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Lemma RB, Fuglerud BM, Frampton J, Gabrielsen OS. MYB: A Key Transcription Factor in the Hematopoietic System Subject to Many Levels of Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:3-29. [PMID: 39017837 DOI: 10.1007/978-3-031-62731-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
MYB is a master regulator and pioneer factor highly expressed in hematopoietic progenitor cells (HPCs) where it contributes to the reprogramming processes operating during hematopoietic development. MYB plays a complex role being involved in several lineages of the hematopoietic system. At the molecular level, the MYB gene is subject to intricate regulation at many levels through several enhancer and promoter elements, through transcriptional elongation control, as well as post-transcriptional regulation. The protein is modulated by post-translational modifications (PTMs) such as SUMOylation restricting the expression of its downstream targets. Together with a range of interaction partners, cooperating transcription factors (TFs) and epigenetic regulators, MYB orchestrates a fine-tuned symphony of genes expressed during various stages of haematopoiesis. At the same time, the complex MYB system is vulnerable, being a target for unbalanced control and cancer development.
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Affiliation(s)
- Roza Berhanu Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | | | - Jon Frampton
- Department of Cancer & Genomic Sciences, College of Medicine & Health, University of Birmingham, Edgbaston, Birmingham, UK
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2
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Lountos GT, Cherry S, Tropea JE, Wlodawer A, Miller M. Structural basis for cell type specific DNA binding of C/EBPβ: The case of cell cycle inhibitor p15INK4b promoter. J Struct Biol 2022; 214:107918. [PMID: 36343842 PMCID: PMC9909937 DOI: 10.1016/j.jsb.2022.107918] [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: 07/27/2022] [Revised: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
C/EBPβ is a key regulator of numerous cellular processes, but it can also contribute to tumorigenesis and viral diseases. It binds to specific DNA sequences (C/EBP sites) and interacts with other transcription factors to control expression of multiple eukaryotic genes in a tissue and cell-type dependent manner. A body of evidence has established that cell-type-specific regulatory information is contained in the local DNA sequence of the binding motif. In human epithelial cells, C/EBPβ is an essential cofactor for TGFβ signaling in the case of Smad2/3/4 and FoxO-dependent induction of the cell cycle inhibitor, p15INK4b. In the TGFβ-responsive region 2 of the p15INK4b promoter, the Smad binding site is flanked by a C/EBP site, CTTAA•GAAAG, which differs from the canonical, palindromic ATTGC•GCAAT motif. The X-ray crystal structure of C/EBPβ bound to the p15INK4b promoter fragment shows how GCGC-to-AAGA substitution generates changes in the intermolecular interactions in the protein-DNA interface that enhances C/EBPβ binding specificity, limits possible epigenetic regulation of the promoter, and generates a DNA element with a unique pattern of methyl groups in the major groove. Significantly, CT/GA dinucleotides located at the 5'ends of the double stranded element maintain local narrowing of the DNA minor groove width that is necessary for DNA recognition. Our results suggest that C/EBPβ would accept all forms of modified cytosine in the context of the CpT site. This contrasts with the effect on the consensus motif, where C/EBPβ binding is modestly increased by cytosine methylation, but substantially decreased by hydroxymethylation.
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Affiliation(s)
- George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Scott Cherry
- Protein Purification Core, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Joseph E Tropea
- Protein Purification Core, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Alexander Wlodawer
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201 USA
| | - Maria Miller
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201 USA
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3
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Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics Chromatin 2022; 15:13. [PMID: 35440061 PMCID: PMC9016969 DOI: 10.1186/s13072-022-00444-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression-methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.
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Affiliation(s)
- Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Emily Martinsen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marit Ledsaak
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vessela Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild Eskeland
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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4
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Schmidt TJ, Klempnauer KH. Natural Products with Antitumor Potential Targeting the MYB-C/EBPβ-p300 Transcription Module. Molecules 2022; 27:molecules27072077. [PMID: 35408476 PMCID: PMC9000602 DOI: 10.3390/molecules27072077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022] Open
Abstract
The transcription factor MYB is expressed predominantly in hematopoietic progenitor cells, where it plays an essential role in the development of most lineages of the hematopoietic system. In the myeloid lineage, MYB is known to cooperate with members of the CCAAT box/enhancer binding protein (C/EBP) family of transcription factors. MYB and C/EBPs interact with the co-activator p300 or its paralog CREB-binding protein (CBP), to form a transcriptional module involved in myeloid-specific gene expression. Recent work has demonstrated that MYB is involved in the development of human leukemia, especially in acute T-cell leukemia (T-ALL) and acute myeloid leukemia (AML). Chemical entities that inhibit the transcriptional activity of the MYB-C/EBPβ-p300 transcription module may therefore be of use as potential anti-tumour drugs. In searching for small molecule inhibitors, studies from our group over the last 10 years have identified natural products belonging to different structural classes, including various sesquiterpene lactones, a steroid lactone, quinone methide triterpenes and naphthoquinones that interfere with the activity of this transcriptional module in different ways. This review gives a comprehensive overview on the various classes of inhibitors and the inhibitory mechanisms by which they affect the MYB-C/EBPβ-p300 transcriptional module as a potential anti-tumor target. We also focus on the current knowledge on structure-activity relationships underlying these biological effects and on the potential of these compounds for further development.
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Affiliation(s)
- Thomas J. Schmidt
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Münster, PharmaCampus-Corrensstraße 48, D-48149 Munster, Germany
- Correspondence: (T.J.S.); (K.-H.K.)
| | - Karl-Heinz Klempnauer
- Institute of Biochemistry, University of Münster, Corrensstraße 36, D-48149 Munster, Germany
- Correspondence: (T.J.S.); (K.-H.K.)
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5
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Chen L, Jung HJ, Datta A, Park E, Poll BG, Kikuchi H, Leo KT, Mehta Y, Lewis S, Khundmiri SJ, Khan S, Chou CL, Raghuram V, Yang CR, Knepper MA. Systems Biology of the Vasopressin V2 Receptor: New Tools for Discovery of Molecular Actions of a GPCR. Annu Rev Pharmacol Toxicol 2022; 62:595-616. [PMID: 34579536 PMCID: PMC10676752 DOI: 10.1146/annurev-pharmtox-052120-011012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Systems biology can be defined as the study of a biological process in which all of the relevant components are investigated together in parallel to discover the mechanism. Although the approach is not new, it has come to the forefront as a result of genome sequencing projects completed in the first few years of the current century. It has elements of large-scale data acquisition (chiefly next-generation sequencing-based methods and protein mass spectrometry) and large-scale data analysis (big data integration and Bayesian modeling). Here we discuss these methodologies and show how they can be applied to understand the downstream effects of GPCR signaling, specifically looking at how the neurohypophyseal peptide hormone vasopressin, working through the V2 receptor and PKA activation, regulates the water channel aquaporin-2. The emerging picture provides a detailedframework for understanding the molecular mechanisms involved in water balance disorders, pointing the way to improved treatment of both polyuric disorders and water-retention disorders causing dilutional hyponatremia.
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Affiliation(s)
- Lihe Chen
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Hyun Jun Jung
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Arnab Datta
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
- Yenepoya Research Center, Yenepoya, Mangalore 575018, Karnataka, India
| | - Euijung Park
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Brian G Poll
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Hiroaki Kikuchi
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Kirby T Leo
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Yash Mehta
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Spencer Lewis
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Syed J Khundmiri
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Shaza Khan
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
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6
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AlSudais H, Wiper-Bergeron N. From quiescence to repair: C/EBPβ as a regulator of muscle stem cell function in health and disease. FEBS J 2021; 289:6518-6530. [PMID: 34854237 DOI: 10.1111/febs.16307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/21/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022]
Abstract
CCAAT/Enhancer Binding protein beta (C/EBPβ) is a transcriptional regulator involved in numerous physiological processes. Herein, we describe a role for C/EBPβ as a regulator of skeletal muscle stem cell function. In particular, C/EBPβ is expressed in muscle stem cells in healthy muscle where it inhibits myogenic differentiation. Downregulation of C/EBPβ expression at the protein and transcriptional level allows for differentiation. Persistence of C/EBPβ promotes stem cell self-renewal and C/EBPβ expression is required for mitotic quiescence in this cell population. As a critical regulator of skeletal muscle homeostasis, C/EBPβ expression is stimulated in pathological conditions such as cancer cachexia, which perturbs muscle regeneration and promotes myofiber atrophy in the context of systemic inflammation. C/EBPβ is also an important regulator of cytokine expression and immune response genes, a mechanism by which it can influence muscle stem cell function. In this viewpoint, we describe a role for C/EBPβ in muscle stem cells and propose a functional intersection between C/EBPβ and NF-kB action in the regulation of cancer cachexia.
