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Budzyński MA, Wong AK, Faghihi A, Teves SS. A dynamic role for transcription factors in restoring transcription through mitosis. Biochem Soc Trans 2024; 52:821-830. [PMID: 38526206 PMCID: PMC11088908 DOI: 10.1042/bst20231022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Mitosis involves intricate steps, such as DNA condensation, nuclear membrane disassembly, and phosphorylation cascades that temporarily halt gene transcription. Despite this disruption, daughter cells remarkably retain the parent cell's gene expression pattern, allowing for efficient transcriptional memory after division. Early studies in mammalian cells suggested that transcription factors (TFs) mark genes for swift reactivation, a phenomenon termed 'mitotic bookmarking', but conflicting data emerged regarding TF presence on mitotic chromosomes. Recent advancements in live-cell imaging and fixation-free genomics challenge the conventional belief in universal formaldehyde fixation, revealing dynamic TF interactions during mitosis. Here, we review recent studies that provide examples of at least four modes of TF-DNA interaction during mitosis and the molecular mechanisms that govern these interactions. Additionally, we explore the impact of these interactions on transcription initiation post-mitosis. Taken together, these recent studies call for a paradigm shift toward a dynamic model of TF behavior during mitosis, underscoring the need for incorporating dynamics in mechanistic models for re-establishing transcription post-mitosis.
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Affiliation(s)
- Marek A. Budzyński
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Alexander K.L. Wong
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Armin Faghihi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Sheila S. Teves
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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2
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Rose JT, Moskovitz E, Boyd JR, Gordon JA, Bouffard NA, Fritz AJ, Illendula A, Bushweller JH, Lian JB, Stein JL, Zaidi SK, Stein GS. Inhibition of the RUNX1-CBFβ transcription factor complex compromises mammary epithelial cell identity: a phenotype potentially stabilized by mitotic gene bookmarking. Oncotarget 2020; 11:2512-2530. [PMID: 32655837 PMCID: PMC7335667 DOI: 10.18632/oncotarget.27637] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
RUNX1 has recently been shown to play an important role in determination of mammary epithelial cell identity. However, mechanisms by which loss of the RUNX1 transcription factor in mammary epithelial cells leads to epithelial-to-mesenchymal transition (EMT) are not known. Here, we report that interaction between RUNX1 and its heterodimeric partner CBFβ is essential for sustaining mammary epithelial cell identity. Disruption of RUNX1-CBFβ interaction, DNA binding, and association with mitotic chromosomes alters cell morphology, global protein synthesis, and phenotype-related gene expression. During interphase, RUNX1 is organized as punctate, predominantly nuclear, foci that are dynamically redistributed during mitosis, with a subset localized to mitotic chromosomes. Genome-wide RUNX1 occupancy profiles for asynchronous, mitotically enriched, and early G1 breast epithelial cells reveal RUNX1 associates with RNA Pol II-transcribed protein coding and long non-coding RNA genes and RNA Pol I-transcribed ribosomal genes critical for mammary epithelial proliferation, growth, and phenotype maintenance. A subset of these genes remains occupied by the protein during the mitosis to G1 transition. Together, these findings establish that the RUNX1-CBFβ complex is required for maintenance of the normal mammary epithelial phenotype and its disruption leads to EMT. Importantly, our results suggest, for the first time, that RUNX1 mitotic bookmarking of a subset of epithelial-related genes may be an important epigenetic mechanism that contributes to stabilization of the mammary epithelial cell identity.
