1
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Yamamoto T, Fujimura A, Wei FY, Shinojima N, Kuroda JI, Mukasa A, Tomizawa K. 2-Methylthio Conversion of N6-Isopentenyladenosine in Mitochondrial tRNAs by CDK5RAP1 Promotes the Maintenance of Glioma-Initiating Cells. iScience 2019; 21:42-56. [PMID: 31654853 PMCID: PMC6820277 DOI: 10.1016/j.isci.2019.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 12/26/2022] Open
Abstract
2-Methylthio-N6-isopentenyl modification of adenosine (ms2i6A) is an evolutionally conserved modification found in mitochondrial (mt)-tRNAs. Cdk5 regulatory subunit-associated protein 1 (CDK5RAP1) specifically converts N6-isopentenyladenosine (i6A) to ms2i6A at position A37 of four mt-DNA-encoded tRNAs, and the modification regulates efficient mitochondrial translation and energy metabolism in mammals. Here, we report that the ms2 conversion mediated by CDK5RAP1 in mt-tRNAs is required to sustain glioma-initiating cell (GIC)-related traits. CDK5RAP1 maintained the self-renewal capacity, undifferentiated state, and tumorigenic potential of GICs. This regulation was not related to the translational control of mt-proteins. CDK5RAP1 abrogated the antitumor effect of i6A by converting i6A to ms2i6A and protected GICs from excessive autophagy triggered by i6A. The elevated activity of CDK5RAP1 contributed to the amelioration of the tumor-suppressive effect of i6A and promoted GIC maintenance. This work demonstrates that CDK5RAP1 is crucial for the detoxification of endogenous i6A and that GICs readily utilize this mechanism for survival. CDK5RAP1 is required to sustain the growth of GICs through ms2 modification of i6A Deficit of CDK5RAP1 inhibits the growth of GIC through i6A accumulation CDK5RAP1 detoxifies i6A by conversion into ms2i6A in the mitochondria of GICs Mitochondria serve as antidotal machinery against i6A in GICs
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Affiliation(s)
- Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Atsushi Fujimura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Neutron Therapy Research Center, Okayama University, Okayama 700-8558, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Naoki Shinojima
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Jun-Ichiro Kuroda
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Neutron Therapy Research Center, Okayama University, Okayama 700-8558, Japan.
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2
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Fritz AJ, Gillis NE, Gerrard DL, Rodriguez PD, Hong D, Rose JT, Ghule PN, Bolf EL, Gordon JA, Tye CE, Boyd JR, Tracy KM, Nickerson JA, van Wijnen AJ, Imbalzano AN, Heath JL, Frietze SE, Zaidi SK, Carr FE, Lian JB, Stein JL, Stein GS. Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer. Genes Chromosomes Cancer 2019; 58:484-499. [PMID: 30873710 DOI: 10.1002/gcc.22731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022] Open
Abstract
Cells establish and sustain structural and functional integrity of the genome to support cellular identity and prevent malignant transformation. In this review, we present a strategic overview of epigenetic regulatory mechanisms including histone modifications and higher order chromatin organization (HCO) that are perturbed in breast cancer onset and progression. Implications for dysfunctions that occur in hormone regulation, cell cycle control, and mitotic bookmarking in breast cancer are considered, with an emphasis on epithelial-to-mesenchymal transition and cancer stem cell activities. The architectural organization of regulatory machinery is addressed within the contexts of translating cancer-compromised genomic organization to advances in breast cancer risk assessment, diagnosis, prognosis, and identification of novel therapeutic targets with high specificity and minimal off target effects.
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Affiliation(s)
- A J Fritz
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - N E Gillis
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - D L Gerrard
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - P D Rodriguez
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - D Hong
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - J T Rose
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - P N Ghule
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - E L Bolf
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J A Gordon
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - C E Tye
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J R Boyd
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - K M Tracy
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J A Nickerson
- Division of Genes and Development of the Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts
| | - A J van Wijnen
- Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic Minnesota, Rochester, Minnesota
| | - A N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - J L Heath
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pediatrics, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - S E Frietze
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - S K Zaidi
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - F E Carr
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J B Lian
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J L Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - G S Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
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3
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Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A, Simon I. Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns. Genome Res 2018; 28:1455-1466. [PMID: 30166406 PMCID: PMC6169886 DOI: 10.1101/gr.230300.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 08/27/2018] [Indexed: 01/23/2023]
Abstract
Mitosis encompasses key molecular changes including chromatin condensation, nuclear envelope breakdown, and reduced transcription levels. Immediately after mitosis, the interphase chromatin structure is reestablished and transcription resumes. The reestablishment of the interphase chromatin is probably achieved by "bookmarking," i.e., the retention of at least partial information during mitosis. To gain a deeper understanding of the contribution of histone modifications to the mitotic bookmarking process, we merged proteomics, immunofluorescence, and ChIP-seq approaches. We focused on key histone modifications and employed HeLa-S3 cells as a model system. Generally, in spite of the general hypoacetylation observed during mitosis, we observed a global concordance between the genomic organization of histone modifications in interphase and mitosis, suggesting that the epigenomic landscape may serve as a component of the mitotic bookmarking process. Next, we investigated the nucleosome that enters nucleosome depleted regions (NDRs) during mitosis. We observed that in ∼60% of the NDRs, the entering nucleosome is distinct from the surrounding highly acetylated nucleosomes and appears to have either low levels of acetylation or high levels of phosphorylation in adjacent residues (since adjacent phosphorylation may interfere with the ability to detect acetylation). Inhibition of histone deacetylases (HDACs) by the small molecule TSA reverts this pattern, suggesting that these nucleosomes are specifically deacetylated during mitosis. Altogether, by merging multiple approaches, our study provides evidence to support a model where histone modifications may play a role in mitotic bookmarking and uncovers new insights into the deposition of nucleosomes during mitosis.