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Affiliation(s)
- Hamood AlSudais
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Canada.,Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Saudi Arabia
| | - Nadine Wiper-Bergeron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Canada
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7
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Yusenko MV, Trentmann A, Casolari DA, Abdel Ghani L, Lenz M, Horn M, Dörner W, Klempnauer S, Mootz HD, Arteaga MF, Mikesch JH, D'Andrea RJ, Gonda TJ, Müller-Tidow C, Schmidt TJ, Klempnauer KH. C/EBPβ is a MYB- and p300-cooperating pro-leukemogenic factor and promising drug target in acute myeloid leukemia. Oncogene 2021; 40:4746-4758. [PMID: 33958723 PMCID: PMC8298201 DOI: 10.1038/s41388-021-01800-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/29/2021] [Accepted: 04/14/2021] [Indexed: 02/05/2023]
Abstract
Transcription factor MYB has recently emerged as a promising drug target for the treatment of acute myeloid leukemia (AML). Here, we have characterized a group of natural sesquiterpene lactones (STLs), previously shown to suppress MYB activity, for their potential to decrease AML cell proliferation. Unlike what was initially thought, these compounds inhibit MYB indirectly via its cooperation partner C/EBPβ. C/EBPβ-inhibitory STLs affect the expression of a large number of MYB-regulated genes, suggesting that the cooperation of MYB and C/EBPβ broadly shapes the transcriptional program of AML cells. We show that expression of GFI1, a direct MYB target gene, is controlled cooperatively by MYB, C/EBPβ, and co-activator p300, and is down-regulated by C/EBPβ-inhibitory STLs, exemplifying that they target the activity of composite MYB-C/EBPβ-p300 transcriptional modules. Ectopic expression of GFI1, a zinc-finger protein that is required for the maintenance of hematopoietic stem and progenitor cells, partially abrogated STL-induced myelomonocytic differentiation, implicating GFI1 as a relevant target of C/EBPβ-inhibitory STLs. Overall, our data identify C/EBPβ as a pro-leukemogenic factor in AML and suggest that targeting of C/EBPβ may have therapeutic potential against AML.
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MESH Headings
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/drug therapy
- Humans
- CCAAT-Enhancer-Binding Protein-beta/metabolism
- CCAAT-Enhancer-Binding Protein-beta/genetics
- Proto-Oncogene Proteins c-myb/metabolism
- Proto-Oncogene Proteins c-myb/genetics
- Transcription Factors/metabolism
- Transcription Factors/genetics
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/genetics
- Cell Proliferation
- E1A-Associated p300 Protein/metabolism
- E1A-Associated p300 Protein/genetics
- Cell Line, Tumor
- Lactones/pharmacology
- Gene Expression Regulation, Leukemic/drug effects
- Sesquiterpenes/pharmacology
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Affiliation(s)
- Maria V Yusenko
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Amke Trentmann
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Debora A Casolari
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Luca Abdel Ghani
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Mairin Lenz
- Institute for Pharmaceutical Biology and Phytochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Melanie Horn
- Department of Medicine V, Hematology, Oncology, Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Wolfgang Dörner
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | | | - Henning D Mootz
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Maria Francisca Arteaga
- Department of Medicine A, Hematology and Oncology, University Hospital, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Jan-Henrik Mikesch
- Department of Medicine A, Hematology and Oncology, University Hospital, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Richard J D'Andrea
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Thomas J Gonda
- Cancer Research Institute, University of South Australia, Adelaide, SA, Australia
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology, Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas J Schmidt
- Institute for Pharmaceutical Biology and Phytochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
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Vitkov L, Muñoz LE, Knopf J, Schauer C, Oberthaler H, Minnich B, Hannig M, Herrmann M. Connection between Periodontitis-Induced Low-Grade Endotoxemia and Systemic Diseases: Neutrophils as Protagonists and Targets. Int J Mol Sci 2021; 22:4647. [PMID: 33925019 PMCID: PMC8125370 DOI: 10.3390/ijms22094647] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
Periodontitis is considered a promoter of many systemic diseases, but the signaling pathways of this interconnection remain elusive. Recently, it became evident that certain microbial challenges promote a heightened response of myeloid cell populations to subsequent infections either with the same or other pathogens. This phenomenon involves changes in the cell epigenetic and transcription, and is referred to as ''trained immunity''. It acts via modulation of hematopoietic stem and progenitor cells (HSPCs). A main modulation driver is the sustained, persistent low-level transmission of lipopolysaccharide from the periodontal pocket into the peripheral blood. Subsequently, the neutrophil phenotype changes and neutrophils become hyper-responsive and prone to boosted formation of neutrophil extracellular traps (NET). Cytotoxic neutrophil proteases and histones are responsible for ulcer formations on the pocket epithelium, which foster bacteremia and endoxemia. The latter promote systemic low-grade inflammation (SLGI), a precondition for many systemic diseases and some of them, e.g., atherosclerosis, diabetes etc., can be triggered by SLGI alone. Either reverting the polarized neutrophils back to the homeostatic state or attenuation of neutrophil hyper-responsiveness in periodontitis might be an approach to diminish or even to prevent systemic diseases.
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Affiliation(s)
- Ljubomir Vitkov
- Vascular & Exercise Biology Unit, Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (L.V.); (H.O.); (B.M.)
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66424 Homburg, Germany
| | - Luis E. Muñoz
- Department of Internal Medicine 3—Rheumatology and Immunology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany; (L.E.M.); (J.K.); (C.S.); (M.H.)
| | - Jasmin Knopf
- Department of Internal Medicine 3—Rheumatology and Immunology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany; (L.E.M.); (J.K.); (C.S.); (M.H.)
| | - Christine Schauer
- Department of Internal Medicine 3—Rheumatology and Immunology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany; (L.E.M.); (J.K.); (C.S.); (M.H.)
| | - Hannah Oberthaler
- Vascular & Exercise Biology Unit, Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (L.V.); (H.O.); (B.M.)
| | - Bernd Minnich
- Vascular & Exercise Biology Unit, Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria; (L.V.); (H.O.); (B.M.)
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66424 Homburg, Germany
| | - Martin Herrmann
- Department of Internal Medicine 3—Rheumatology and Immunology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany; (L.E.M.); (J.K.); (C.S.); (M.H.)
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9
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Transcriptional Regulation of Inflammasomes. Int J Mol Sci 2020; 21:ijms21218087. [PMID: 33138274 PMCID: PMC7663688 DOI: 10.3390/ijms21218087] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Inflammasomes are multimolecular complexes with potent inflammatory activity. As such, their activity is tightly regulated at the transcriptional and post-transcriptional levels. In this review, we present the transcriptional regulation of inflammasome genes from sensors (e.g., NLRP3) to substrates (e.g., IL-1β). Lineage-determining transcription factors shape inflammasome responses in different cell types with profound consequences on the responsiveness to inflammasome-activating stimuli. Pro-inflammatory signals (sterile or microbial) have a key transcriptional impact on inflammasome genes, which is largely mediated by NF-κB and that translates into higher antimicrobial immune responses. Furthermore, diverse intrinsic (e.g., circadian clock, metabolites) or extrinsic (e.g., xenobiotics) signals are integrated by signal-dependent transcription factors and chromatin structure changes to modulate transcriptionally inflammasome responses. Finally, anti-inflammatory signals (e.g., IL-10) counterbalance inflammasome genes induction to limit deleterious inflammation. Transcriptional regulations thus appear as the first line of inflammasome regulation to raise the defense level in front of stress and infections but also to limit excessive or chronic inflammation.