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Affiliation(s)
- Joshua T. Rose
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- These authors contributed equally to this work
| | - Eliana Moskovitz
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- These authors contributed equally to this work
| | - Joseph R. Boyd
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Jonathan A. Gordon
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Nicole A. Bouffard
- Microscopy Imaging Center at the Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Andrew J. Fritz
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Anuradha Illendula
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - John H. Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jane B. Lian
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Janet L. Stein
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Sayyed K. Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Gary S. Stein
- Department of Biochemistry and University of Vermont Cancer Center, Robert Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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3
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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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4
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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: 17] [Impact Index Per Article: 2.8] [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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5
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Shao Z, Yao C, Khodadadi-Jamayran A, Xu W, Townes TM, Crowley MR, Hu K. Reprogramming by De-bookmarking the Somatic Transcriptional Program through Targeting of BET Bromodomains. Cell Rep 2018; 16:3138-3145. [PMID: 27653680 DOI: 10.1016/j.celrep.2016.08.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/19/2016] [Accepted: 08/18/2016] [Indexed: 01/11/2023] Open
Abstract
One critical event in reprogramming to pluripotency is erasure of the somatic transcriptional program of starting cells. Here, we present the proof of principle of a strategy for reprogramming to pluripotency facilitated by small molecules that interfere with the somatic transcriptional memory. We show that mild chemical targeting of the acetyllysine-binding pockets of the BET bromodomains, the transcriptional bookmarking domains, robustly enhances reprogramming. Furthermore, we show that chemical targeting of the transcriptional bookmarking BET bromodomains downregulates or turns off the expression of somatic genes in both naive and reprogramming fibroblasts. Chemical blocking of the BET bromodomains also results in loss of fibroblast morphology early in reprogramming. We therefore experimentally demonstrate that cell fate conversion can be achieved by chemically targeting the transcriptional bookmarking BET bromodomains responsible for transcriptional memory.
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Affiliation(s)
- Zhicheng Shao
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Chunping Yao
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA; Department of Radiation Oncology, Shandong Cancer Hospital, Shandong University, Jinan, Shandong 250117, China
| | - Alireza Khodadadi-Jamayran
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Weihua Xu
- Longyan University, Fujian 364012, China
| | - Tim M Townes
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Michael R Crowley
- Howell and Elizabeth Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Kejin Hu
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA.
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7
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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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8
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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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9
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Arora M, Packard CZ, Banerjee T, Parvin JD. RING1A and BMI1 bookmark active genes via ubiquitination of chromatin-associated proteins. Nucleic Acids Res 2015; 44:2136-44. [PMID: 26578590 PMCID: PMC4797268 DOI: 10.1093/nar/gkv1223] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 10/29/2015] [Indexed: 01/27/2023] Open
Abstract
During mitosis the chromatin undergoes dramatic architectural changes with the halting of the transcriptional processes and evacuation of nearly all transcription associated machinery from genes and promoters. Molecular bookmarking of genes during mitosis is a mechanism of faithfully transmitting cell-specific transcription patterns through cell division. We previously discovered chromatin ubiquitination at active promoters as a potential mitotic bookmark. In this study, we identify the enzymes involved in the deposition of ubiquitin before mitosis. We find that the polycomb complex proteins BMI1 and RING1A regulate the ubiquitination of chromatin associated proteins bound to promoters, and this modification is necessary for the expression of marked genes once the cells enter G1. Depletion of RING1A, and thus inactivation of mitotic bookmarking by ubiquitination, is deleterious to progression through G1, cell survival and proliferation. Though the polycomb complex proteins are thought to primarily regulate gene expression by transcriptional repression, in this study, we discover that these two polycomb proteins regulate the transcription of active genes during the mitosis to G1 transition.
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Affiliation(s)
- Mansi Arora
- Department of Biomedical Informatics, OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Colin Z Packard
- Department of Biomedical Informatics, OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Tapahsama Banerjee
- Department of Biomedical Informatics, OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Jeffrey D Parvin
- Department of Biomedical Informatics, OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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10
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Affiliation(s)
- Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri 64110;
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11
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Bouwman BAM, de Laat W. Getting the genome in shape: the formation of loops, domains and compartments. Genome Biol 2015; 16:154. [PMID: 26257189 PMCID: PMC4536798 DOI: 10.1186/s13059-015-0730-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The hierarchical levels of genome architecture exert transcriptional control by tuning the accessibility and proximity of genes and regulatory elements. Here, we review current insights into the trans-acting factors that enable the genome to flexibly adopt different functionally relevant conformations.
