of the extracellular matrix. We demonstrate by luciferase assays that these novel biological targets are regulated by Runx2 occupancy at non-promoter regions. CONCLUSIONS Our data establish that Runx2 interactions with chromatin across the genome reveal novel genes, pathways and transcriptional mechanisms that contribute to the regulation of osteoblastogenesis.
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Abstract
In this issue of Genes & Development, Grob and colleagues (pp. 220-230) identify the minimal molecular requirements to assemble a fully functional nucleolus in human cells and demonstrate the importance of the nucleolar transcription factor upstream binding factor (UBF) as a mitotic bookmark at the ribosomal DNA (rDNA).
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Lake RJ, Tsai PF, Choi I, Won KJ, Fan HY. RBPJ, the major transcriptional effector of Notch signaling, remains associated with chromatin throughout mitosis, suggesting a role in mitotic bookmarking. PLoS Genet 2014; 10:e1004204. [PMID: 24603501 PMCID: PMC3945225 DOI: 10.1371/journal.pgen.1004204] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 01/13/2014] [Indexed: 01/07/2023] Open
Abstract
Mechanisms that maintain transcriptional memory through cell division are important to maintain cell identity, and sequence-specific transcription factors that remain associated with mitotic chromatin are emerging as key players in transcriptional memory propagation. Here, we show that the major transcriptional effector of Notch signaling, RBPJ, is retained on mitotic chromatin, and that this mitotic chromatin association is mediated through the direct association of RBPJ with DNA. We further demonstrate that RBPJ binds directly to nucleosomal DNA in vitro, with a preference for sites close to the entry/exit position of the nucleosomal DNA. Genome-wide analysis in the murine embryonal-carcinoma cell line F9 revealed that roughly 60% of the sites occupied by RBPJ in asynchronous cells were also occupied in mitotic cells. Among them, we found that a fraction of RBPJ occupancy sites shifted between interphase and mitosis, suggesting that RBPJ can be retained on mitotic chromatin by sliding on DNA rather than disengaging from chromatin during mitotic chromatin condensation. We propose that RBPJ can function as a mitotic bookmark, marking genes for efficient transcriptional activation or repression upon mitotic exit. Strikingly, we found that sites of RBPJ occupancy were enriched for CTCF-binding motifs in addition to RBPJ-binding motifs, and that RBPJ and CTCF interact. Given that CTCF regulates transcription and bridges long-range chromatin interactions, our results raise the intriguing hypothesis that by collaborating with CTCF, RBPJ may participate in establishing chromatin domains and/or long-range chromatin interactions that could be propagated through cell division to maintain gene expression programs. How does a cell remember what it should be after cell division? One mechanism that is beginning to emerge is the retention of a few key regulatory proteins on the highly condensed mitotic chromatin during cell division. These proteins are called mitotic bookmarks, as they are believed to offer critical information as to how genetic information should be read immediately after mitosis. We have found that a protein called RBPJ, which plays pivotal roles in regulating cell-fate choices, is retained on mitotic chromatin. RBPJ transmits to DNA signals elicited by the Notch pathway: a pathway that conveys information resulting from the communication between two adjacent cells. Unlike many other factors, we found that RBPJ can bind to nucleosomes, which are the basic unit of packaged DNA consisting of DNA wrapped around eight histone proteins. We also found that RBPJ interacts with and binds to DNA sites regulated by the CTCF protein, which plays important roles in regulating long-range DNA interactions. Together, our results suggest that RBPJ can function as a mitotic bookmarking factor, to help maintain genetic programs, higher-order structural information and consequently the memory of cell identity through cell division.