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10
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Werwein E, Biyanee A, Klempnauer KH. Intramolecular interaction of B-MYB is regulated through Ser-577 phosphorylation. FEBS Lett 2020; 594:4266-4279. [PMID: 32979888 DOI: 10.1002/1873-3468.13940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/11/2020] [Accepted: 09/08/2020] [Indexed: 02/02/2023]
Abstract
The transcription factor B-MYB is an important regulator of cell cycle-related processes that is activated by step-wise phosphorylation of multiple sites by cyclin-dependent kinases (CDKs) and conformational changes induced by the peptidylprolyl cis/trans isomerase Pin1. Here, we show that a conserved amino acid sequence around Ser-577 in the C-terminal part of B-MYB is able to interact with the B-MYB DNA-binding domain. Phosphorylation of Ser-577 disrupts this interaction and is regulated by the interplay of CDKs and the phosphatase CDC14B. Deletion of sequences surrounding Ser-577 hyperactivates the transactivation potential of B-MYB, decreases its proteolytic stability, and causes cell cycle defects. Overall, we show for the first time that B-MYB can undergo an intramolecular interaction that is controlled by the phosphorylation state of Ser-577.
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Affiliation(s)
- Eugen Werwein
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Abhiruchi Biyanee
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
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11
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Wu H, Gu J, Zhou D, Cheng W, Wang Y, Wang Q, Wang X. LINC00160 mediated paclitaxel-And doxorubicin-resistance in breast cancer cells by regulating TFF3 via transcription factor C/EBPβ. J Cell Mol Med 2020; 24:8589-8602. [PMID: 32652877 PMCID: PMC7412707 DOI: 10.1111/jcmm.15487] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 05/07/2020] [Accepted: 05/24/2020] [Indexed: 12/11/2022] Open
Abstract
Chemoresistance represents a major challenge in breast cancer (BC) treatment. This study aimed to probe the roles of LINC00160 in paclitaxel‐ and doxorubicin‐resistant BC cells. Three pairs of BC and adjacent normal tissue were used for lncRNA microarray analysis. Paclitaxel‐resistant MCF‐7 (MCF‐7/Tax) and doxorubicin‐resistant BT474 (BT474/Dox) cells were generated by exposure of parental drug‐sensitive MCF‐7 or BT474 cells to gradient concentrations of drugs. Correlation between LINC00160 expression and clinical response to paclitaxel in BC patients was examined. Short interfering RNAs specifically targeting LINC00160 or TFF3 were designed to construct LINC00160‐ and TFF3‐depleted BC cells to discuss their effects on biological episodes of MCF‐7/Tax and BT474/Dox cells. Interactions among LINC00160, transcription factor C/EBPβ and TFF3 were identified. MCF‐7/Tax and BT474/Dox cells stable silencing of LINC00160 were transplanted into nude mice. Consequently, up‐regulated LINC00160 led to poor clinical response to paclitaxel in BC patients. LINC00160 knockdown reduced drug resistance in MCF‐7/Tax and BT474/Dox cells and reduced cell migration and invasion. LINC00160 recruited C/EBPβ into the promoter region of TFF3 and increased TFF3 expression. LINC00160‐depleted MCF‐7/Tax and BT474/Dox cells showed decreased tumour growth rates in nude mice. Overall, we identified a novel mechanism of LINC00160‐mediated chemoresistance via the C/EBPβ/TFF3 axis, highlighting the potential of LINC00160 for treating BC with chemoresistance.
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Affiliation(s)
- Huaiguo Wu
- Center for Precision Medicine, Anhui No.2 Provincial People's Hospital, Hefei, China
| | - Juan Gu
- Department of Medical Laboratory Science, The Fifth People's Hospital of Wuxi, Nanjing Medical University, Wuxi, China.,Department of Pathology, The Fifth People's Hospital of Wuxi, The Medical School of Jiangnan University, Wuxi, China
| | - Daoping Zhou
- Center for Precision Medicine, Anhui No.2 Provincial People's Hospital, Hefei, China.,Department of Medical Laboratory Science, The Fifth People's Hospital of Wuxi, Nanjing Medical University, Wuxi, China
| | - Wei Cheng
- Center for Precision Medicine, Anhui No.2 Provincial People's Hospital, Hefei, China
| | - Yueping Wang
- Center for Precision Medicine, Anhui No.2 Provincial People's Hospital, Hefei, China.,Department of Medical Laboratory Science, The Fifth People's Hospital of Wuxi, Nanjing Medical University, Wuxi, China.,Department of Biology, College of Arts & Science, Massachusetts University, Boston, MA, USA
| | - Qingping Wang
- Center for Precision Medicine, Anhui No.2 Provincial People's Hospital, Hefei, China.,Department of Medical Laboratory Science, The Fifth People's Hospital of Wuxi, Nanjing Medical University, Wuxi, China
| | - Xuedong Wang
- Center for Precision Medicine, Anhui No.2 Provincial People's Hospital, Hefei, China.,Department of Medical Laboratory Science, The Fifth People's Hospital of Wuxi, Nanjing Medical University, Wuxi, China
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12
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Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T. MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. Nucleic Acids Res 2020; 47:D145-D154. [PMID: 30380113 PMCID: PMC6323897 DOI: 10.1093/nar/gky1005] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/10/2018] [Indexed: 12/17/2022] Open
Abstract
Several recent studies have portrayed DNA methylation as a new player in the recruitment of transcription factors (TF) within chromatin, highlighting a need to connect TF binding sites (TFBS) with their respective DNA methylation profiles. However, current TFBS databases are restricted to DNA binding motif sequences. Here, we present MethMotif, a two-dimensional TFBS database that records TFBS position weight matrices along with cell type specific CpG methylation information computed from a combination of ChIP-seq and whole genome bisulfite sequencing datasets. Integrating TFBS motifs with TFBS DNA methylation better portrays the features of DNA loci recognised by TFs. In particular, we found that DNA methylation patterns within TFBS can be cell specific (e.g. MAFF). Furthermore, for a given TF, different DNA methylation profiles are associated with different DNA binding motifs (e.g. REST). To date, MethMotif database records over 500 TFBSs computed from over 2000 ChIP-seq datasets in 11 different cell types. MethMotif portal is accessible through an open source web interface (https://bioinfo-csi.nus.edu.sg/methmotif) that allows users to intuitively explore the entire dataset and perform both single, and batch queries.
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Affiliation(s)
- Quy Xiao Xuan Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Stephanie Sian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Denis Thieffry
- Computational Systems Biology Team, Institut de Biologie de l'École Normale Supérieure (IBENS), INSERM, École Normale Supérieure, PSL Research University, Paris, France
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
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13
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de Laval B, Maurizio J, Kandalla PK, Brisou G, Simonnet L, Huber C, Gimenez G, Matcovitch-Natan O, Reinhardt S, David E, Mildner A, Leutz A, Nadel B, Bordi C, Amit I, Sarrazin S, Sieweke MH. C/EBPβ-Dependent Epigenetic Memory Induces Trained Immunity in Hematopoietic Stem Cells. Cell Stem Cell 2020; 26:657-674.e8. [PMID: 32169166 DOI: 10.1016/j.stem.2020.01.017] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/23/2019] [Accepted: 01/23/2020] [Indexed: 02/08/2023]
Abstract
Hematopoietic stem cells (HSCs) maintain life-long production of immune cells and can directly respond to infection, but sustained effects on the immune response remain unclear. We show that acute immune stimulation with lipopolysaccharide (LPS) induced only transient changes in HSC abundance, composition, progeny, and gene expression, but persistent alterations in accessibility of specific myeloid lineage enhancers occurred, which increased responsiveness of associated immune genes to secondary stimulation. Functionally, this was associated with increased myelopoiesis of pre-exposed HSCs and improved innate immunity against the gram-negative bacterium P. aeruginosa. The accessible myeloid enhancers were enriched for C/EBPβ targets, and C/EBPβ deletion erased the long-term inscription of LPS-induced epigenetic marks and gene expression. Thus, short-term immune signaling can induce C/EBPβ-dependent chromatin accessibility, resulting in HSC-trained immunity, during secondary infection. This establishes a mechanism for how infection history can be epigenetically inscribed in HSCs as an integral memory function of innate immunity.