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Affiliation(s)
- Elisheva Javasky
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Inbal Shamir
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Shashi Gandhi
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Shawn Egri
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Oded Sandler
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Noam Kaplan
- Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, 31096, Israel
| | - Jacob D Jaffe
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Alon Goren
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
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4
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Zaidi SK, Fritz AJ, Tracy KM, Gordon JA, Tye CE, Boyd J, Van Wijnen AJ, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS. Nuclear organization mediates cancer-compromised genetic and epigenetic control. Adv Biol Regul 2018; 69:1-10. [PMID: 29759441 PMCID: PMC6102062 DOI: 10.1016/j.jbior.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/13/2018] [Accepted: 05/02/2018] [Indexed: 12/19/2022]
Abstract
Nuclear organization is functionally linked to genetic and epigenetic regulation of gene expression for biological control and is modified in cancer. Nuclear organization supports cell growth and phenotypic properties of normal and cancer cells by facilitating physiologically responsive interactions of chromosomes, genes and regulatory complexes at dynamic three-dimensional microenvironments. We will review nuclear structure/function relationships that include: 1. Epigenetic bookmarking of genes by phenotypic transcription factors to control fidelity and plasticity of gene expression as cells enter and exit mitosis; 2. Contributions of chromatin remodeling to breast cancer nuclear morphology, metabolism and effectiveness of chemotherapy; 3. Relationships between fidelity of nuclear organization and metastasis of breast cancer to bone; 4. Dynamic modifications of higher-order inter- and intra-chromosomal interactions in breast cancer cells; 5. Coordinate control of cell growth and phenotype by tissue-specific transcription factors; 6. Oncofetal epigenetic control by bivalent histone modifications that are functionally related to sustaining the stem cell phenotype; and 7. Noncoding RNA-mediated regulation in the onset and progression of breast cancer. The discovery of components to nuclear organization that are functionally related to cancer and compromise gene expression have the potential for translation to innovative cancer diagnosis and targeted therapy.
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Affiliation(s)
- Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Jonathan A Gordon
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Joseph Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Andre J Van Wijnen
- Departments of Orthopedic Surgery, Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Jeffrey A Nickerson
- Department of Pediatrics, UMass Medical School, Worcester, MA, United States
| | - Antony N Imbalzano
- Graduate Program in Cell Biology and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, United States
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
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5
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Zaidi SK, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS. Mitotic Gene Bookmarking: An Epigenetic Program to Maintain Normal and Cancer Phenotypes. Mol Cancer Res 2018; 16:1617-1624. [PMID: 30002192 DOI: 10.1158/1541-7786.mcr-18-0415] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/24/2018] [Accepted: 06/22/2018] [Indexed: 01/06/2023]
Abstract
Reconfiguration of nuclear structure and function during mitosis presents a significant challenge to resume the next cell cycle in the progeny cells without compromising structural and functional identity of the cells. Equally important is the requirement for cancer cells to retain the transformed phenotype, that is, unrestricted proliferative potential, suppression of cell phenotype, and activation of oncogenic pathways. Mitotic gene bookmarking retention of key regulatory proteins that include sequence-specific transcription factors, chromatin-modifying factors, and components of RNA Pol (RNAP) I and II regulatory machineries at gene loci on mitotic chromosomes plays key roles in coordinate control of cell phenotype, growth, and proliferation postmitotically. There is growing recognition that three distinct protein types, mechanistically, play obligatory roles in mitotic gene bookmarking: (i) Retention of phenotypic transcription factors on mitotic chromosomes is essential to sustain lineage commitment; (ii) Select chromatin modifiers and posttranslational histone modifications/variants retain competency of mitotic chromatin for gene reactivation as cells exit mitosis; and (iii) Functional components of RNAP I and II transcription complexes (e.g., UBF and TBP, respectively) are retained on genes poised for reactivation immediately following mitosis. Importantly, recent findings have identified oncogenes that are associated with target genes on mitotic chromosomes in cancer cells. The current review proposes that mitotic gene bookmarking is an extensively utilized epigenetic mechanism for stringent control of proliferation and identity in normal cells and hypothesizes that bookmarking plays a pivotal role in maintenance of tumor phenotypes, that is, unrestricted proliferation and compromised control of differentiation. Mol Cancer Res; 16(11); 1617-24. ©2018 AACR.