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Affiliation(s)
- Robert J. Lake
- Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Pei-Fang Tsai
- Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Inchan Choi
- Institute for Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kyoung-Jae Won
- Institute for Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (KJW); (HYF)
| | - Hua-Ying Fan
- Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (KJW); (HYF)
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83
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Kim HS, Mukhopadhyay R, Rothbart SB, Silva AC, Vanoosthuyse V, Radovani E, Kislinger T, Roguev A, Ryan CJ, Xu J, Jahari H, Hardwick KG, Greenblatt JF, Krogan NJ, Fillingham JS, Strahl BD, Bouhassira EE, Edelmann W, Keogh MC. Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function. Cell Rep 2014; 6:892-905. [PMID: 24565511 DOI: 10.1016/j.celrep.2014.01.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 10/20/2013] [Accepted: 01/23/2014] [Indexed: 11/26/2022] Open
Abstract
Condensin is a central regulator of mitotic genome structure with mutants showing poorly condensed chromosomes and profound segregation defects. Here, we identify NCT, a complex comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), casein kinase II (CKII), and several TAFs, as a regulator of condensin function. We show that NCT and condensin bind similar genomic regions but only briefly colocalize during the periods of chromosome condensation and decondensation. This pattern of NCT binding at the core centromere, the region of maximal condensin enrichment, tracks the abundance of acetylated histone H4, as regulated by the Hat1-Mis16 acetyltransferase complex and recognized by the first Nrc1 bromodomain. Strikingly, mutants in NCT or Hat1-Mis16 restore the formation of segregation-competent chromosomes in cells containing defective condensin. These results are consistent with a model where NCT targets CKII to chromatin in a cell-cycle-directed manner in order to modulate the activity of condensin during chromosome condensation and decondensation.
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Affiliation(s)
- Hyun-Soo Kim
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10454, USA
| | - Rituparna Mukhopadhyay
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10454, USA
| | - Scott B Rothbart
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, NC 27599, USA
| | - Andrea C Silva
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10454, USA
| | - Vincent Vanoosthuyse
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3QR, Scotland
| | - Ernest Radovani
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | | | - Assen Roguev
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
| | - Colm J Ryan
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA; School of Medicine & Medical Science, University College, Dublin 4, Ireland
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
| | - Harlizawati Jahari
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA; Malaysian Institute of Pharmaceuticals and Nutraceuticals, 11800 USM Penang, Malaysia
| | - Kevin G Hardwick
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3QR, Scotland
| | - Jack F Greenblatt
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jeffrey S Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, NC 27599, USA
| | - Eric E Bouhassira
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10454, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10454, USA
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84
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Abstract
A conserved organizational feature of eukaryotic nuclei is the peripheral heterochromatin compartment, which provides a protected area for epigenetically silent genes and gene-poor DNA. In metazoan cells this compartment is associated with the nuclear lamina, the protein meshwork at the inner edge of the nucleus. Heterochromatin-nuclear lamina interactions promote epigenetic gene silencing, which may drive many normal and diseased biological processes. We recently obtained evidence that a previously unstudied human protein, PRR14, participates in the tethering of heterochromatin to the inner nuclear periphery. PRR14 associates with the nuclear lamina and attaches to heterochromatin through its binding partner, heterochromatin protein 1 (HP1). After disassembly early in mitosis, PRR14 reassembles in two steps, first binding to anaphase chromosomes through HP1, followed by association with the nuclear lamina in telophase. PRR14 may thereby play a role in specifying HP1-bound heterochromatin for reattachment to the nuclear lamina at mitotic exit. Here we review the relevant literature, summarize our initial work, and provide additional comments and findings.
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Affiliation(s)
- Andrey Poleshko
- Fox Chase Cancer Center; Institute for Cancer Research; Philadelphia, PA USA
| | - Richard A Katz
- Fox Chase Cancer Center; Institute for Cancer Research; Philadelphia, PA USA
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85
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Grob A, Colleran C, McStay B. Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division. Genes Dev 2014; 28:220-30. [PMID: 24449107 PMCID: PMC3923965 DOI: 10.1101/gad.234591.113] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/17/2013] [Indexed: 01/22/2023]
Abstract
Human cell nuclei are functionally organized into structurally stable yet dynamic bodies whose cell cycle inheritance is poorly understood. Here, we investigate the biogenesis and propagation of nucleoli, sites of ribosome biogenesis and key regulators of cellular growth. Nucleolar and cell cycles are intimately connected. Nucleoli disappear during mitosis, reforming around prominent uncharacterized chromosomal features, nucleolar organizer regions (NORs). By examining the effects of UBF depletion on both endogenous NORs and synthetic pseudo-NORs, we reveal its essential role in maintaining competency and establishing a bookmark on mitotic NORs. Furthermore, we demonstrate that neo-NORs, UBF-binding site arrays coupled with rDNA transcription units, direct the de novo biogenesis of functional compartmentalized neonucleoli irrespective of their site of chromosomal integration. For the first time, we establish the sequence requirements for nucleolar biogenesis and provide proof that this is a staged process where UBF-dependent mitotic bookmarking precedes function-dependent nucleolar assembly.