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Affiliation(s)
| | - Julien Maurizio
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France; Inovarion, 75005 Paris, France
| | - Prashanth K Kandalla
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany
| | - Gabriel Brisou
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France
| | - Louise Simonnet
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France
| | - Caroline Huber
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France
| | - Gregory Gimenez
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France; Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, Germany
| | | | - Susanne Reinhardt
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alexander Mildner
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, Germany
| | - Achim Leutz
- Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany; Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, Germany
| | - Bertrand Nadel
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France
| | - Christophe Bordi
- Institut de Microbiologie de la Méditerranée, CNRS, 13009 Marseille, France
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sandrine Sarrazin
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France.
| | - Michael H Sieweke
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), 13125 Berlin, Germany.
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14
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Abstract
Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. The degree to which the arrangement of motif sites within regulatory elements determines their function remains unclear. Here, we show that the positional distribution of TF motif sites within nucleosome-depleted regions of DNA fall into six distinct classes. These patterns are highly consistent across cell types and bring together factors that have similar functional and binding properties. Furthermore, the position of motif sites appears to be related to their known functions. Our results suggest that TFs play distinct roles in forming a functional enhancer, facilitated by their position within a regulatory sequence. Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known about where within these regions specific TFs tend to be found. Here, we characterize the positional bias of inferred binding sites for 103 TFs within ∼500,000 NDRs across 47 cell types. We find that distinct classes of TFs display different binding preferences: Some tend to have binding sites toward the edges, some toward the center, and some at other positions within the NDR. These patterns are highly consistent across cell types, suggesting that they may reflect TF-specific intrinsic structural or functional characteristics. In particular, TF classes with binding sites at NDR edges are enriched for those known to interact with histones and chromatin remodelers, whereas TFs with central enrichment interact with other TFs and cofactors such as p300. Our results suggest distinct regiospecific binding patterns and functions of TF classes within enhancers.
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15
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Fuglerud BM, Ledsaak M, Rogne M, Eskeland R, Gabrielsen OS. The pioneer factor activity of c-Myb involves recruitment of p300 and induction of histone acetylation followed by acetylation-induced chromatin dissociation. Epigenetics Chromatin 2018; 11:35. [PMID: 29954426 PMCID: PMC6022509 DOI: 10.1186/s13072-018-0208-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background The concept of pioneer transcription factors is emerging as an essential part of the epigenetic regulation, taking place during cell development and differentiation. However, the precise molecular mechanism underlying pioneer factor activity remains poorly understood. We recently reported that the transcription factor c-Myb acts as a pioneer factor in haematopoiesis, and a point mutation in its DNA binding domain, D152V, is able to abrogate this function. Results Here, we show that specific histone modifications, including H3K27ac, prevent binding of c-Myb to histone tails, representing a novel effect of histone modifications, namely restricting binding of a pioneer factor to chromatin. Furthermore, we have taken advantage of the pioneer-defect D152V mutant to investigate mechanisms of c-Myb’s pioneer factor activity. We show that c-Myb-dependent transcriptional activation of a gene in inaccessible chromatin relies on c-Myb binding to histones, as well as on c-Myb interacting with the histone acetyltransferase p300. ChIP assays show that both wild type and the D152V mutant of c-Myb bind to a selected target gene at its promoter and enhancer, but only wild-type c-Myb causes opening and activation of the locus. Enhancement of histone acetylation restores activation of the same gene in the absence of c-Myb, suggesting that facilitating histone acetylation is a crucial part of the pioneer factor function of c-Myb. Conclusions We suggest a pioneer factor model in which c-Myb binds to regions of closed chromatin and then recruits histone acetyltransferases. By binding to histones, c-Myb facilitates histone acetylation, acting as a cofactor for p300 at c-Myb bound sites. The resulting H3K27ac leads to chromatin opening and detachment of c-Myb from the acetylated chromatin. We propose that the latter phenomenon, acetylation-induced chromatin dissociation, represents a mechanism for controlling the dynamics of pioneer factor binding to chromatin. Electronic supplementary material The online version of this article (10.1186/s13072-018-0208-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bettina M Fuglerud
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Marit Ledsaak
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Marie Rogne
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway
| | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, 0379, Norway
| | - Odd S Gabrielsen
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Blindern, Oslo, Norway.
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16
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Tamura I, Jozaki K, Sato S, Shirafuta Y, Shinagawa M, Maekawa R, Taketani T, Asada H, Tamura H, Sugino N. The distal upstream region of insulin-like growth factor-binding protein-1 enhances its expression in endometrial stromal cells during decidualization. J Biol Chem 2018; 293:5270-5280. [PMID: 29453285 DOI: 10.1074/jbc.ra117.000234] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/06/2018] [Indexed: 11/06/2022] Open
Abstract
We have previously shown that decidualization of human endometrial stromal cells (ESCs) causes a genome-wide increase in the levels of acetylation of histone-H3 Lys-27 (H3K27ac). We also reported that the distal gene regions, more than 3 kb up- or downstream of gene transcription start sites have increased H3K27ac levels. Insulin-like growth factor-binding protein-1 (IGFBP-1) is a specific decidualization marker and has increased H3K27ac levels in its distal upstream region (-4701 to -7501 bp). Here, using a luciferase reporter gene construct containing this IGFBP-1 upstream region, we tested the hypothesis that it is an IGFBP-1 enhancer. To induce decidualization, we incubated ESCs with cAMP and found that cAMP increased luciferase expression, indicating that decidualization increased the transcriptional activity from the IGFBP-1 upstream region. Furthermore, CRISPR/Cas9-mediated deletion of this region in HepG2 cells significantly reduced IGFBP-1 expression, confirming its role as an IGFBP-1 enhancer. A ChIP assay revealed that cAMP increased the recruitment of the transcriptional regulators CCAAT enhancer-binding protein β (C/EBPβ), forkhead box O1 (FOXO1), and p300 to the IGFBP-1 enhancer in ESCs. Of note, C/EBPβ knockdown inhibited the stimulatory effects of cAMP on the levels of H3K27ac, chromatin opening, and p300 recruitment at the IGFBP-1 enhancer. These results indicate that the region -4701 to -7501 bp upstream of IGFBP-1 functions as an enhancer for IGFBP-1 expression in ESCs undergoing decidualization, that C/EBPβ and FOXO1 bind to the enhancer region to up-regulate IGFBP-1 expression, and that C/EBPβ induces H3K27ac by recruiting p300 to the IGFBP-1 enhancer.
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Affiliation(s)
- Isao Tamura
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Kosuke Jozaki
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Shun Sato
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Yuichiro Shirafuta
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Masahiro Shinagawa
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Ryo Maekawa
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Toshiaki Taketani
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Hiromi Asada
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Hiroshi Tamura
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
| | - Norihiro Sugino
- From the Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Minamikogushi 1-1-1, Ube 755-8505, Japan
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17
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Coulibaly A, Haas A, Steinmann S, Jakobs A, Schmidt TJ, Klempnauer KH. The natural anti-tumor compound Celastrol targets a Myb-C/EBPβ-p300 transcriptional module implicated in myeloid gene expression. PLoS One 2018; 13:e0190934. [PMID: 29394256 PMCID: PMC5796697 DOI: 10.1371/journal.pone.0190934] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022] Open
Abstract
Myb is a key regulator of hematopoietic progenitor cell proliferation and differentiation and has emerged as a potential target for the treatment of acute leukemia. Using a myeloid cell line with a stably integrated Myb-inducible reporter gene as a screening tool we have previously identified Celastrol, a natural compound with anti-tumor activity, as a potent Myb inhibitor that disrupts the interaction of Myb with the co-activator p300. We showed that Celastrol inhibits the proliferation of acute myeloid leukemia (AML) cells and prolongs the survival of mice in an in vivo model of AML, demonstrating that targeting Myb with a small-molecule inhibitor is feasible and might have potential as a therapeutic approach against AML. Recently we became aware that the reporter system used for Myb inhibitor screening also responds to inhibition of C/EBPβ, a transcription factor known to cooperate with Myb in myeloid cells. By re-investigating the inhibitory potential of Celastrol we have found that Celastrol also strongly inhibits the activity of C/EBPβ by disrupting its interaction with the Taz2 domain of p300. Together with previous studies our work reveals that Celastrol independently targets Myb and C/EBPβ by disrupting the interaction of both transcription factors with p300. Myb, C/EBPβ and p300 cooperate in myeloid-specific gene expression and, as shown recently, are associated with so-called super-enhancers in AML cells that have been implicated in the maintenance of the leukemia. We hypothesize that the ability of Celastrol to disrupt the activity of a transcriptional Myb-C/EBPβ-p300 module might explain its promising anti-leukemic activity.