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Affiliation(s)
- Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Jeffrey A Nickerson
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Anthony N Imbalzano
- Graduate Program in Cell Biology and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Centre, University of Vermont, Burlington Vermont.
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6
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Ghule PN, Seward DJ, Fritz AJ, Boyd JR, van Wijnen AJ, Lian JB, Stein JL, Stein GS. Higher order genomic organization and regulatory compartmentalization for cell cycle control at the G1/S-phase transition. J Cell Physiol 2018; 233:6406-6413. [PMID: 29744889 DOI: 10.1002/jcp.26741] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 01/19/2023]
Abstract
Fidelity of histone gene regulation, and ultimately of histone protein biosynthesis, is obligatory for packaging of newly replicated DNA into chromatin. Control of histone gene expression within the 3-dimensional context of nuclear organization is reflected by two well documented observations. DNA replication-dependent histone mRNAs are synthesized at specialized subnuclear domains designated histone locus bodies (HLBs), in response to activation of the growth factor dependent Cyclin E/CDK2/HINFP/NPAT pathway at the G1/S transition in mammalian cells. Complete loss of the histone gene regulatory factors HINFP or NPAT disrupts HLB integrity that is necessary for coordinate control of DNA replication and histone gene transcription. Here we review the molecular histone-related requirements for G1/S-phase progression during the cell cycle. Recently developed experimental strategies, now enable us to explore mechanisms involved in dynamic control of histone gene expression in the context of the temporal (cell cycle) and spatial (HLBs) remodeling of the histone gene loci.
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Affiliation(s)
- Prachi N Ghule
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - David J Seward
- Department of Pathology, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Joseph R Boyd
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Andre J van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, Vermont
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7
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Mitotic Gene Bookmarking: An Epigenetic Mechanism for Coordination of Lineage Commitment, Cell Identity and Cell Growth. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:95-102. [PMID: 28299653 DOI: 10.1007/978-981-10-3233-2_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Epigenetic control of gene expression contributes to dynamic responsiveness of cellular processes that include cell cycle, cell growth and differentiation. Mitotic gene bookmarking, retention of sequence-specific transcription factors at target gene loci, including the RUNX regulatory proteins, provide a novel dimension to epigenetic regulation that sustains cellular identity in progeny cells following cell division. Runx transcription factor retention during mitosis coordinates physiological control of cell growth and differentiation in a broad spectrum of biological conditions, and is associated with compromised gene expression in pathologies that include cancer.
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8
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Luo H, Xi Y, Li W, Li J, Li Y, Dong S, Peng L, Liu Y, Yu W. Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle. Hum Mol Genet 2017; 26:4231-4243. [DOI: 10.1093/hmg/ddx312] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/02/2017] [Indexed: 12/29/2022] Open
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9
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Mazumdar C, Majeti R. The role of mutations in the cohesin complex in acute myeloid leukemia. Int J Hematol 2017; 105:31-36. [PMID: 27796738 PMCID: PMC5516647 DOI: 10.1007/s12185-016-2119-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/20/2016] [Indexed: 11/25/2022]
Abstract
Mutations in the members of the cohesin complex have recently been identified as early events in acute myeloid leukemia (AML) pathogenesis. Studies conducted by our lab and others have shown that cohesin mutations or knockdown of cohesin subunits impair hematopoietic differentiation and enforce stem cell programs in both human and mouse hematopoiesis. Furthermore, studies in both models demonstrated global changes in chromatin accessibility and structure, in particular increased accessibility at binding sites for hematopoietic stem and progenitor cell (HSPC) transcription factors. These results suggest that mutations in the cohesin complex may contribute to leukemogenesis through modulation of HSPC chromatin accessibility. Future studies will be necessary to determine the detailed mechanisms mediating these phenotypes.
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Affiliation(s)
- Claire Mazumdar
- Division of Hematology, Department of Medicine, Cancer Institute, Stanford University School of Medicine, Stanford, USA
- Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lokey Stem Cell Building, 265 Campus Drive, Stanford, CA, 94305, USA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute, Stanford University School of Medicine, Stanford, USA.
- Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lokey Stem Cell Building, 265 Campus Drive, Stanford, CA, 94305, USA.
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10
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Deluz C, Friman ET, Strebinger D, Benke A, Raccaud M, Callegari A, Leleu M, Manley S, Suter DM. A role for mitotic bookmarking of SOX2 in pluripotency and differentiation. Genes Dev 2016; 30:2538-2550. [PMID: 27920086 PMCID: PMC5159668 DOI: 10.1101/gad.289256.116] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/28/2016] [Indexed: 11/24/2022]
Abstract
Mitotic bookmarking transcription factors remain bound to chromosomes during mitosis and were proposed to regulate phenotypic maintenance of stem and progenitor cells at the mitosis-to-G1 (M-G1) transition. However, mitotic bookmarking remains largely unexplored in most stem cell types, and its functional relevance for cell fate decisions remains unclear. Here we screened for mitotic chromosome binding within the pluripotency network of embryonic stem (ES) cells and show that SOX2 and OCT4 remain bound to mitotic chromatin through their respective DNA-binding domains. Dynamic characterization using photobleaching-based methods and single-molecule imaging revealed quantitatively similar specific DNA interactions, but different nonspecific DNA interactions, of SOX2 and OCT4 with mitotic chromatin. Using ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) to assess the genome-wide distribution of SOX2 on mitotic chromatin, we demonstrate the bookmarking activity of SOX2 on a small set of genes. Finally, we investigated the function of SOX2 mitotic bookmarking in cell fate decisions and show that its absence at the M-G1 transition impairs pluripotency maintenance and abrogates its ability to induce neuroectodermal differentiation but does not affect reprogramming efficiency toward induced pluripotent stem cells. Our study demonstrates the mitotic bookmarking property of SOX2 and reveals its functional importance in pluripotency maintenance and ES cell differentiation.