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Affiliation(s)
- Alice Grob
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Christine Colleran
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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86
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Collas P, Lund EG, Oldenburg AR. Closing the (nuclear) envelope on the genome: how nuclear lamins interact with promoters and modulate gene expression. Bioessays 2013; 36:75-83. [PMID: 24272858 DOI: 10.1002/bies.201300138] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nuclear envelope shapes the functional organization of the nucleus. Increasing evidence indicates that one of its main components, the nuclear lamina, dynamically interacts with the genome, including the promoter region of specific genes. This seems to occur in a manner that accords developmental significance to these interactions. This essay addresses key issues raised by recent data on the association of nuclear lamins with the genome. We discuss how lamins interact with large chromatin domains and with spatially restricted regions on gene promoters. We address the relationship between these interactions, chromatin modifications and gene expression outcomes. Lamin-genome contacts are redistributed after cell division and during stem cell differentiation, with evidence of lineage specificity. Thus, we also speculate on a developmental role of lamin interactions with specific genes. Finally, we highlight how concepts arising from this recent work lay the foundations of future challenges and investigations.
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Affiliation(s)
- Philippe Collas
- Stem Cell Epigenetics Laboratory, Faculty of Medicine, Institute of Basic Medical Sciences, Norwegian Center for Stem Cell Research, University of Oslo, Oslo, Norway
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87
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He S, Khan DH, Winter S, Seiser C, Davie JR. Dynamic distribution of HDAC1 and HDAC2 during mitosis: association with F-actin. J Cell Physiol 2013; 228:1525-35. [PMID: 23280436 DOI: 10.1002/jcp.24311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 12/10/2012] [Indexed: 11/05/2022]
Abstract
During mitosis, histone deacetylase 2 (HDAC2) becomes highly phosphorylated through the action of CK2, and HDAC1 and 2 are displaced from mitotic chromosomes. HDAC1 and 2 are components of corepressor complexes, which function with lysine acetyltransferases to catalyze dynamic protein acetylation and regulate gene expression. In this study, we show that HDAC1 and 2 associate with F-actin in mitotic cells. Inhibition of Aurora B or protein kinase CK2 did not prevent the displacement of HDAC1 and 2 from mitotic chromosomes in HeLa cells. Further, proteins of the HDAC1 and 2 corepressor complexes and transcription factors recruiting these corepressors to chromatin were dissociated from mitotic chromosomes independent of Aurora B activity. HDAC1 and 2 returned to the nuclei of daughter cells during lamin A/C reassembly and before Sp1, Sp3, and RNA polymerase II. Our results show that HDAC1 and 2 corepressor complexes are removed from the mitotic chromosomes and are available early in the events leading to the re-establishment of the gene expression program in daughter cells.
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Affiliation(s)
- Shihua He
- Manitoba Institute of Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
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88
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Rosenberg M, Fan AX, Lin IJ, Liang SY, Bungert J. Cell-cycle specific association of transcription factors and RNA polymerase ii with the human β-globin gene locus. J Cell Biochem 2013; 114:1997-2006. [PMID: 23519692 DOI: 10.1002/jcb.24542] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 03/05/2013] [Indexed: 12/28/2022]
Abstract
The human β-globin genes are regulated by a locus control region (LCR) and are expressed at extremely high levels in erythroid cells. How transcriptional fidelity of highly expressed genes is regulated and maintained during the cell cycle is not completely understood. Here, we analyzed the association of transcription factor USF, the co-activator CBP, topoisomerase I (Topo I), basal transcription factor TFIIB, and RNA polymerase II (Pol II) with the β-globin gene locus at specific cell-cycle stages. The data demonstrate that while association of Pol II with globin locus associated chromatin decreased in mitotically arrested cells, it remained bound at lower levels at the γ-globin gene promoter. During early S-phase, association of CBP, USF, and Pol II with the globin gene locus decreased. The re-association of CBP and USF2 with the LCR preceded re-association of Pol II, suggesting that these proteins together mediate recruitment of Pol II to the β-globin gene locus during S-phase. Finally, we analyzed the association of Topo I with the globin gene locus during late S-phase. In general, Topo I association correlated with the binding of Pol II. Inhibition of Topo I activity reduced Pol II binding at the LCR and intergenic regions but not at the γ-globin gene promoter. The data demonstrate dynamic associations of transcription factors with the globin gene locus during the cell cycle and support previous results showing that specific components of transcription complexes remain associated with highly transcribed genes during mitosis.