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Affiliation(s)
- Anna Coulibaly
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Astrid Haas
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Simone Steinmann
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Anke Jakobs
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Thomas J. Schmidt
- Institute for Pharmaceutical Biology and Phytochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Karl-Heinz Klempnauer
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
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18
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Fuglerud BM, Lemma RB, Wanichawan P, Sundaram AYM, Eskeland R, Gabrielsen OS. A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function. Nucleic Acids Res 2017; 45:7681-7696. [PMID: 28472346 PMCID: PMC5570105 DOI: 10.1093/nar/gkx364] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/26/2017] [Indexed: 12/21/2022] Open
Abstract
The transcription factor c-Myb is involved in early differentiation and proliferation of haematopoietic cells, where it operates as a regulator of self-renewal and multi-lineage differentiation. Deregulated c-Myb plays critical roles in leukaemias and other human cancers. Due to its role as a master regulator, we hypothesized it might function as a pioneer transcription factor. Our approach to test this was to analyse a mutant of c-Myb, D152V, previously reported to cause haematopoietic defects in mice by an unknown mechanism. Our transcriptome data from K562 cells indicates that this mutation specifically affects c-Myb's ability to regulate genes involved in differentiation, causing failure in c-Myb's ability to block differentiation. Furthermore, we see a major effect of this mutation in assays where chromatin opening is involved. We show that each repeat in the minimal DNA-binding domain of c-Myb binds to histones and that D152V disrupts histone binding of the third repeat. ATAC-seq data indicates this mutation impairs the ability of c-Myb to cause chromatin opening at specific sites. Taken together, our findings support that c-Myb acts as a pioneer factor and show that D152V impairs this function. The D152V mutant is the first mutant of a transcription factor specifically destroying pioneer factor function.
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Affiliation(s)
- Bettina M Fuglerud
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway
| | - Roza B Lemma
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway
| | - Pimthanya Wanichawan
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway.,Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, P.O.Box 4956 Nydalen, N-0424 Oslo, Norway.,Center for Heart Failure Research, Oslo University Hospital and University of Oslo, P.O.Box 4956 Nydalen, N-0424 Oslo, Norway
| | - Arvind Y M Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, P.O.Box 4950 Nydalen, N-0424 Oslo, Norway
| | - Ragnhild Eskeland
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway.,Norwegian Center for Stem Cell Research, Department of Immunology, Oslo University Hospital, P.O.Box 1112 Blindern, N-0317 Oslo, Norway
| | - Odd S Gabrielsen
- Department of Biosciences, University of Oslo, P.O.Box 1066 Blindern, N-0316 Oslo, Norway
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19
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Falkenberg KD, Jakobs A, Matern JC, Dörner W, Uttarkar S, Trentmann A, Steinmann S, Coulibaly A, Schomburg C, Mootz HD, Schmidt TJ, Klempnauer KH. Withaferin A, a natural compound with anti-tumor activity, is a potent inhibitor of transcription factor C/EBPβ. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1349-1358. [PMID: 28476645 DOI: 10.1016/j.bbamcr.2017.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023]
Abstract
Recent work has shown that deregulation of the transcription factor Myb contributes to the development of leukemia and several other human cancers, making Myb and its cooperation partners attractive targets for drug development. By employing a myeloid Myb-reporter cell line we have identified Withaferin A (WFA), a natural compound that exhibits anti-tumor activities, as an inhibitor of Myb-dependent transcription. Analysis of the inhibitory mechanism of WFA showed that WFA is a significantly more potent inhibitor of C/EBPβ, a transcription factor cooperating with Myb in myeloid cells, than of Myb itself. We show that WFA covalently modifies specific cysteine residues of C/EBPβ, resulting in the disruption of the interaction of C/EBPβ with the co-activator p300. Our work identifies C/EBPβ as a novel direct target of WFA and highlights the role of p300 as a crucial co-activator of C/EBPβ. The finding that WFA is a potent inhibitor of C/EBPβ suggests that inhibition of C/EBPβ might contribute to the biological activities of WFA.
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Affiliation(s)
- Kim D Falkenberg
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Anke Jakobs
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Julian C Matern
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Wolfgang Dörner
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Sagar Uttarkar
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Amke Trentmann
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Simone Steinmann
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Anna Coulibaly
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Caroline Schomburg
- Institute for Pharmaceutical Biology and Phytochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Henning D Mootz
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Thomas J Schmidt
- Institute for Pharmaceutical Biology and Phytochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Karl-Heinz Klempnauer
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany.
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20
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Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility. PLoS Comput Biol 2017; 13:e1005311. [PMID: 28118358 PMCID: PMC5261565 DOI: 10.1371/journal.pcbi.1005311] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/15/2016] [Indexed: 11/29/2022] Open
Abstract
To better understand genome regulation, it is important to uncover the role of transcription factors in the process of chromatin structure establishment and maintenance. Here we present a data-driven approach to systematically characterise transcription factors that are relevant for this process. Our method uses a linear mixed modelling approach to combine datasets of transcription factor binding motif enrichments in open chromatin and gene expression across the same set of cell lines. Applying this approach to the ENCODE dataset, we confirm already known and imply numerous novel transcription factors that play a role in the establishment or maintenance of open chromatin. In particular, our approach rediscovers many factors that have been annotated as pioneer factors. Transcription factor binding occurs mainly in regions of open chromatin. For many transcription factors, it is unclear whether binding is the cause or the consequence of open chromatin. Here, we used datasets on open chromatin and gene expression provided by the ENCODE project to predict which transcription factors drive transitions between open and closed states. A signature of such a factor is that its expression values are correlated to chromatin accessibility at its motif across the same set of cell lines. Our method assesses this correlation while accounting for the fact that some tested cell lines are more related than others. We find many transcription factors showing evidence of driving transitions and a high proportion of these transcription factors are known pioneer factors, i.e., they play a role in opening up closed chromatin.