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Affiliation(s)
- Cédric Deluz
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Elias T Friman
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Daniel Strebinger
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Alexander Benke
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland.,Institute of Physics, Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Mahé Raccaud
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Andrea Callegari
- Institute of Physics, Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marion Leleu
- Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Suliana Manley
- Institute of Physics, Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - David M Suter
- UPSUTER, The Institute of Bioengineering (IBI), School of Life Sciences, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
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11
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The loading of condensin in the context of chromatin. Curr Genet 2016; 63:577-589. [PMID: 27909798 DOI: 10.1007/s00294-016-0669-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 11/24/2016] [Accepted: 11/25/2016] [Indexed: 12/23/2022]
Abstract
The packaging of DNA into chromosomes is a ubiquitous process that enables living organisms to structure and transmit their genome accurately through cell divisions. In the three kingdoms of life, the architecture and dynamics of chromosomes rely upon ring-shaped SMC (Structural Maintenance of Chromosomes) condensin complexes. To understand how condensin rings organize chromosomes, it is essential to decipher how they associate with chromatin filaments. Here, we use recent evidence to discuss the role played by nucleosomes and transcription factors in the loading of condensin at transcribed genes. We propose a model whereby cis-acting features nestled in the promoters of active genes synergistically attract condensin rings and promote their association with DNA.
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12
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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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13
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Bengoechea-Alonso MT, Ericsson J. The phosphorylation-dependent regulation of nuclear SREBP1 during mitosis links lipid metabolism and cell growth. Cell Cycle 2016; 15:2753-65. [PMID: 27579997 PMCID: PMC5053579 DOI: 10.1080/15384101.2016.1220456] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/13/2016] [Accepted: 07/31/2016] [Indexed: 01/02/2023] Open
Abstract
The SREBP transcription factors are major regulators of lipid metabolism. Disturbances in lipid metabolism are at the core of several health issues facing modern society, including cardiovascular disease, obesity and diabetes. In addition, the role of lipid metabolism in cancer cell growth is receiving increased attention. Transcriptionally active SREBP molecules are unstable and rapidly degraded in a phosphorylation-dependent manner by Fbw7, a ubiquitin ligase that targets several cell cycle regulatory proteins for degradation. We have previously demonstrated that active SREBP1 is stabilized during mitosis. We have now delineated the mechanisms involved in the stabilization of SREBP1 in mitotic cells. This process is initiated by the phosphorylation of a specific serine residue in nuclear SREBP1 by the mitotic kinase Cdk1. The phosphorylation of this residue creates a docking site for a separate mitotic kinase, Plk1. Plk1 interacts with nuclear SREBP1 in mitotic cells and phosphorylates a number of residues in the C-terminal domain of the protein, including a threonine residue in close proximity of the Fbw7 docking site in SREBP1. The phosphorylation of these residues by Plk1 blocks the interaction between SREBP1 and Fbw7 and attenuates the Fbw7-dependent degradation of nuclear SREBP1 during cell division. Inactivation of SREBP1 results in a mitotic defect, suggesting that SREBP1 could regulate cell division. We propose that the mitotic phosphorylation and stabilization of nuclear SREBP1 during cell division provides a link between lipid metabolism and cell proliferation. Thus, the current study provides additional support for the emerging hypothesis that SREBP-dependent lipid metabolism may be important for cell growth.
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Affiliation(s)
| | - Johan Ericsson
- University College Dublin, School of Medicine and Medical Science, UCD Conway Institute, Dublin, Ireland
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14
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A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer. Cell Res 2016; 26:946-62. [PMID: 27364684 DOI: 10.1038/cr.2016.84] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 12/16/2015] [Accepted: 03/22/2016] [Indexed: 12/16/2022] Open
Abstract
Progression through the cell cycle is largely dependent on waves of periodic gene expression, and the regulatory networks for these transcriptome dynamics have emerged as critical points of vulnerability in various aspects of tumor biology. Through RNA-sequencing of human cells during two continuous cell cycles (>2.3 billion paired reads), we identified over 1 000 mRNAs, non-coding RNAs and pseudogenes with periodic expression. Periodic transcripts are enriched in functions related to DNA metabolism, mitosis, and DNA damage response, indicating these genes likely represent putative cell cycle regulators. Using our set of periodic genes, we developed a new approach termed "mitotic trait" that can classify primary tumors and normal tissues by their transcriptome similarity to different cell cycle stages. By analyzing >4 000 tumor samples in The Cancer Genome Atlas (TCGA) and other expression data sets, we found that mitotic trait significantly correlates with genetic alterations, tumor subtype and, notably, patient survival. We further defined a core set of 67 genes with robust periodic expression in multiple cell types. Proteins encoded by these genes function as major hubs of protein-protein interaction and are mostly required for cell cycle progression. The core genes also have unique chromatin features including increased levels of CTCF/RAD21 binding and H3K36me3. Loss of these features in uterine and kidney cancers is associated with altered expression of the core 67 genes. Our study suggests new chromatin-associated mechanisms for periodic gene regulation and offers a predictor of cancer patient outcomes.