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Affiliation(s)
- Michael Rosenberg
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Alex Xiucheng Fan
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - I-Ju Lin
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Shermi Y Liang
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
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89
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Zaidi SK, Van Wijnen AJ, Lian JB, Stein JL, Stein GS. Targeting deregulated epigenetic control in cancer. J Cell Physiol 2013; 228:2103-8. [PMID: 23589100 DOI: 10.1002/jcp.24387] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 04/02/2013] [Indexed: 12/12/2022]
Abstract
Cancer is a multifaceted disease that involves acquisition of genetic mutations, deletions, and amplifications as well as deregulation of epigenetic mechanisms that fine-tune gene regulation. Key epigenetic mechanisms that include histone modifications, DNA methylation, and non-coding RNA-mediated gene silencing are often deregulated in a variety of cancers. Subnuclear localization of key proteins in the interphase nucleus and bookmarking of genes by lineage commitment factors in mitosis-a new dimension to epigenetic control of fundamental biological processes-is also modified in cancer. In this review, we discuss the various aspects of epigenetic control that are operative in a variety of cancers and their potential for risk assessment, early detection, targeted therapy, and personalized medicine.
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Affiliation(s)
- Sayyed K Zaidi
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
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90
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Yan J, Enge M, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, Taipale J. Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 2013; 154:801-13. [PMID: 23953112 DOI: 10.1016/j.cell.2013.07.034] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/23/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
Abstract
During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered and that the clusters are enriched in binding motifs for several major TF classes. Strikingly, almost all clusters are formed around cohesin, and loss of cohesin decreases both DNA accessibility and binding of TFs to clusters. We show that cohesin remains bound in S phase, holding the nascent sister chromatids together at the TF cluster sites. Furthermore, cohesin remains bound to the cluster sites when TFs are evicted in early M phase. These results suggest that cohesin-binding functions as a cellular memory that promotes re-establishment of TF clusters after DNA replication and chromatin condensation.
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Affiliation(s)
- Jian Yan
- Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 14183, Sweden
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91
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Henriquez B, Bustos FJ, Aguilar R, Becerra A, Simon F, Montecino M, van Zundert B. Ezh1 and Ezh2 differentially regulate PSD-95 gene transcription in developing hippocampal neurons. Mol Cell Neurosci 2013; 57:130-43. [PMID: 23932971 DOI: 10.1016/j.mcn.2013.07.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 07/12/2013] [Accepted: 07/30/2013] [Indexed: 01/04/2023] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) mediates transcriptional silencing by catalyzing histone H3 lysine 27 trimethylation (H3K27me3), but its role in the maturation of postmitotic mammalian neurons remains largely unknown. We report that the PRC2 paralogs Ezh1 and Ezh2 are differentially expressed during hippocampal development. We show that depletion of Ezh2 leads to increased expression of PSD-95, a critical plasticity gene, and that reduced PSD-95 gene transcription is correlated with enrichment of Ezh2 at the PSD-95 gene promoter; however, the H3K27me3 epigenetic mark is not present at the PSD-95 gene promoter, likely due to the antagonizing effects of the H3S28P and H3K27Ac marks and the activity of the H3K27 demethylases JMJD3 and UTX. In contrast, increased PSD-95 gene transcription is accompanied by the presence of Ezh1 and elongation-engaged RNA Polymerase II complexes at the PSD-95 gene promoter, while knock-down of Ezh1 reduces PSD-95 transcription. These results indicate that Ezh1 and Ezh2 have antagonistic roles in regulating PSD-95 transcription.
