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Affar M, Bottardi S, Quansah N, Lemarié M, Ramón AC, Affar EB, Milot E. IKAROS: from chromatin organization to transcriptional elongation control. Cell Death Differ 2023:10.1038/s41418-023-01212-2. [PMID: 37620540 DOI: 10.1038/s41418-023-01212-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
IKAROS is a master regulator of cell fate determination in lymphoid and other hematopoietic cells. This transcription factor orchestrates the association of epigenetic regulators with chromatin, ensuring the expression pattern of target genes in a developmental and lineage-specific manner. Disruption of IKAROS function has been associated with the development of acute lymphocytic leukemia, lymphoma, chronic myeloid leukemia and immune disorders. Paradoxically, while IKAROS has been shown to be a tumor suppressor, it has also been identified as a key therapeutic target in the treatment of various forms of hematological malignancies, including multiple myeloma. Indeed, targeted proteolysis of IKAROS is associated with decreased proliferation and increased death of malignant cells. Although the molecular mechanisms have not been elucidated, the expression levels of IKAROS are variable during hematopoiesis and could therefore be a key determinant in explaining how its absence can have seemingly opposite effects. Mechanistically, IKAROS collaborates with a variety of proteins and complexes controlling chromatin organization at gene regulatory regions, including the Nucleosome Remodeling and Deacetylase complex, and may facilitate transcriptional repression or activation of specific genes. Several transcriptional regulatory functions of IKAROS have been proposed. An emerging mechanism of action involves the ability of IKAROS to promote gene repression or activation through its interaction with the RNA polymerase II machinery, which influences pausing and productive transcription at specific genes. This control appears to be influenced by IKAROS expression levels and isoform production. In here, we summarize the current state of knowledge about the biological roles and mechanisms by which IKAROS regulates gene expression. We highlight the dynamic regulation of this factor by post-translational modifications. Finally, potential avenues to explain how IKAROS destruction may be favorable in the treatment of certain hematological malignancies are also explored.
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Affiliation(s)
- Malik Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Norreen Quansah
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Maud Lemarié
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Ailyn C Ramón
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - El Bachir Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
| | - Eric Milot
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
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2
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EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release. Cell Rep 2022; 41:111830. [PMID: 36543143 PMCID: PMC9879271 DOI: 10.1016/j.celrep.2022.111830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/06/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
EKLF/Klf1 is a zinc-finger transcription activator essential for erythroid lineage commitment and terminal differentiation. Using ChIP-seq, we investigate EKLF DNA binding and transcription activation mechanisms during mouse embryonic erythropoiesis. We utilize the Nan/+ mouse that expresses the EKLF-E339D (Nan) variant mutated in its conserved zinc-finger region and address the mechanism of hypomorphic and neomorphic changes in downstream gene expression. First, we show that Nan-EKLF limits normal EKLF binding to a subset of its sites. Second, we find that ectopic binding of Nan-EKLF occurs largely at enhancers and activates transcription through pioneering activity. Third, we find that for a subset of ectopic targets, gene activation is achieved in Nan/+ only by Nan-EKLF binding to distal enhancers, leading to RNA polymerase II pause-release. These results have general applicability to understanding how a DNA binding variant factor confers dominant disruptive effects on downstream gene expression even in the presence of its normal counterpart.
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Naidu SR, Capitano M, Ropa J, Cooper S, Huang X, Broxmeyer HE. Chromatin remodeling subunit BRM and valine regulate hematopoietic stem/progenitor cell function and self-renewal via intrinsic and extrinsic effects. Leukemia 2022; 36:821-833. [PMID: 34599272 PMCID: PMC9212754 DOI: 10.1038/s41375-021-01426-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023]
Abstract
Little is known of hematopoietic stem (HSC) and progenitor (HPC) cell self-renewal. The role of Brahma (BRM), a chromatin remodeler, in HSC function is unknown. Bone marrow (BM) from Brm-/- mice manifested increased numbers of long- and short-term HSCs, GMPs, and increased numbers and cycling of functional HPCs. However, increased Brm-/- BM HSC numbers had decreased secondary and tertiary engraftment, suggesting BRM enhances HSC self-renewal. Valine was elevated in lineage negative Brm-/- BM cells, linking intracellular valine with Brm expression. Valine enhanced HPC colony formation, replating of human cord blood (CB) HPC-derived colonies, mouse BM and human CB HPC survival in vitro, and ex vivo expansion of normal mouse BM HSCs and HPCs. Valine increased oxygen consumption rates of WT cells. BRM through CD98 was linked to regulated import of branched chain amino acids, such as valine, in HPCs. Brm-/- LSK cells exhibited upregulated interferon response/cell cycle gene programs. Effects of BRM depletion are less apparent on isolated HSCs compared to HSCs in the presence of HPCs, suggesting cell extrinsic effects on HSCs. Thus, intracellular valine is regulated by BRM expression in HPCs, and the BRM/valine axis regulates HSC and HPC self-renewal, proliferation, and possibly differentiation fate decisions.