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15
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Varela N, Aranguiz A, Lizama C, Sepulveda H, Antonelli M, Thaler R, Moreno RD, Montecino M, Stein GS, van Wijnen AJ, Galindo M. Mitotic Inheritance of mRNA Facilitates Translational Activation of the Osteogenic-Lineage Commitment Factor Runx2 in Progeny of Osteoblastic Cells. J Cell Physiol 2016; 231:1001-14. [PMID: 26381402 PMCID: PMC5812339 DOI: 10.1002/jcp.25188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 12/24/2022]
Abstract
Epigenetic mechanisms mediate the acquisition of specialized cellular phenotypes during tissue development, maintenance and repair. When phenotype-committed cells transit through mitosis, chromosomal condensation counteracts epigenetic activation of gene expression. Subsequent post-mitotic re-activation of transcription depends on epigenetic DNA and histone modifications, as well as other architecturally bound proteins that "bookmark" the genome. Osteogenic lineage commitment, differentiation and progenitor proliferation require the bone-related runt-related transcription factor Runx2. Here, we characterized a non-genomic mRNA mediated mechanism by which osteoblast precursors retain their phenotype during self-renewal. We show that osteoblasts produce maximal levels of Runx2 mRNA, but not protein, prior to mitotic cell division. Runx2 mRNA partitions symmetrically between daughter cells in a non-chromosomal tubulin-containing compartment. Subsequently, transcription-independent de novo synthesis of Runx2 protein in early G1 phase results in increased functional interactions of Runx2 with a representative osteoblast-specific target gene (osteocalcin/BGLAP2) in chromatin. Somatic transmission of Runx2 mRNAs in osteoblasts and osteosarcoma cells represents a versatile mechanism for translational rather than transcriptional induction of this principal gene regulator to maintain osteoblast phenotype identity after mitosis.
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Affiliation(s)
- Nelson Varela
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Medical Technology, Faculty of Medicine, University of Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, University of Chile, Santiago, Chile
| | - Alejandra Aranguiz
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, University of Chile, Santiago, Chile
| | - Carlos Lizama
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Hugo Sepulveda
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
| | - Marcelo Antonelli
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Roman Thaler
- Departments of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street S.W., MSB 3-69, Rochester, MN 55905
| | - Ricardo D. Moreno
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Martin Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
| | - Gary S. Stein
- Department of Biochemistry, HSRF 326, Vermont Cancer Center for Basic and Translational Research, University of Vermont Medical School, Burlington, VT
| | - Andre J. van Wijnen
- Departments of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street S.W., MSB 3-69, Rochester, MN 55905
| | - Mario Galindo
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, University of Chile, Santiago, Chile
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16
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Davie JR, Xu W, Delcuve GP. Histone H3K4 trimethylation: dynamic interplay with pre-mRNA splicing. Biochem Cell Biol 2016; 94:1-11. [DOI: 10.1139/bcb-2015-0065] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is often stated as a mark of transcriptionally active promoters. However, closer study of the positioning of H3K4me3 shows the mark locating primarily after the first exon at the 5′ splice site and overlapping with a CpG island in mammalian cells. There are several enzyme complexes that are involved in the placement of the H3K4me3 mark, including multiple protein complexes containing SETD1A, SETD1B, and MLL1 enzymes (writers). CXXC1, which is associated with SETD1A and SETD1B, target these enzymes to unmethylated CpG islands. Lysine demethylases (KDM5 family members, erasers) demethylate H3K4me3. The H3K4me3 mark is recognized by several proteins (readers), including lysine acetyltransferase complexes, chromatin remodelers, and RNA bound proteins involved in pre-mRNA splicing. Interestingly, attenuation of H3K4me3 impacts pre-mRNA splicing, and inhibition of pre-mRNA splicing attenuates H3K4me3.