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Affiliation(s)
- Berta Henriquez
- Center for Biomedical Research, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile; Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile
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92
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Park CS, Rehrauer H, Mansuy IM. Genome-wide analysis of H4K5 acetylation associated with fear memory in mice. BMC Genomics 2013; 14:539. [PMID: 23927422 PMCID: PMC3751108 DOI: 10.1186/1471-2164-14-539] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 08/03/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone acetylation has been implicated in learning and memory in the brain, however, its function at the level of the genome and at individual genetic loci remains poorly investigated. This study examines a key acetylation mark, histone H4 lysine 5 acetylation (H4K5ac), genome-wide and its role in activity-dependent gene transcription in the adult mouse hippocampus following contextual fear conditioning. RESULTS Using ChIP-Seq, we identified 23,235 genes in which H4K5ac correlates with absolute gene expression in the hippocampus. However, in the absence of transcription factor binding sites 150 bp upstream of the transcription start site, genes were associated with higher H4K5ac and expression levels. We further establish H4K5ac as a ubiquitous modification across the genome. Approximately one-third of all genes have above average H4K5ac, of which ~15% are specific to memory formation and ~65% are co-acetylated for H4K12. Although H4K5ac is prevalent across the genome, enrichment of H4K5ac at specific regions in the promoter and coding region are associated with different levels of gene expression. Additionally, unbiased peak calling for genes differentially acetylated for H4K5ac identified 114 unique genes specific to fear memory, over half of which have not previously been associated with memory processes. CONCLUSIONS Our data provide novel insights into potential mechanisms of gene priming and bookmarking by histone acetylation following hippocampal memory activation. Specifically, we propose that hyperacetylation of H4K5 may prime genes for rapid expression following activity. More broadly, this study strengthens the importance of histone posttranslational modifications for the differential regulation of transcriptional programs in cognitive processes.
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Affiliation(s)
- C Sehwan Park
- Department of Health Science and Technology, ETH Zürich, Zürich, Switzerland.
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93
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Lucero CMJ, Vega OA, Osorio MM, Tapia JC, Antonelli M, Stein GS, van Wijnen AJ, Galindo MA. The cancer-related transcription factor Runx2 modulates cell proliferation in human osteosarcoma cell lines. J Cell Physiol 2013; 228:714-23. [PMID: 22949168 DOI: 10.1002/jcp.24218] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 11/09/2022]
Abstract
Runx2 regulates osteogenic differentiation and bone formation, but also suppresses pre-osteoblast proliferation by affecting cell cycle progression in the G(1) phase. The growth suppressive potential of Runx2 is normally inactivated in part by protein destabilization, which permits cell cycle progression beyond the G(1)/S phase transition, and Runx2 is again up-regulated after mitosis. Runx2 expression also correlates with metastasis and poor chemotherapy response in osteosarcoma. Here we show that six human osteosarcoma cell lines (SaOS, MG63, U2OS, HOS, G292, and 143B) have different growth rates, which is consistent with differences in the lengths of the cell cycle. Runx2 protein levels are cell cycle-regulated with respect to the G(1)/S phase transition in U2OS, HOS, G292, and 143B cells. In contrast, Runx2 protein levels are constitutively expressed during the cell cycle in SaOS and MG63 cells. Forced expression of Runx2 suppresses growth in all cell lines indicating that accumulation of Runx2 in excess of its pre-established levels in a given cell type triggers one or more anti-proliferative pathways in osteosarcoma cells. Thus, regulatory mechanisms controlling Runx2 expression in osteosarcoma cells must balance Runx2 protein levels to promote its putative oncogenic functions, while avoiding suppression of bone tumor growth.
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Affiliation(s)
- Claudia M J Lucero
- Millennium Institute on Immunology and Immunotherapy, University of Chile, Santiago, Chile
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94
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Gurudatta BV, Yang J, Van Bortle K, Donlin-Asp PG, Corces VG. Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle. Cell Cycle 2013; 12:1605-15. [PMID: 23624840 DOI: 10.4161/cc.24742] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DREF was first characterized for its role in the regulation of transcription of genes encoding proteins involved in DNA replication and found to interact with sequences similar to the DNA recognition motif of the BEAF-32 insulator protein. Insulators are DNA-protein complexes that mediate intra- and inter-chromosome interactions. Several DNA-binding insulator proteins have been described in Drosophila, including BEAF-32, dCTCF and Su(Hw). Here we find that DREF and BEAF-32 co-localize at the same genomic sites, but their enrichment shows an inverse correlation. Furthermore, DREF co-localizes in the genome with other insulator proteins, suggesting that the function of this protein may require components of Drosophila insulators. This is supported by the finding that mutations in insulator proteins modulate DREF-induced cell proliferation. DREF persists bound to chromatin during mitosis at a subset of sites where it also co-localizes with dCTCF, BEAF-32 and CP190. These sites are highly enriched for sites where Orc2 and Mcm2 are present during interphase and at the borders of topological domains of chromosomes defined by Hi-C. The results suggest that DREF and insulator proteins may help maintain chromosome organization during the cell cycle and mark a subset of genomic sites for the assembly of pre-replication complexes and gene bookmarking during the M/G1 transition.