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Affiliation(s)
- Britta A M Bouwman
- Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Wouter de Laat
- Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
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12
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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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13
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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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14
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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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15
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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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16
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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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17
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Cohen-Zinder M, Zinder-Cohen M, Karasik D, Onn I. Structural maintenance of chromosome complexes and bone development: the beginning of a wonderful relationship? BONEKEY REPORTS 2013; 2:388. [PMID: 24422108 DOI: 10.1038/bonekey.2013.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/25/2013] [Indexed: 11/09/2022]
Abstract
Bone development depends on environmental, nutritional and hormonal factors. Yet, an ordered and timed activation of genes and their associated molecular pathways are central for the growth and development of healthy bones. The correct expression of genes depends on both cis- and trans-regulatory elements. Of these, the elusive role of chromatin ultrastructure is just beginning to become appreciated. Changes in the higher-order structure of chromatin are affecting the expression of genes in response to intrinsic and environmental signals. Cohesin and condensin are members of the structural maintenance of chromosome (SMC) family of protein complexes, which mediate higher-order chromatin structure by tethering distinct regions of chromatin either inter- or intra-molecularly. In recent years, SMCs had been identified for their function in the regulation of gene expression and developmental processes, whereas malfunction of cohesin or condensin has an impact on human health. However, little is known about the specific roles of SMC complexes in bone development and their possible effect on bone health. Here, we review studies that suggest an intimate link between SMCs and bone development, as well as a plausible effect, direct or indirect, on the bone health. We describe genetic syndromes associated with SMCs with distinctive bone phenotypes and identify links between SMCs and bone-related molecular pathways. Future studies of the relationship between SMCs and bone development will reveal new understandings of both the cellular and molecular roles of SMC complexes and provide new insights into the growth and developmental processes in the bone.
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Affiliation(s)
| | - Miri Zinder-Cohen
- Faculty of Medicine in the Galilee, Bar-Ilan University , Safed, Israel
| | - David Karasik
- Faculty of Medicine in the Galilee, Bar-Ilan University , Safed, Israel ; Hebrew SeniorLife, Harvard Medical School , Boston, MA, USA
| | - Itay Onn
- Faculty of Medicine in the Galilee, Bar-Ilan University , Safed, Israel
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18
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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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19
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Kadauke S, Blobel GA. Mitotic bookmarking by transcription factors. Epigenetics Chromatin 2013; 6:6. [PMID: 23547918 PMCID: PMC3621617 DOI: 10.1186/1756-8935-6-6] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/11/2013] [Indexed: 11/30/2022] Open
Abstract
Mitosis is accompanied by dramatic changes in chromatin organization and nuclear architecture. Transcription halts globally and most sequence-specific transcription factors and co-factors are ejected from mitotic chromatin. How then does the cell maintain its transcriptional identity throughout the cell division cycle? It has become clear that not all traces of active transcription and gene repression are erased within mitotic chromatin. Many histone modifications are stable or only partially diminished throughout mitosis. In addition, some sequence-specific DNA binding factors have emerged that remain bound to select sites within mitotic chromatin, raising the possibility that they function to transmit regulatory information through the transcriptionally silent mitotic phase, a concept that has been termed “mitotic bookmarking.” Here we review recent approaches to studying potential bookmarking factors with regards to their mitotic partitioning, and summarize emerging ideas concerning the in vivo functions of mitotically bound nuclear factors.
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Affiliation(s)
- Stephan Kadauke
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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20
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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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21
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Vagnarelli P. Chromatin reorganization through mitosis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 90:179-224. [PMID: 23582205 DOI: 10.1016/b978-0-12-410523-2.00006-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome condensation is one of the major chromatin-remodeling events that occur during cell division. The changes in chromatin compaction and higher-order structure organization are essential requisites for ensuring a faithful transmission of the replicated genome to daughter cells. Although the observation of mitotic chromosome condensation has fascinated Scientists for a century, we are still far away from understanding how the process works from a molecular point of view. In this chapter, I will analyze our current understanding of chromatin condensation during mitosis with particular attention to the major molecular players that trigger and maintain this particular chromatin conformation. However, within the chromosome, not all regions of the chromatin are organized in the same manner. I will address separately the structure and functions of particular chromatin domains such as the centromere. Finally, the transition of the chromatin through mitosis represents just an interlude for gene expression between two cell cycles. How the transcriptional information that governs cell linage identity is transmitted from mother to daughter represents a big and interesting question. I will present how cells take care of the aspect ensuring that mitotic chromosome condensation and the block of transcription does not wipe out the cell identity.