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Affiliation(s)
- James R. Davie
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Wayne Xu
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Genevieve P. Delcuve
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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17
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Survivin and cycline D1 expressions are associated with malignant potential in mucinous ovarian neoplasms. J Mol Histol 2016; 47:145-52. [PMID: 26815661 DOI: 10.1007/s10735-016-9661-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
Abstract
The most prevalent malignant ovarian neoplasms are epithelial ovarian cancers which is the most common cause of death among all gynecologic malignancies and a result of complex interaction of multiple oncogenes and tumor suppressor genes. The aim of this study was to evaluate expression of survivin and cycline D1 biomarkers in mucinous ovarian neoplasms and their correlations with clinicopathological variables in mucinous ovarian cancers. We analyzed pathological specimens of 98 patients with benign (n = 34), borderline (n = 22) and malignant (n = 42) mucinous ovarian neoplasms. Immunohistochemical analysis was performed on formalin-fixed paraffin-embedded specimens. Immunohistochemical analysis revealed that survivin and cyclin D1 expressions were located primarily in the nucleus of ovarian tumor cells and relatively weaker cytoplasmic staining. Survivin expression was significantly higher in malignant tumors (88.1 %) than those found in borderline (18.2 %) and benign tumors (8.8 %) (p < 0.001). Similarly, higher cyclin D1 expression was observed in malignant tumors (100 %) compared to borderline (36.4 %) and benign tumors (5.9 %) (p < 0.001). Expression of all biomarkers analyzed significantly and gradually increased from benign to borderline and borderline to malignant mucinous tumors. In terms of clinicopathological variables, tumor grade, FIGO stage and lymph node methastasis were associated with the expression of both biomarkers. Whereas age exhibited no different correlations in mucinous ovarian cancers. The expressions of survivin and cycline D1 are positively correlated with the malignant potential of mucinous ovarian neoplasms.
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18
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Philip R, Heiler S, Mu W, Büchler MW, Zöller M, Thuma F. Claudin-7 promotes the epithelial-mesenchymal transition in human colorectal cancer. Oncotarget 2015; 6:2046-63. [PMID: 25514462 PMCID: PMC4385835 DOI: 10.18632/oncotarget.2858] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/02/2014] [Indexed: 12/14/2022] Open
Abstract
In colorectal cancer (CoCa) EpCAM is frequently associated with claudin-7. There is evidence that tumor-promoting EpCAM activities are modulated by the association with claudin-7. To support this hypothesis, claudin-7 was knocked-down (kd) in HT29 and SW948 cells. HT29-cld7kd and SW948-cld7kd cells display decreased anchorage-independent growth and the capacity for holoclone-, respectively, sphere-formation is reduced. Tumor growth is delayed and cld7kd cells poorly metastasize. In line with this, migratory and invasive potential of cld7kd clones is strongly impaired, migration being inhibited by anti-CD49c, but not anti-EpCAM, although motility is reduced in EpCAM siRNA-treated cells. This is due to claudin-7 recruiting EpCAM in glycolipid-enriched membrane fractions towards claudin-7-associated TACE and presenilin2, which cleave EpCAM. The cleaved intracellular domain, EpIC, promotes epithelial-mesenchymal transition (EMT)-associated transcription factor expression, which together with fibronectin and vimentin are reduced in claudin-7kd cells. But, uptake of HT29wt and SW948wt exosomes by the claudin-7kd lines sufficed for transcription factor upregulation and for restoring motility. Thus, claudin-7 contributes to motility and invasion and is required for recruiting EpCAM towards TACE/presenilin2. EpIC generation further supports motility by promoting a shift towards EMT. Notably, EMT features of cld7-competent metastatic CoCa cells can be transferred via exosomes to poorly metastatic cells.
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Affiliation(s)
- Rahel Philip
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg
| | - Sarah Heiler
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg
| | - Wei Mu
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg
| | | | - Margot Zöller
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg
| | - Florian Thuma
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg
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19
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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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20
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Martins NMC, Bergmann JH, Shono N, Kimura H, Larionov V, Masumoto H, Earnshaw WC. Epigenetic engineering shows that a human centromere resists silencing mediated by H3K27me3/K9me3. Mol Biol Cell 2015; 27:177-96. [PMID: 26564795 PMCID: PMC4694756 DOI: 10.1091/mbc.e15-08-0605] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/03/2015] [Indexed: 12/14/2022] Open
Abstract
Centromeres are embedded within heterochromatin but are transcriptionally active. Centromeric transcription and the centromere function of a human artificial chromosome resist repression mediated by nucleation of repressive marks H3K27me3 or H3K9me3 via tethering of EZH2 or the SET domain of Suv39h1, respectively. Centromeres are characterized by the centromere-specific H3 variant CENP-A, which is embedded in chromatin with a pattern characteristic of active transcription that is required for centromere identity. It is unclear how centromeres remain transcriptionally active despite being flanked by repressive pericentric heterochromatin. To further understand centrochromatin’s response to repressive signals, we nucleated a Polycomb-like chromatin state within the centromere of a human artificial chromosome (HAC) by tethering the methyltransferase EZH2. This led to deposition of the H3K27me3 mark and PRC1 repressor binding. Surprisingly, this state did not abolish HAC centromere function or transcription, and this apparent resistance was not observed on a noncentromeric locus, where transcription was silenced. Directly tethering the reader/repressor PRC1 bypassed this resistance, inactivating the centromere. We observed analogous responses when tethering the heterochromatin Editor Suv39h1-methyltransferase domain (centromere resistance) or reader HP1α (centromere inactivation), respectively. Our results reveal that the HAC centromere can resist repressive pathways driven by H3K9me3/H3K27me3 and may help to explain how centromeres are able to resist inactivation by flanking heterochromatin.