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Affiliation(s)
- B V Gurudatta
- Department of Biology, Emory University, Atlanta, GA, USA
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95
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Halley-Stott RP, Gurdon JB. Epigenetic memory in the context of nuclear reprogramming and cancer. Brief Funct Genomics 2013; 12:164-73. [PMID: 23585580 PMCID: PMC3662891 DOI: 10.1093/bfgp/elt011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Epigenetic memory represents a natural mechanism whereby the identity of a cell is maintained through successive cell cycles, allowing the specification and maintenance of differentiation during development and in adult cells. Cancer is a loss or reversal of the stable differentiated state of adult cells and may be mediated in part by epigenetic changes. The identity of somatic cells can also be reversed experimentally by nuclear reprogramming. Nuclear reprogramming experiments reveal the mechanisms required to activate embryonic gene expression in adult cells and thus provide insight into the reversal of epigenetic memory. In this article, we will introduce epigenetic memory and the mechanisms by which it may operate. We limit our discussion primarily to the context of nuclear reprogramming and briefly discuss the relevance of memory and reprogramming to cancer biology.
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Affiliation(s)
- Richard P Halley-Stott
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN United Kingdom
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96
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Li H, Sheridan R, Williams T. Analysis of TFAP2A mutations in Branchio-Oculo-Facial Syndrome indicates functional complexity within the AP-2α DNA-binding domain. Hum Mol Genet 2013; 22:3195-206. [PMID: 23578821 DOI: 10.1093/hmg/ddt173] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multiple lines of evidence indicate that the AP-2 transcription factor family has an important regulatory function in human craniofacial development. Notably, mutations in TFAP2A, the gene encoding AP-2α, have been identified in patients with Branchio-Oculo-Facial Syndrome (BOFS). BOFS is an autosomal-dominant trait that commonly presents with facial clefting, eye defects and branchial skin anomalies. Examination of multiple cases has suggested either simple haploinsufficiency or more complex genetic causes for BOFS, especially as the clinical manifestations are variable, with no clear genotype-phenotype correlation. Mutations occur throughout TFAP2A, but mostly within conserved sequences within the DNA contact domain of AP-2α. However, the consequences of the various mutations for AP-2α protein function have not been evaluated. Therefore, it remains unclear if all BOFS mutations result in similar changes to the AP-2α protein or if they each produce specific alterations that underlie the spectrum of phenotypes. Here, we have investigated the molecular consequences of the mutations that localize to the DNA-binding region. We show that although individual mutations have different effects on DNA binding, they all demonstrate significantly reduced transcriptional activities. Moreover, all mutant derivatives have an altered nuclear:cytoplasmic distribution compared with the predominantly nuclear localization of wild-type AP-2α and several can exert a dominant-negative activity on the wild-type AP-2α protein. Overall, our data suggest that the individual TFAP2A BOFS mutations can generate null, hypomorphic or antimorphic alleles and that these differences in activity, combined with a role for AP-2α in epigenetic events, may influence the resultant pathology and the phenotypic variability.