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Affiliation(s)
- Paola Vagnarelli
- Heinz Wolff Building, Brunel University, Uxbridge, United Kingdom.
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22
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Fukuoka M, Uehara A, Niki K, Goto S, Kato D, Utsugi T, Ohtsu M, Murakami Y. Identification of preferentially reactivated genes during early G1 phase using nascent mRNA as an index of transcriptional activity. Biochem Biophys Res Commun 2012; 430:1005-10. [PMID: 23261446 DOI: 10.1016/j.bbrc.2012.12.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 12/11/2012] [Indexed: 11/19/2022]
Abstract
During mammalian mitosis, transcription is silenced due to dissociation of transcription factors from DNA and chromosome condensation. At the end of mitosis, transcription is reactivated through chromosome relaxation and reloading of these factors to the DNA. Early G1 genes, which are preferentially reactivated during M/G1 transition, are important for maintenance of cellular function and are known to be strictly regulated. As only few early G1 genes have been identified to date, screening for early G1 genes by genome-wide analysis using nascent mRNA could contribute to the elucidation of the regulatory mechanisms during early G1. Here, we performed a detailed expression analysis for the M/G1 transition of mammalian cells by microarray analysis of nascent mRNA, and identified 298 early G1 genes. Analysis of these genes provides two important insights. Firstly, certain motifs are enriched in the upstream sequences of early G1 genes; from this we could predict candidate cognate transcription factors, including Sp1, which is recruited to the DNA in the early G1 phase. Secondly, we discovered that neighboring genes of early G1 genes were also frequently up-regulated in the G1 phase. Information about these numerous newly identified early G1 genes will likely contribute to an understanding of the regulatory mechanisms of the early G1 genes.
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Affiliation(s)
- Masashi Fukuoka
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
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23
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Kumar S, Tyagi RK. Androgen receptor association with mitotic chromatin - analysis with introduced deletions and disease-inflicting mutations. FEBS J 2012; 279:4598-614. [DOI: 10.1111/febs.12046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 09/24/2012] [Accepted: 10/25/2012] [Indexed: 12/17/2022]
Affiliation(s)
- Sanjay Kumar
- Special Centre for Molecular Medicine; Jawaharlal Nehru University; New Delhi; India
| | - Rakesh K. Tyagi
- Special Centre for Molecular Medicine; Jawaharlal Nehru University; New Delhi; India
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24
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Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, Cheng Y, Hardison RC, Blobel GA. Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Cell 2012; 150:725-37. [PMID: 22901805 DOI: 10.1016/j.cell.2012.06.038] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 03/11/2012] [Accepted: 06/04/2012] [Indexed: 12/21/2022]
Abstract
Tissue-specific transcription patterns are preserved throughout cell divisions to maintain lineage fidelity. We investigated whether transcription factor GATA1 plays a role in transmitting hematopoietic gene expression programs through mitosis when transcription is transiently silenced. Live-cell imaging revealed that a fraction of GATA1 is retained focally within mitotic chromatin. ChIP-seq of highly purified mitotic cells uncovered that key hematopoietic regulatory genes are occupied by GATA1 in mitosis. The GATA1 coregulators FOG1 and TAL1 dissociate from mitotic chromatin, suggesting that GATA1 functions as platform for their postmitotic recruitment. Mitotic GATA1 target genes tend to reactivate more rapidly upon entry into G1 than genes from which GATA1 dissociates. Mitosis-specific destruction of GATA1 delays reactivation selectively of genes that retain GATA1 during mitosis. These studies suggest a requirement of mitotic "bookmarking" by GATA1 for the faithful propagation of cell-type-specific transcription programs through cell division.