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Affiliation(s)
- Nuno M C Martins
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Jan H Bergmann
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Nobuaki Shono
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Vladimir Larionov
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Hiroshi Masumoto
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
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21
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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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22
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Dudakovic A, Camilleri ET, Xu F, Riester SM, McGee-Lawrence ME, Bradley EW, Paradise CR, Lewallen EA, Thaler R, Deyle DR, Larson AN, Lewallen DG, Dietz AB, Stein GS, Montecino MA, Westendorf JJ, van Wijnen AJ. Epigenetic Control of Skeletal Development by the Histone Methyltransferase Ezh2. J Biol Chem 2015; 290:27604-17. [PMID: 26424790 DOI: 10.1074/jbc.m115.672345] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 11/06/2022] Open
Abstract
Epigenetic control of gene expression is critical for normal fetal development. However, chromatin-related mechanisms that activate bone-specific programs during osteogenesis have remained underexplored. Therefore, we investigated the expression profiles of a large cohort of epigenetic regulators (>300) during osteogenic differentiation of human mesenchymal cells derived from the stromal vascular fraction of adipose tissue (AMSCs). Molecular analyses establish that the polycomb group protein EZH2 (enhancer of zeste homolog 2) is down-regulated during osteoblastic differentiation of AMSCs. Chemical inhibitor and siRNA knockdown studies show that EZH2, a histone methyltransferase that catalyzes trimethylation of histone 3 lysine 27 (H3K27me3), suppresses osteogenic differentiation. Blocking EZH2 activity promotes osteoblast differentiation and suppresses adipogenic differentiation of AMSCs. High throughput RNA sequence (mRNASeq) analysis reveals that EZH2 inhibition stimulates cell cycle inhibitory proteins and enhances the production of extracellular matrix proteins. Conditional genetic loss of Ezh2 in uncommitted mesenchymal cells (Prrx1-Cre) results in multiple defects in skeletal patterning and bone formation, including shortened forelimbs, craniosynostosis, and clinodactyly. Histological analysis and mRNASeq profiling suggest that these effects are attributable to growth plate abnormalities and premature cranial suture closure because of precocious maturation of osteoblasts. We conclude that the epigenetic activity of EZH2 is required for skeletal patterning and development, but EZH2 expression declines during terminal osteoblast differentiation and matrix production.
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Affiliation(s)
| | | | - Fuhua Xu
- From the Departments of Orthopedic Surgery
| | | | - Meghan E McGee-Lawrence
- the Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, Georgia 30912
| | | | | | | | | | | | | | | | - Allan B Dietz
- the Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905
| | - Gary S Stein
- the Department of Biochemistry, University of Vermont Medical School, Burlington, Vermont 05405, and
| | - Martin A Montecino
- the Centro de Investigaciones Biomedicas and Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias Center for Genome Regulation, Universidad Andres Bello, Santiago 837-0146, Chile
| | | | - Andre J van Wijnen
- From the Departments of Orthopedic Surgery, Biochemistry & Molecular Biology,
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23
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Bernard P, Vanoosthuyse V. Does transcription play a role in creating a condensin binding site? Transcription 2015; 6:12-6. [PMID: 25634470 DOI: 10.1080/21541264.2015.1012980] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The highly conserved condensin complex is essential for the condensation and integrity of chromosomes through cell division. Published data argue that high levels of transcription contribute to specify some condensin-binding sites on chromosomes but the exact role of transcription in this process remains elusive. Here we discuss our recent data addressing the role of transcription in establishing a condensin-binding site.
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Affiliation(s)
- Pascal Bernard
- a CNRS, Université Lyon 01, UMR5239, LBMC; Ecole Normale Supérieure de Lyon , Lyon , France
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24
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Dudakovic A, Camilleri ET, Lewallen EA, McGee-Lawrence ME, Riester SM, Kakar S, Montecino M, Stein GS, Ryoo HM, Dietz AB, Westendorf JJ, van Wijnen AJ. Histone deacetylase inhibition destabilizes the multi-potent state of uncommitted adipose-derived mesenchymal stromal cells. J Cell Physiol 2015; 230:52-62. [PMID: 24912092 DOI: 10.1002/jcp.24680] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 05/20/2014] [Indexed: 12/31/2022]
Abstract
Human adipose-derived mesenchymal stromal cells (AMSCs) grown in platelet lysate are promising agents for therapeutic tissue regeneration. Here, we investigated whether manipulation of epigenetic events by the clinically relevant histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) alters differentiation of AMSCs. The multipotency of AMSCs was validated by their ability to differentiate into osteogenic, chondrogenic, and adipogenic lineages. High-throughput RNA sequencing and RT-qPCR established that human histone deacetylases (HDAC1 to HDAC11, and SIRT1 to SIRT7) are differentially expressed in AMSCs. SAHA induces hyper-acetylation of histone H3 and H4, stimulates protein expression of the HDAC-responsive gene SLC9A3R1/NHERF1 and modulates the AKT/FOXO1 pathway. Biologically, SAHA interferes with osteogenic, chondrogenic and adipogenic lineage commitment of multipotent AMSCs. Mechanistically, SAHA-induced loss of differentiation potential of uncommitted AMSCs correlates with multiple changes in the expression of principal transcription factors that control mesenchymal or pluripotent states. We propose that SAHA destabilizes the multi-potent epigenetic state of uncommitted human AMSCs by hyper-acetylation and perturbation of key transcription factor pathways. Furthermore, AMSCs grown in platelet lysate may provide a useful biological model for screening of new HDAC inhibitors that control the biological fate of human mesenchymal stromal cells.