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Bhaumik P, Davis J, Tropea JE, Cherry S, Johnson PF, Miller M. Structural insights into interactions of C/EBP transcriptional activators with the Taz2 domain of p300. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1914-21. [PMID: 25004968 PMCID: PMC4089485 DOI: 10.1107/s1399004714009262] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/24/2014] [Indexed: 11/10/2022]
Abstract
Members of the C/EBP family of transcription factors bind to the Taz2 domain of p300/CBP and mediate its phosphorylation through the recruitment of specific kinases. Short sequence motifs termed homology boxes A and B, which comprise their minimal transactivation domains (TADs), are conserved between C/EBP activators and are necessary for specific p300/CBP binding. A possible mode of interaction between C/EBP TADs and the p300 Taz2 domain was implied by the crystal structure of a chimeric protein composed of residues 1723-1818 of p300 Taz2 and residues 37-61 of C/EBPℇ. The segment corresponding to the C/EBPℇ TAD forms two orthogonally disposed helices connected by a short linker and interacts with the core structure of Taz2 from a symmetry-related molecule. It is proposed that other members of the C/EBP family interact with the Taz2 domain in the same manner. The position of the C/EBPℇ peptide on the Taz2 protein interaction surface suggests that the N-termini of C/EBP proteins are unbound in the C/EBP-p300 Taz2 complex. This observation is in agreement with the known location of the docking site of protein kinase HIPK2 in the C/EBPβ N-terminus, which associates with the C/EBPβ-p300 complex.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Jamaine Davis
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Joseph E. Tropea
- Protein Purification Core, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Scott Cherry
- Protein Purification Core, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Peter F. Johnson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Maria Miller
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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Tamura I, Sato S, Okada M, Tanabe M, Lee L, Maekawa R, Asada H, Yamagata Y, Tamura H, Sugino N. Importance of C/EBPβ binding and histone acetylation status in the promoter regions for induction of IGFBP-1, PRL, and Mn-SOD by cAMP in human endometrial stromal cells. Endocrinology 2014; 155:275-86. [PMID: 24248464 DOI: 10.1210/en.2013-1569] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Dynamic changes of gene expressions occur in human endometrial stromal cells (ESCs) during decidualization. CCAAT/enhancer-binding proteinβ (C/EBPβ) regulates the expression of a number of decidualization-related genes. In addition to transcription factors, it is important to know the role of epigenetic mechanisms, such as histone modifications in the regulation of decidualization-related genes. This study investigated the molecular and epigenetic mechanisms by which cAMP up-regulates the expression of IGF-binding protein-1 (IGFBP-1), prolactin (PRL), and manganese superoxide dismutase (Mn-SOD) in ESC. ESCs isolated from proliferative phase endometrium were incubated with cAMP to induce decidualization. IGFBP-1, PRL, and Mn-SOD mRNA expressions were determined by real-time RT-PCR. The C/EBPβ binding and histone modification status (acetylation of histone-H3 lysine-27 [H3K27ac]) in the promoter were examined by chromatin immunoprecipitation assay. Knockdowns of C/EBPβ were performed using the small interfering RNA method. cAMP induced mRNA expressions of IGFBP-1 and PRL accompanied by the increases in both C/EBPβ binding activities and H3K27ac levels in the promoters. The stimulatory effects of cAMP on mRNA levels and H3K27ac levels were completely abolished by C/EBPβ knockdown. cAMP increased Mn-SOD mRNA levels and C/EBPβ binding activities in the enhancer region. C/EBPβ knockdown inhibited Mn-SOD mRNA levels. The H3K27ac levels in the enhancer were high before cAMP stimulus but were not further increased by cAMP and were not inhibited by C/EBPβ knockdown. These results show that C/EBPβ regulates the expression of IGFBP-1 and PRL by altering the histone acetylation status of their promoters but differently regulates Mn-SOD gene expression in human ESC during decidualization.
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Affiliation(s)
- Isao Tamura
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
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Yang Z, Yoshioka H, McCarrey JR. Sequence-specific promoter elements regulate temporal-specific changes in chromatin required for testis-specific activation of the Pgk2 gene. Reproduction 2013; 146:501-16. [PMID: 24000349 DOI: 10.1530/rep-13-0311] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The phosphoglycerate kinase-2 (Pgk2) gene is regulated in a tissue-, cell type-, and developmental stage-specific manner during spermatogenesis and is required for normal sperm motility and fertility in mammals. Activation of Pgk2 transcription is regulated by testis-specific demethylation of DNA and binding of testis-specific transcription factors to enhancer and core promoter elements. Here, we show that chromatin remodeling including reconfiguration of nucleosomes and changes in histone modifications is also associated with transcriptional activation of the Pgk2 gene during spermatogenesis. Developmental studies indicate that the order of events involved in transcriptional activation of the Pgk2 gene includes demethylation of DNA in T₁- and T₂-prospermatogonia, binding of a factor to the CAAT box in type A and B spermatogonia, followed by recruitment of chromatin remodeling factors, displacement of a nucleosome from the Pgk2 promoter region, binding of factors to the Pgk2 core promoter and enhancer regions, and, finally, initiation of transcription in primary spermatocytes. Transgene studies show that Pgk2 core promoter elements are required to direct demethylation of DNA and reconfiguration of nucleosomes, whereas both enhancer and core promoter elements are required to direct changes in histone modifications and initiation of transcription. These results provide novel insight into the developmental order of molecular events required to activate tissue-specific transcription of the Pgk2 gene, the distinct elements in the 5'-regulatory region of the Pgk2 gene that regulate each of these events, and the relationship among these events in that each step in this process appears to be a necessary prerequisite for the subsequent step.
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Affiliation(s)
- Zhangsheng Yang
- Department of Biology, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, Texas 78249, USA
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Steinmann S, Coulibaly A, Ohnheiser J, Jakobs A, Klempnauer KH. Interaction and cooperation of the CCAAT-box enhancer-binding protein β (C/EBPβ) with the homeodomain-interacting protein kinase 2 (Hipk2). J Biol Chem 2013; 288:22257-69. [PMID: 23782693 DOI: 10.1074/jbc.m113.487769] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CCAAT box/enhancer-binding protein β (C/EBPβ) is a bZip transcription factor that plays crucial roles in important cellular processes such as differentiation and proliferation of specific cell types. Previously, we showed that C/EBPβ cooperates with the coactivator p300 through a novel mechanism that involves the C/EBPβ-induced phosphorylation of multiple sites in the carboxyl-terminal domain of p300 by protein kinase Hipk2. We have now examined the interaction and cooperation of C/EBPβ, p300, and Hipk2 in more detail. We show that Hipk2 and C/EBPβ are direct physical binding partners whose interaction is mediated by sequences located in the amino-terminal and central domains of Hipk2 and the amino-terminal part of C/EBPβ. In addition to phosphorylating p300 recruited to C/EBPβ, Hipk2 also phosphorylates C/EBPβ at sites that have previously been shown to plays key roles in the regulation of C/EBPβ activity. Silencing of Hipk2 expression disrupts adipocyte differentiation of 3T3-L1 cells, a physiological C/EBPβ-dependent differentiation process indicating that the cooperation of C/EBPβ and Hipk2 is functionally relevant. Finally, we demonstrate that C/EBPα, a related C/EBP family member whose amino-terminal sequences differ significantly from that of C/EBPβ, is unable to interact and cooperate with Hipk2. Instead, our data suggest that C/EBPα cooperates with the protein kinase Jnk to induce phosphorylation of p300. Overall, our data identify Hipk2 as a novel regulator of C/EBPβ and implicate different protein kinases in the cooperation of p300 with C/EBPβ and C/EBPα.
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Affiliation(s)
- Simone Steinmann
- Institut für Biochemie, Westfälische-Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 2, D-48149 Münster, Germany
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Shan J, Fu L, Balasubramanian MN, Anthony T, Kilberg MS. ATF4-dependent regulation of the JMJD3 gene during amino acid deprivation can be rescued in Atf4-deficient cells by inhibition of deacetylation. J Biol Chem 2012; 287:36393-403. [PMID: 22955275 DOI: 10.1074/jbc.m112.399600] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Following amino acid deprivation, the amino acid response (AAR) induces transcription from specific genes through a collection of signaling mechanisms, including the GCN2-eIF2-ATF4 pathway. The present report documents that the histone demethylase JMJD3 is an activating transcription factor 4 (ATF4)-dependent target gene. The JMJD3 gene contains two AAR-induced promoter activities and chromatin immunoprecipitation (ChIP) analysis showed that the AAR leads to enhanced ATF4 recruitment to the C/EBP-ATF response element (CARE) upstream of Promoter-1. AAR-induced histone modifications across the JMJD3 gene locus occur upon ATF4 binding. Jmjd3 transcription is not induced in Atf4-knock-out cells, but the AAR-dependent activation was rescued by inhibition of histone deacetylation with trichostatin A (TSA). The TSA rescue of AAR activation in the absence of Atf4 also occurred for the Atf3 and C/EBP homology protein (Chop) genes, but not for the asparagine synthetase gene. ChIP analysis of the Jmjd3, Atf3, and Chop genes in Atf4 knock-out cells documented that activation of the AAR in the presence of TSA led to specific changes in acetylation of histone H4. The results suggest that a primary function of ATF4 is to recruit histone acetyltransferase activity to a sub-set of AAR target genes. Thus, absolute binding of ATF4 to these particular genes is not required and no ATF4 interaction with the general transcription machinery is necessary. The data are consistent with the hypothesis that ATF4 functions as a pioneer factor to alter chromatin structure and thus, enhance transcription in a gene-specific manner.