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Affiliation(s)
- Stephan Kadauke
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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25
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Similarities between the Epstein-Barr Virus (EBV) Nuclear Protein EBNA1 and the Pioneer Transcription Factor FoxA: Is EBNA1 a "Bookmarking" Oncoprotein that Alters the Host Cell Epigenotype? Pathogens 2012; 1:37-51. [PMID: 25436603 PMCID: PMC4235684 DOI: 10.3390/pathogens1010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 08/21/2012] [Accepted: 09/04/2012] [Indexed: 11/19/2022] Open
Abstract
EBNA1, a nuclear protein expressed in all EBV-associated neoplasms is indispensable for the maintenance of the viral episomes in latently infected cells. EBNA1 may induce genetic alterations by upregulating cellular recombinases, production of reactive oxygen species (ROS) and affecting p53 levels and function. All these changes may contribute to tumorigenesis. In this overview we focus, however, on the epigenetic alterations elicited by EBNA1 by drawing a parallel between EBNA1 and the FoxA family of pioneer transcription factors. Both EBNA1 and FoxA induce local DNA demethylation, nucleosome destabilization and bind to mitotic chromosomes. Local DNA demethylation and nucleosome rearrangement mark active promoters and enhancers. In addition, EBNA1 and FoxA, when associated with mitotic chromatin may “bookmark” active genes and ensure their reactivation in postmitotic cells (epigenetic memory). We speculate that DNA looping induced by EBNA1-EBNA1 interactions may reorganize the cellular genome. Such chromatin loops, sustained in mitotic chromatin similarly to the long-distance interactions mediated by the insulator protein CTCF, may also mediate the epigenetic inheritance of gene expression patterns. We suggest that EBNA1 has the potential to induce patho-epigenetic alterations contributing to tumorigenesis.
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26
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Arora M, Zhang J, Heine GF, Ozer G, Liu HW, Huang K, Parvin JD. Promoters active in interphase are bookmarked during mitosis by ubiquitination. Nucleic Acids Res 2012; 40:10187-202. [PMID: 22941662 PMCID: PMC3488253 DOI: 10.1093/nar/gks820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We analyzed modification of chromatin by ubiquitination in human cells and whether this mark changes through the cell cycle. HeLa cells were synchronized at different stages and regions of the genome with ubiquitinated chromatin were identified by affinity purification coupled with next-generation sequencing. During interphase, ubiquitin marked the chromatin on the transcribed regions of ∼70% of highly active genes and deposition of this mark was sensitive to transcriptional inhibition. Promoters of nearly half of the active genes were highly ubiquitinated specifically during mitosis. The ubiquitination at the coding regions in interphase but not at promoters during mitosis was enriched for ubH2B and dependent on the presence of RNF20. Ubiquitin labeling of both promoters during mitosis and transcribed regions during interphase, correlated with active histone marks H3K4me3 and H3K36me3 but not a repressive histone modification, H3K27me3. The high level of ubiquitination at the promoter chromatin during mitosis was transient and was removed within 2 h after the cells exited mitosis and entered the next cell cycle. These results reveal that the ubiquitination of promoter chromatin during mitosis is a bookmark identifying active genes during chromosomal condensation in mitosis, and we suggest that this process facilitates transcriptional reactivation post-mitosis.
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Affiliation(s)
- Mansi Arora
- Department of Biomedical Informatics and the Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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27
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Ali SA, Dobson JR, Lian JB, Stein JL, van Wijnen AJ, Zaidi SK, Stein GS. A RUNX2-HDAC1 co-repressor complex regulates rRNA gene expression by modulating UBF acetylation. J Cell Sci 2012; 125:2732-9. [PMID: 22393235 DOI: 10.1242/jcs.100909] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The osteogenic and oncogenic transcription factor RUNX2 downregulates the RNA polymerase I (RNA Pol I)-mediated transcription of rRNAs and changes histone modifications associated with the rDNA repeat. However, the mechanisms by which RUNX2 suppresses rRNA transcription are not well understood. RUNX2 cofactors such as histone deacetylases (HDACs) play a key role in chromatin remodeling and regulation of gene transcription. Here, we show that RUNX2 recruits HDAC1 to the rDNA repeats in osseous cells. This recruitment alters the histone modifications associated with active rRNA-encoding genes and causes deacetylation of the protein upstream binding factor (UBF, also known as UBTF). Downregulation of RUNX2 expression reduces the localization of HDAC1 to the nucleolar periphery and also decreases the association between HDAC1 and UBF. Functionally, depletion of HDAC1 relieves the RUNX2-mediated repression of rRNA-encoding genes and concomitantly increases cell proliferation and global protein synthesis in osseous cells. Our findings collectively identify a RUNX2-HDAC1-dependent mechanism for the regulation of rRNA-encoding genes and suggest that there is plasticity to RUNX2-mediated epigenetic control, which is mediated through selective mitotic exclusion of co-regulatory factors.