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Affiliation(s)
- Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
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25
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Gordon JAR, Montecino MA, Aqeilan RI, Stein JL, Stein GS, Lian JB. Epigenetic pathways regulating bone homeostasis: potential targeting for intervention of skeletal disorders. Curr Osteoporos Rep 2014; 12:496-506. [PMID: 25260661 PMCID: PMC4216616 DOI: 10.1007/s11914-014-0240-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation utilizes different mechanisms to convey heritable traits to progeny cells that are independent of DNA sequence, including DNA silencing, post-translational modifications of histone proteins, and the post-transcriptional modulation of RNA transcript levels by non-coding RNAs. Although long non-coding RNAs have recently emerged as important regulators of gene imprinting, their functions during osteogenesis are as yet unexplored. In contrast, microRNAs (miRNAs) are well characterized for their control of osteogenic and osteoclastic pathways; thus, further defining how gene regulatory networks essential for skeleton functions are coordinated and finely tuned through the activities of miRNAs. Roles of miRNAs are constantly expanding as new studies uncover associations with skeletal disorders. The distinct functions of epigenetic regulators and evidence for integrating their activities to control normal bone gene expression and bone disease will be presented. In addition, potential for using "signature miRNAs" to identify, manage, and therapeutically treat osteosarcoma will be discussed in this review.
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Affiliation(s)
- Jonathan A. R. Gordon
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Martin A. Montecino
- Centro de Investigaciones Biomedicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile
| | - Rami I. Aqeilan
- Lautenberg Center for Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, PO Box 12272, Ein Karem Campus, Jerusalem 91120, Israel
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
- Corresponding Author: Jane B. Lian – P: 802-656-4872, F: 802-656-8216,
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The expression of HER-2/neu (c-erbB2), survivin and cycline D1 in serous ovarian neoplasms: their correlation with clinicopathological variables. J Mol Histol 2014; 45:679-87. [DOI: 10.1007/s10735-014-9591-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/29/2014] [Indexed: 11/25/2022]
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Grob A, McStay B. Construction of synthetic nucleoli and what it tells us about propagation of sub-nuclear domains through cell division. Cell Cycle 2014; 13:2501-8. [PMID: 25486191 PMCID: PMC4614152 DOI: 10.4161/15384101.2014.949124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 11/19/2022] Open
Abstract
The cell nucleus is functionally compartmentalized into numerous membraneless and dynamic, yet defined, bodies. The cell cycle inheritance of these nuclear bodies (NBs) is poorly understood at the molecular level. In higher eukaryotes, their propagation is challenged by cell division through an "open" mitosis, where the nuclear envelope disassembles along with most NBs. A deeper understanding of the mechanisms involved can be achieved using the engineering principles of synthetic biology to construct artificial NBs. Successful biogenesis of such synthetic NBs demonstrates knowledge of the basic mechanisms involved. Application of this approach to the nucleolus, a paradigm of nuclear organization, has highlighted a key role for mitotic bookmarking in the cell cycle propagation of NBs.
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Key Words
- 1°, primary
- 2°, secondary
- CBs, Cajal bodies
- CDK, cyclin-dependent kinase
- DFC, dense fibrillar component
- DJ, distal junction
- FCs, fibrillar centers
- GC, granular component
- HLBs, histone locus bodies
- HMG, high mobility group
- IGS, intergenic spacers
- NBs, nuclear bodies
- NORs, nucleolar organizer regions
- Nucleolar Organizer Region (NOR)
- PJ, proximal junction
- PML, promyelocytic leukemia
- PNBs, pre-nucleolar bodies
- TFs, transcription factors
- UBF
- UBF, Upstream binding factor
- XEn, Xenopus enhancer
- cell cycle
- mitotic bookmarking
- neo-NOR
- neonucleoli
- nuclear bodies
- nucleolus
- pol, RNA polymerase
- pre-rRNA, precursor rRNA
- pseudo-NOR
- rDNA, ribosomal genes
- rRNA, ribosomal RNA; RNP, ribonucleoprotein
- synthetic biology
- t-UTPs, transcription U 3 proteins
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Affiliation(s)
- Alice Grob
- Center for Chromosome Biology; School of Natural Sciences; National University of Ireland; Galway, Ireland
| | - Brian McStay
- Center for Chromosome Biology; School of Natural Sciences; National University of Ireland; Galway, Ireland
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