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Affiliation(s)
- Hong Li
- Department of Craniofacial Biology and Cell and Developmental Biology, University of Colorado Denver, Aurora, CO 80045, USA
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97
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98
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Arampatzi P, Gialitakis M, Makatounakis T, Papamatheakis J. Gene-specific factors determine mitotic expression and bookmarking via alternate regulatory elements. Nucleic Acids Res 2013; 41:2202-15. [PMID: 23303784 PMCID: PMC4230186 DOI: 10.1093/nar/gks1365] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcriptional silencing during mitosis is caused by inactivation of critical transcriptional regulators and/or chromatin condensation. Inheritance of gene expression patterns through cell division involves various bookmarking mechanisms. In this report, we have examined the mitotic and post-mitotic expression of the DRA major histocompatibility class II (MHCII) gene in different cell types. During mitosis the constitutively MHCII-expressing B lymphoblastoid cells showed sustained occupancy of the proximal promoter by the cognate enhanceosome and general transcription factors. In contrast, although mitotic epithelial cells were depleted of these proteins irrespectively of their MHCII transcriptional activity, a distal enhancer selectively recruited the PP2A phosphatase via NFY and maintained chromatin accessibility. Based on our data, we propose a novel chromatin anti-condensation role for this element in mitotic bookmarking and timing of post-mitotic transcriptional reactivation.
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Affiliation(s)
- Panagiota Arampatzi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 70013, Greece
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99
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Maze I, Noh KM, Allis CD. Histone regulation in the CNS: basic principles of epigenetic plasticity. Neuropsychopharmacology 2013; 38:3-22. [PMID: 22828751 PMCID: PMC3521967 DOI: 10.1038/npp.2012.124] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/07/2012] [Accepted: 05/08/2012] [Indexed: 12/25/2022]
Abstract
Postmitotic neurons are subject to a vast array of environmental influences that require the nuclear integration of intracellular signaling events to promote a wide variety of neuroplastic states associated with synaptic function, circuit formation, and behavioral memory. Over the last decade, much attention has been paid to the roles of transcription and chromatin regulation in guiding fundamental aspects of neuronal function. A great deal of this work has centered on neurodevelopmental and adulthood plasticity, with increased focus in the areas of neuropharmacology and molecular psychiatry. Here, we attempt to provide a broad overview of chromatin regulation, as it relates to central nervous system (CNS) function, with specific emphasis on the modes of histone posttranslational modifications, chromatin remodeling, and histone variant exchange. Understanding the functions of chromatin in the context of the CNS will aid in the future development of pharmacological therapeutics aimed at alleviating devastating neurological disorders.
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Affiliation(s)
- Ian Maze
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Kyung-Min Noh
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
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100
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Kapinas K, Grandy R, Ghule P, Medina R, Becker K, Pardee A, Zaidi SK, Lian J, Stein J, van Wijnen A, Stein G. The abbreviated pluripotent cell cycle. J Cell Physiol 2013; 228:9-20. [PMID: 22552993 PMCID: PMC3667593 DOI: 10.1002/jcp.24104] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human embryonic stem cells (hESCs) and induced pluripotent stem cells proliferate rapidly and divide symmetrically producing equivalent progeny cells. In contrast, lineage committed cells acquire an extended symmetrical cell cycle. Self-renewal of tissue-specific stem cells is sustained by asymmetric cell division where one progeny cell remains a progenitor while the partner progeny cell exits the cell cycle and differentiates. There are three principal contexts for considering the operation and regulation of the pluripotent cell cycle: temporal, regulatory, and structural. The primary temporal context that the pluripotent self-renewal cell cycle of hESCs is a short G1 period without reducing periods of time allocated to S phase, G2, and mitosis. The rules that govern proliferation in hESCs remain to be comprehensively established. However, several lines of evidence suggest a key role for the naïve transcriptome of hESCs, which is competent to stringently regulate the embryonic stem cell (ESC) cell cycle. This supports the requirements of pluripotent cells to self-propagate while suppressing expression of genes that confer lineage commitment and/or tissue specificity. However, for the first time, we consider unique dimensions to the architectural organization and assembly of regulatory machinery for gene expression in nuclear microenviornments that define parameters of pluripotency. From both fundamental biological and clinical perspectives, understanding control of the abbreviated ESC cycle can provide options to coordinate control of proliferation versus differentiation. Wound healing, tissue engineering, and cell-based therapy to mitigate developmental aberrations illustrate applications that benefit from knowledge of the biology of the pluripotent cell cycle.
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Affiliation(s)
- Kristina Kapinas
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Rodrigo Grandy
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Prachi Ghule
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Ricardo Medina
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Klaus Becker
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Arthur Pardee
- Department of Biological Chemistry and Molecular Pharmacology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Sayyed K. Zaidi
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Jane Lian
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Janet Stein
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Andre van Wijnen
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Gary Stein
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655
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