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Affiliation(s)
- Jixiu Shan
- Department of Biochemistry and Molecular Biology, Genetics Institute, Shands Cancer Center, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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26
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Regulation of C/EBPβ and resulting functions in cells of the monocytic lineage. Cell Signal 2012; 24:1287-96. [DOI: 10.1016/j.cellsig.2012.02.007] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 02/14/2012] [Indexed: 01/10/2023]
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27
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Bujnicki T, Wilczek C, Schomburg C, Feldmann F, Schlenke P, Müller-Tidow C, Schmidt TJ, Klempnauer KH. Inhibition of Myb-dependent gene expression by the sesquiterpene lactone mexicanin-I. Leukemia 2011; 26:615-22. [PMID: 21986841 DOI: 10.1038/leu.2011.275] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The c-myb proto-oncogene encodes a transcription factor that is highly expressed in the progenitor cells of the hematopoietic system, where it regulates the expression of genes important for lineage determination, cell proliferation and differentiation. There is strong evidence that deregulation of c-myb expression is involved in the development of human tumors, particularly of certain types of leukemia, and breast and colon cancer. The c-Myb protein is therefore an interesting therapeutic target. Here, we have investigated the potential of natural sesquiterpene lactones (STLs), a class of compounds that are active constituents of a variety of medicinal plants, to suppress Myb-dependent gene expression. We have developed a test system that allows screening of compounds for their ability to interfere with the activation of Myb target genes. Using this assay system, we have identified the STL mexicanin-I as the first cell-permeable, low-molecular-weight inhibitor of Myb-induced gene expression.
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Affiliation(s)
- T Bujnicki
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
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28
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Abstract
Pdcd4 is a novel tumor suppressor protein that functions in the nucleus and the cytoplasm, and appears to be involved in the regulation of transcription and translation. In the cytoplasm, Pdcd4 has been implicated in the suppression of translation of mRNAs containing structured 5'-untranslated regions; however, the mechanisms that recruit Pdcd4 to specific target mRNAs and the identities of these mRNAs are mostly unknown. In this study, we have identified c-myb mRNA as the first natural translational target mRNA of Pdcd4. We have found that translational suppression of c-myb mRNA by Pdcd4 is dependent on sequences located within the c-myb-coding region. Furthermore, we have found that the N-terminal domain of Pdcd4 has an important role in targeting Pdcd4 to c-myb RNA by mediating preferential RNA binding to the Pdcd4-responsive region of c-myb mRNA. Overall, our work demonstrates for the first time that Pdcd4 is directly involved in translational suppression of a natural mRNA and provides the first evidence for a key role of the RNA-binding domain in targeting Pdcd4 to a specific mRNA.
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Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis. EMBO J 2011; 30:1459-72. [PMID: 21427703 DOI: 10.1038/emboj.2011.65] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 02/17/2011] [Indexed: 12/27/2022] Open
Abstract
Adipogenesis is tightly controlled by a complex network of transcription factors acting at different stages of differentiation. Peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein (C/EBP) family members are key regulators of this process. We have employed DNase I hypersensitive site analysis to investigate the genome-wide changes in chromatin structure that accompany the binding of adipogenic transcription factors. These analyses revealed a dramatic and dynamic modulation of the chromatin landscape during the first hours of adipocyte differentiation that coincides with cooperative binding of multiple early transcription factors (including glucocorticoid receptor, retinoid X receptor, Stat5a, C/EBPβ and -δ) to transcription factor 'hotspots'. Our results demonstrate that C/EBPβ marks a large number of these transcription factor 'hotspots' before induction of differentiation and chromatin remodelling and is required for their establishment. Furthermore, a subset of early remodelled C/EBP-binding sites persists throughout differentiation and is later occupied by PPARγ, indicating that early C/EBP family members, in addition to their well-established role in activation of PPARγ transcription, may act as pioneering factors for PPARγ binding.
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Abstract
Sequence-specific transcription factors (TFs) play a central role in regulating transcription initiation by directing the recruitment and activity of the general transcription machinery and accessory factors. It is now well established that many of the effects exerted by TFs in eukaryotes are mediated through interactions with a host of coregulators that modify the chromatin state, resulting in a more open (in case of activation) or closed conformation (in case of repression). The relationship between TFs and chromatin is a two-way street, however, as chromatin can in turn influence the recognition and binding of target sequences by TFs. The aim of this chapter is to highlight how this dynamic interplay between TF-directed remodelling of chromatin and chromatin-adjusted targeting of TF binding determines where and how transcription is initiated, and to what degree it is productive.
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31
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Santilli G, Almarza E, Brendel C, Choi U, Beilin C, Blundell MP, Haria S, Parsley KL, Kinnon C, Malech HL, Bueren JA, Grez M, Thrasher AJ. Biochemical correction of X-CGD by a novel chimeric promoter regulating high levels of transgene expression in myeloid cells. Mol Ther 2010; 19:122-32. [PMID: 20978475 DOI: 10.1038/mt.2010.226] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
X-linked chronic granulomatous disease (X-CGD) is a primary immunodeficiency caused by mutations in the CYBB gene encoding the phagocyte nicotinamide adenine dinucleotide phosphate (NADPH)-oxidase catalytic subunit gp91(phox). A recent clinical trial for X-CGD using a spleen focus-forming virus (SFFV)-based γ-retroviral vector has demonstrated clear therapeutic benefits in several patients although complicated by enhancer-mediated mutagenesis and diminution of effectiveness over time due to silencing of the viral long terminal repeat (LTR). To improve safety and efficacy, we have designed a lentiviral vector that directs transgene expression primarily in myeloid cells. To this end, we created a synthetic chimeric promoter that contains binding sites for myeloid transcription factors CAAT box enhancer-binding family proteins (C/EBPs) and PU.1, which are highly expressed during granulocytic differentiation. As predicted, the chimeric promoter regulated higher reporter gene expression in myeloid than in nonmyeloid cells, and in human hematopoietic progenitors upon granulocytic differentiation. In a murine model of stem cell gene therapy for X-CGD, the chimeric vector resulted in high levels of gp91(phox) expression in committed myeloid cells and granulocytes, and restored normal NADPH-oxidase activity. These findings were recapitulated in human neutrophils derived from transduced X-CGD CD34(+) cells in vivo, and suggest that the chimeric promoter will have utility for gene therapy of myeloid lineage disorders such as CGD.
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Affiliation(s)
- Giorgia Santilli
- Molecular Immunology Unit, Institute of Child Health, London, UK
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32
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Wilczek C, Chayka O, Plachetka A, Klempnauer KH. Myb-induced chromatin remodeling at a dual enhancer/promoter element involves non-coding rna transcription and is disrupted by oncogenic mutations of v-myb. J Biol Chem 2010; 284:35314-24. [PMID: 19841477 DOI: 10.1074/jbc.m109.066175] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The oncogene v-myb of avian myeloblastosis virus (AMV) encodes a transcription factor (v-Myb) that transforms myelomonocytic cells by deregulating the expression of specific target genes. v-myb has acquired its oncogenic potential by truncation as well as by a number of point mutations of its cellular progenitor c-myb. As a result of these changes, the target gene spectrum v-Myb differs from that of c-Myb. We recently showed that the chicken mim-1 gene, a c-Myb target gene that is not activated by v-Myb harbors a powerful cell type-specific and Myb-inducible enhancer in addition to a Myb-responsive promoter. We now show that Myb-dependent activation of the mim-1 gene is accompanied by extensive remodeling of the nucleosomal architecture at the enhancer. We found that the mim-1 enhancer region also harbors a promoter whose activity is stimulated by Myb and which directs the transcription of an apparently non-coding RNA. Furthermore, our data show that the oncogenic mutations of AMV have disrupted the ability of v-Myb to induce remodeling of chromatin structure at the mim-1 enhancer. Together, our results demonstrate for the first time directly that Myb induces alterations of the nucleosomal organization at a relevant target site and provide new insight into the functional consequences of the oncogenic amino acid substitutions.