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Affiliation(s)
- Syed A Ali
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, MA 01655, USA
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28
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Abstract
During mitosis, most transcription ceases. Mitotic gene bookmarking marks genes for reactivation to ensure reestablishment of transcription states and cell-cycle progression. In a recent issue of Nature Cell Biology, Zhao et al. (2011) investigate how gene bookmarking leads to accelerated kinetics of transcriptional reactivation after mitosis.
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Affiliation(s)
- Nicole E Follmer
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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29
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Regulation of primary response genes. Mol Cell 2011; 44:348-60. [PMID: 22055182 DOI: 10.1016/j.molcel.2011.09.014] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/29/2011] [Accepted: 09/22/2011] [Indexed: 12/24/2022]
Abstract
Primary response genes (PRGs) are a set of genes that are induced in response to both cell-extrinsic and cell-intrinsic signals and do not require de novo protein synthesis for their expression. These "first responders" in the waves of transcription of signal-responsive genes play pivotal roles in a wide range of biological responses, including neuronal survival and plasticity, cardiac stress response, innate and adaptive immune responses, glucose metabolism, and oncogeneic transformation. Here we bring together recent advances and our current understanding of the signal-induced transcriptional and epigenetic regulation of PRGs.
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30
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Zhao R, Nakamura T, Fu Y, Lazar Z, Spector DL. Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nat Cell Biol 2011; 13:1295-304. [PMID: 21983563 PMCID: PMC3210065 DOI: 10.1038/ncb2341] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/10/2011] [Indexed: 12/12/2022]
Abstract
Although transmission of the gene expression program from mother to daughter cells has been suggested to be mediated by gene bookmarking, the precise mechanism by which bookmarking mediates post-mitotic transcriptional re-activation has been unclear. Here, we used a real-time gene expression system to quantitatively demonstrate that transcriptional activation of the same genetic locus occurs with a significantly more rapid kinetics in post-mitotic cells versus interphase cells. RNA polymerase II large subunit (Pol II) and bromodomain protein 4 (BRD4) were recruited to the locus in a different sequential order on interphase initiation versus post-mitotic re-activation resulting from the recognition by BRD4 of increased levels of histone H4 Lys 5 acetylation (H4K5ac) on the previously activated locus. BRD4 accelerated the dynamics of messenger RNA synthesis by de-compacting chromatin and hence facilitating transcriptional re-activation. Using a real-time quantitative approach, we identified differences in the kinetics of transcriptional activation between interphase and post-mitotic cells that are mediated by a chromatin-based epigenetic mechanism.
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Affiliation(s)
- Rui Zhao
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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31
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Salbaum JM, Kappen C. Diabetic embryopathy: a role for the epigenome? ACTA ACUST UNITED AC 2011; 91:770-80. [PMID: 21538816 DOI: 10.1002/bdra.20807] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/04/2011] [Accepted: 02/11/2011] [Indexed: 12/28/2022]
Abstract
Embryonic development under adverse conditions, such as maternal diabetes or obesity during pregnancy, constitutes a major risk factor for birth defects, as well as for long-term health consequences and disease susceptibility in the offspring. While contributions from epigenetic changes have been invoked previously to explain the long-term changes in terms of developmental programming, we here review how maternal metabolism may directly affect the embryonic epigenome in relationship to teratogenic processes. We consider four epigenetic modalities--DNA methylation, non-coding RNA, transcription factors, and histone modifications--and their contribution to epigenetic memory, and discuss how epigenomic changes may mediate the altered control of embryonic gene expression brought about by maternal diabetes. In combination, the epigenomic modalities serve to define transcription-permissive domains of the genome, resulting in distinct epigenomic landscapes in different developmental cell types. We evaluate experimental approaches to characterize the epigenome in adverse pregnancy conditions, highlighting the role of next-generation sequencing on the technological side, while emphasizing the necessity to study defined cell populations in terms of biologic impact. Finally, we outline the challenges in moving from findings that correlate epigenomics to developmental phenotypes to scenarios that establish teratogenic causality.