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Affiliation(s)
- Carola Wilczek
- Institut für Biochemie, Westfälische-Wilhelms-Universität Münster, D-48149 Münster, Germany
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Wethkamp N, Klempnauer KH. Daxx is a transcriptional repressor of CCAAT/enhancer-binding protein beta. J Biol Chem 2009; 284:28783-94. [PMID: 19690170 DOI: 10.1074/jbc.m109.041186] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
CCAAT/enhancer-binding Protein beta (C/EBPbeta) is a member of the bZIP transcription factor family that is expressed in various tissues, including cells of the hematopoietic system. C/EBPbeta is involved in tissue-specific gene expression and thereby takes part in fundamental cellular processes such as proliferation and differentiation. Here, we show that the activity of C/EBPbeta is negatively regulated by the transcriptional co-repressor Daxx. C/EBPbeta was found to directly interact with Daxx after overexpression as well as on the endogenous level. Glutathione S-transferase pulldown assays showed that Daxx binds via amino acids 190-400 to the C-terminal part of C/EBPbeta. Co-expression of C/EBPbeta changed the sub-nuclear Daxx distribution pattern from predominantly POD-localized to nucleoplasmic. Daxx suppressed basal and p300-enhanced transcriptional activity of C/EBPbeta. Furthermore, Daxx decreased the C/EBPbeta-dependent phosphorylation of p300, which in turn was associated with a diminished level of p300-mediated C/EBPbeta acetylation. Co-expression of promyelocytic leukemia protein abrogated the repressive effect of Daxx on C/EBPbeta as well as the direct interaction of Daxx and C/EBPbeta, presumably by re-recruiting Daxx to PML-oncogenic domains. In acute promyelocytic leukemia (APL) cells, C/EBPbeta activity is known to be required for all-trans-retinoic acid-induced cell differentiation and disease remission. We show that all-trans-retinoic acid as well as arsenic trioxide treatment leads to a reduced C/EBPbeta fraction associated with Daxx suggesting a relief of Daxx-dependent C/EBPbeta repression as an important molecular event leading to APL cell differentiation. Overall, our data identify Daxx as a new negative regulator of C/EBPbeta and provide first clues for a link between abrogation of Daxx-C/EBPbeta complex formation and APL remission.
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Affiliation(s)
- Nils Wethkamp
- Institut für Biochemie, Westfälische-Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 2, Münster D-48149, Germany
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Ranjan R, Thompson EA, Yoon K, Smart RC. C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint. Oncogene 2009; 28:3235-45. [PMID: 19581927 PMCID: PMC2741539 DOI: 10.1038/onc.2009.176] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We observed that C/EBPα is highly inducible in primary fibroblasts by DNA damaging agents that induce strand breaks, alkylate and crosslink DNA as well as those that produce bulky DNA lesions. Fibroblasts deficient in C/EBPα (C/EBPα-/-) display an impaired G1 checkpoint as evidenced by inappropriate entry into S-phase in response to DNA damage and these cells also display an enhanced G1 to S transition in response to mitogens. The induction of C/EBPα by DNA damage in fibroblasts does not require p53. EMSA analysis of nuclear extracts prepared from UVB- and MNNG-treated fibroblasts revealed increased binding of C/EBPβ to a C/EBP consensus sequence and ChIP analysis revealed increased C/EBPβ binding to the C/EBPα promoter. To determine whether C/EBPβ has a role in the regulation of C/EBPα we treated C/EBPβ-/- fibroblasts with UVB or MNNG. We observed C/EBPα induction was impaired in both UVB- and MNNG- treated C/EBPβ-/- fibroblasts. Our study reveals a novel role for C/EBPβ in the regulation of C/EBPα in response to DNA damage and provides definitive genetic evidence that C/EBPα has a critical role in the DNA damage G1 checkpoint.
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Affiliation(s)
- R Ranjan
- Cell Signaling and Cancer Group, Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, NC 27695-7633, USA
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Cruickshank MN, Fenwick E, Karimi M, Abraham LJ, Ulgiati D. Cell- and stage-specific chromatin structure across the Complement receptor 2 (CR2/CD21) promoter coincide with CBF1 and C/EBP-beta binding in B cells. Mol Immunol 2009; 46:2613-22. [PMID: 19487031 DOI: 10.1016/j.molimm.2009.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 05/01/2009] [Accepted: 05/02/2009] [Indexed: 01/19/2023]
Abstract
Stringent developmental transcription requires multiple transcription factor (TF) binding sites, cell-specific expression of signaling molecules, TFs and co-regulators and appropriate chromatin structure. During B-lymphopoiesis, human Complement receptor 2 (CR2/CD21) is detected on immature and mature B cells but not on B cell precursors and plasma cells. We examined cell- and stage-specific human CR2 gene regulation using cell lines modeling B-lymphopoiesis. Chromatin accessibility assays revealed a region between -409 and -262 with enhanced accessibility in mature B cells and pre-B cells, compared to either non-lymphoid or plasma cell-types, however, accessibility near the transcription start site (TSS) was elevated only in CR2-expressing B cells. A correlation between histone acetylation and CR2 expression was observed, while histone H3K4 dimethylation was enriched near the TSS in both CR2-expressing B cells and non-expressing pre-B cells. Candidate sites within the CR2 promoter were identified which could regulate chromatin, including a matrix attachment region associated with CDP, SATB1/BRIGHT and CEBP-beta sites as well as two CBF1 sites. ChIP assays verified that both CBF1 and C/EBP-beta bind the CR2 promoter in B cells raising the possibility that these factors facilitate or respond to alterations in chromatin structure to control the timing and/or level of CR2 transcription.
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The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood 2009; 113:5456-65. [PMID: 19346495 DOI: 10.1182/blood-2009-01-200048] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The basic helix-loop-helix transcription factor Scl/Tal1 controls the development and subsequent differentiation of hematopoietic stem cells (HSCs). However, because few Scl target genes have been validated to date, the underlying mechanisms have remained largely unknown. In this study, we have used ChIP-Seq technology (coupling chromatin immunoprecipitation with deep sequencing) to generate a genome-wide catalog of Scl-binding events in a stem/progenitor cell line, followed by validation using primary fetal liver cells and comprehensive transgenic mouse assays. Transgenic analysis provided in vivo validation of multiple new direct Scl target genes and allowed us to reconstruct an in vivo validated network consisting of 17 factors and their respective regulatory elements. By coupling ChIP-Seq in model cell lines with in vivo transgenic validation and sophisticated bioinformatic analysis, we have identified a widely applicable strategy for the reconstruction of stem cell regulatory networks in which biologic material is otherwise limiting. Moreover, in addition to revealing multiple previously unrecognized links to known HSC regulators, as well as novel links to genes not previously implicated in HSC function, comprehensive transgenic analysis of regulatory elements provided substantial new insights into the transcriptional control of several important hematopoietic regulators, including Cbfa2t3h/Eto2, Cebpe, Nfe2, Zfpm1/Fog1, Erg, Mafk, Gfi1b, and Myb.
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Epigenetic plasticity of chromatin in embryonic and hematopoietic stem/progenitor cells: therapeutic potential of cell reprogramming. Leukemia 2008; 22:1503-18. [PMID: 18548105 DOI: 10.1038/leu.2008.141] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
During embryonic development and adult life, the plasticity and reversibility of modifications that affect the chromatin structure is important in the expression of genes involved in cell fate decisions and the maintenance of cell-differentiated state. Epigenetic changes in DNA and chromatin, which must occur to allow the accessibility of transcriptional factors at specific DNA-binding sites, are regarded as emerging major players for embryonic and hematopoietic stem cell (HSC) development and lineage differentiation. Epigenetic deregulation of gene expression, whether it be in conjunction with chromosomal alterations and gene mutations or not, is a newly recognized mechanism that leads to several diseases, including leukemia. The reversibility of epigenetic modifications makes DNA and chromatin changes attractive targets for therapeutic intervention. Here we review some of the epigenetic mechanisms that regulate gene expression in pluripotent embryonic and multipotent HSCs but may be deregulated in leukemia, and the clinical approaches designed to target the chromatin structure in leukemic cells.
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