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Affiliation(s)
- J Michael Salbaum
- Pennington Biomedical Research Center, 6400 Perkins Road, Baton Rouge, LA 70808, USA.
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32
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Stein GS, van Wijnen AJ, Imbalzano AN, Montecino M, Zaidi SK, Lian JB, Nickerson JA, Stein JL. Architectural genetic and epigenetic control of regulatory networks: compartmentalizing machinery for transcription and chromatin remodeling in nuclear microenvironments. Crit Rev Eukaryot Gene Expr 2011; 20:149-55. [PMID: 21133844 DOI: 10.1615/critreveukargeneexpr.v20.i2.50] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The regulatory machinery that governs genetic and epigenetic control of gene expression for biological processes and cancer is organized in nuclear microenvironments. Strategic placement of transcription factors at target gene promoters in punctate microenvironments of interphase nuclei supports scaffolding of co- regulatory proteins and the convergence as well as integration of regulatory networks. The organization and localization of regulatory complexes within the nucleus can provide signatures that are linked to regulatory activity. Retention of transcription factors at gene loci in mitotic chromosomes contributes to epigenetic control of cell fate and lineage commitment, as well as to persistence of transformed and tumor phenotypes. Mechanistic understanding of the architectural assembly of regulatory machinery can serve as a basis for treating cancer with high specificity and minimal off-target effects.
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Affiliation(s)
- Gary S Stein
- Department of Cell Biology, University of Massachusetts Medical School and Cancer Center, Worcester, MA 01655, USA.
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33
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Sakurai H, Enoki Y. Novel aspects of heat shock factors: DNA recognition, chromatin modulation and gene expression. FEBS J 2010; 277:4140-9. [PMID: 20945530 DOI: 10.1111/j.1742-4658.2010.07829.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heat shock factor (HSF) is an evolutionarily conserved stress-response regulator that activates the transcription of heat shock protein genes, whose products maintain protein homeostasis under normal physiological conditions, as well as under conditions of stress. The promoter regions of the target genes contain a heat shock element consisting of multiple inverted repeats of the pentanucleotide sequence nGAAn. A single HSF of yeast can bind to heat shock elements that differ in the configuration of the nGAAn units and can regulate the transcription of various genes that function not only in stress resistance, but also in a broad range of biological processes. Mammalian cells have four HSF family members involved in different, but in some cases similar, biological functions, including stress resistance, cell differentiation and development. Mammalian HSF family members exhibit differential specificity for different types of heat shock elements, which, together with cell type-specific expression of HSFs is important in determining the target genes of each HSF. This minireview focuses on the molecular mechanisms of DNA recognition, chromatin modulation and gene expression by yeast and mammalian HSFs.
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Affiliation(s)
- Hiroshi Sakurai
- Department of Clinical Laboratory Science, Kanazawa University Graduate School of Medical Science, Ishikawa, Japan.
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34
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Abstract
Traditional methods for epigenomic analysis provide a static picture of chromatin, which is actually a highly dynamic assemblage. Recent approaches have allowed direct measurements of chromatin dynamics, providing deeper insights into processes such as transcription, DNA replication and epigenetic inheritance.
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Affiliation(s)
- Roger B Deal
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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35
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Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA. H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell 2010; 39:901-11. [PMID: 20864037 PMCID: PMC2947862 DOI: 10.1016/j.molcel.2010.08.026] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 05/26/2010] [Accepted: 07/06/2010] [Indexed: 11/16/2022]
Abstract
Profound chromatin changes occur during mitosis to allow for gene silencing and chromosome segregation followed by reactivation of memorized transcription states in daughter cells. Using genome-wide sequencing, we found H2A.Z-containing +1 nucleosomes of active genes shift upstream to occupy TSSs during mitosis, significantly reducing nucleosome-depleted regions. Single-molecule analysis confirmed nucleosome shifting and demonstrated that mitotic shifting is specific to active genes that are silenced during mitosis and, thus, is not seen on promoters, which are silenced by methylation or mitotically expressed genes. Using the GRP78 promoter as a model, we found H3K4 trimethylation is also maintained while other indicators of active chromatin are lost and expression is decreased. These key changes provide a potential mechanism for rapid silencing and reactivation of genes during the cell cycle.
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Affiliation(s)
- Theresa K. Kelly
- Departments of Urology and Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Tina Branscombe Miranda
- Departments of Urology and Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Gangning Liang
- Departments of Urology and Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Benjamin P. Berman
- USC Epigenome Center, University of Southern California, Los Angeles, CA USA
| | - Joy C. Lin
- Departments of Urology and Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, The Weizmann Institute, Rehovot, Israel
| | - Peter A. Jones
- Departments of Urology and Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
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Chromatin loading of E2F-MLL complex by cancer-associated coregulator ANCCA via reading a specific histone mark. Mol Cell Biol 2010; 30:5260-72. [PMID: 20855524 DOI: 10.1128/mcb.00484-10] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Histone modifications are regarded as the carrier of epigenetic memory through cell divisions. How the marks facilitate cell cycle-dependent gene expression is poorly understood. The evolutionarily conserved AAA ATPase ANCCA (AAA nuclear coregulator cancer-associated protein)/ATAD2 was identified as a direct target of oncogene AIB1/ACTR/SRC-3 and a transcriptional coregulator for estrogen and androgen receptors and is strongly implicated in tumorigenesis. We report here that ANCCA directly interacts with E2F1 to E2F3 and that its N terminus interacts with both the N and C termini of E2F1. ANCCA preferentially associates via its bromodomain with H3 acetylated at lysine 14 (H3K14ac) and is required for key cell cycle gene expression and cancer cell proliferation. ANCCA associates with chromosomes at late mitosis, and its occupancy at E2F targets peaks at the G(1)-to-S transition. Strikingly, ANCCA is required for recruitment of specific E2Fs to their targets and chromatin assembly of the host cell factor 1 (HCF-1)-MLL histone methyltransferase complex. ANCCA depletion results in a marked decrease of the gene activation-linked H3K4me3 mark. Bromodomain mutations disable ANCCA function as an E2F coactivator and its ability to promote cancer cell proliferation, while ANCCA overexpression in tumors correlates with tumor growth. Together, these results suggest that ANCCA acts as a pioneer factor in E2F-dependent gene activation and that a novel mechanism involving ANCCA bromodomain may contribute to cancer cell proliferation.
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37
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Mitotic bookmarking of genes: a novel dimension to epigenetic control. Nat Rev Genet 2010; 11:583-9. [PMID: 20628351 DOI: 10.1038/nrg2827] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Regulatory machinery is focally organized in the interphase nucleus. The information contained in these focal nuclear microenvironments must be inherited during cell division to sustain physiologically responsive gene expression in progeny cells. Recent results suggest that focal mitotic retention of phenotypic transcription factors at promoters together with histone modifications and DNA methylation--a mechanism collectively known as gene bookmarking--is a novel parameter of inherited epigenetic control that sustains cellular identity after mitosis. The epigenetic signatures imposed by bookmarking poise genes for activation or suppression following mitosis. We discuss the implications of phenotypic transcription factor retention on mitotic chromosomes in biological control and disease.
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Transcriptional corepressor TLE1 functions with Runx2 in epigenetic repression of ribosomal RNA genes. Proc Natl Acad Sci U S A 2010; 107:4165-9. [PMID: 20160071 DOI: 10.1073/pnas.1000620107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Epigenetic control of ribosomal RNA (rRNA) gene transcription by cell type-specific regulators, such as the osteogenic transcription factor Runx2, conveys cellular memory of growth and differentiation to progeny cells during mitosis. Here, we examined whether coregulatory proteins contribute to epigenetic functions that are mitotically transmitted by Runx2 in osteoblastic cells. We show that the transcriptional corepressor Transducin Like Enhancer-1 (TLE1) associates with rRNA genes during mitosis and interphase through interaction with Runx2. Mechanistically, depletion of TLE1 relieves Runx2-mediated repression of rRNA genes transcription and selectively increases histone modifications linked to active transcription. Biologically, loss of TLE-dependent rRNA gene repression coincides with increased global protein synthesis and enhanced cell proliferation. Our findings reinforce the epigenetic marking target genes by phenotypic transcription factors in mitosis and demonstrate a requirement for retention of coregulatory factors to sustain physiological control of gene expression during proliferation of lineage committed cells.
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