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Affiliation(s)
- Samisubbu R. Naidu
- Medicine, Indiana University School of Medicine,Indiana University School of Medicine, Department of Microbiology/Immunology, 950 West Walnut Street, Bldg. R2, Room 302, Indianapolis, IN 46202, Indiana University School of Medicine, Department of Medicine, 950 West Walnut Street, Bldg. R2, Room E435,These authors contributed equally to this work
| | - Maegan Capitano
- Departments of Microbiology and Immunology, Indiana University School of Medicine,These authors contributed equally to this work
| | - James Ropa
- Departments of Microbiology and Immunology, Indiana University School of Medicine,These authors contributed equally to this work
| | - Scott Cooper
- Departments of Microbiology and Immunology, Indiana University School of Medicine
| | - Xinxin Huang
- Departments of Microbiology and Immunology, Indiana University School of Medicine
| | - Hal E. Broxmeyer
- Departments of Microbiology and Immunology, Indiana University School of Medicine,Indiana University School of Medicine, Department of Microbiology/Immunology, 950 West Walnut Street, Bldg. R2, Room 302, Indianapolis, IN 46202, Indiana University School of Medicine, Department of Medicine, 950 West Walnut Street, Bldg. R2, Room E435
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4
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Boulad F, Maggio A, Wang X, Moi P, Acuto S, Kogel F, Takpradit C, Prockop S, Mansilla-Soto J, Cabriolu A, Odak A, Qu J, Thummar K, Du F, Shen L, Raso S, Barone R, Di Maggio R, Pitrolo L, Giambona A, Mingoia M, Everett JK, Hokama P, Roche AM, Cantu VA, Adhikari H, Reddy S, Bouhassira E, Mohandas N, Bushman FD, Rivière I, Sadelain M. Lentiviral globin gene therapy with reduced-intensity conditioning in adults with β-thalassemia: a phase 1 trial. Nat Med 2022; 28:63-70. [PMID: 34980909 PMCID: PMC9380046 DOI: 10.1038/s41591-021-01554-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/23/2021] [Indexed: 01/05/2023]
Abstract
β-Thalassemias are inherited anemias that are caused by the absent or insufficient production of the β chain of hemoglobin. Here we report 6-8-year follow-up of four adult patients with transfusion-dependent β-thalassemia who were infused with autologous CD34+ cells transduced with the TNS9.3.55 lentiviral globin vector after reduced-intensity conditioning (RIC) in a phase 1 clinical trial ( NCT01639690) . Patients were monitored for insertional mutagenesis and the generation of a replication-competent lentivirus (safety and tolerability of the infusion product after RIC-primary endpoint) and engraftment of genetically modified autologous CD34+ cells, expression of the transduced β-globin gene and post-transplant transfusion requirements (efficacy-secondary endpoint). No unexpected safety issues occurred during conditioning and cell product infusion. Hematopoietic gene marking was very stable but low, reducing transfusion requirements in two patients, albeit not achieving transfusion independence. Our findings suggest that non-myeloablative conditioning can achieve durable stem cell engraftment but underscore a minimum CD34+ cell transduction requirement for effective therapy. Moderate clonal expansions were associated with integrations near cancer-related genes, suggestive of non-erythroid activity of globin vectors in stem/progenitor cells. These correlative findings highlight the necessity of cautiously monitoring patients harboring globin vectors.
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Affiliation(s)
- Farid Boulad
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aurelio Maggio
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Xiuyan Wang
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Moi
- Ospedale Pediatrico Microcitemie 'A.Cao', A.O. 'G.Brotzu', Cagliari, Italy
| | - Santina Acuto
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Friederike Kogel
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chayamon Takpradit
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pediatrics, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Susan Prockop
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge Mansilla-Soto
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Annalisa Cabriolu
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashlesha Odak
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinrong Qu
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Keyur Thummar
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fang Du
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lingbo Shen
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simona Raso
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Rita Barone
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Rosario Di Maggio
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Lorella Pitrolo
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Antonino Giambona
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Maura Mingoia
- Ospedale Pediatrico Microcitemie 'A.Cao', A.O. 'G.Brotzu', Cagliari, Italy
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Pascha Hokama
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aoife M Roche
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Vito Adrian Cantu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hriju Adhikari
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric Bouhassira
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Narla Mohandas
- Laboratory of Red Cell Physiology, New York Blood Center, New York, NY, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Isabelle Rivière
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Lemarié M, Bottardi S, Mavoungou L, Pak H, Milot E. IKAROS is required for the measured response of NOTCH target genes upon external NOTCH signaling. PLoS Genet 2021; 17:e1009478. [PMID: 33770102 PMCID: PMC8026084 DOI: 10.1371/journal.pgen.1009478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/07/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
The tumor suppressor IKAROS binds and represses multiple NOTCH target genes. For their induction upon NOTCH signaling, IKAROS is removed and replaced by NOTCH Intracellular Domain (NICD)-associated proteins. However, IKAROS remains associated to other NOTCH activated genes upon signaling and induction. Whether IKAROS could participate to the induction of this second group of NOTCH activated genes is unknown. We analyzed the combined effect of IKAROS abrogation and NOTCH signaling on the expression of NOTCH activated genes in erythroid cells. In IKAROS-deleted cells, we observed that many of these genes were either overexpressed or no longer responsive to NOTCH signaling. IKAROS is then required for the organization of bivalent chromatin and poised transcription of NOTCH activated genes belonging to either of the aforementioned groups. Furthermore, we show that IKAROS-dependent poised organization of the NOTCH target Cdkn1a is also required for its adequate induction upon genotoxic insults. These results highlight the critical role played by IKAROS in establishing bivalent chromatin and transcriptional poised state at target genes for their activation by NOTCH or other stress signals. NOTCH1 deregulation can favor hematological malignancies. In addition to RBP-Jκ/NICD/MAML1, other regulators are required for the measured activation of NOTCH target genes. IKAROS is a known repressor of many NOTCH targets. Since it can also favor transcriptional activation and control gene expression levels, we questioned whether IKAROS could participate to the activation of specific NOTCH target genes. We are reporting that upon NOTCH induction, the absence of IKAROS impairs the measured activation of two groups of NOTCH target genes: (i) those overexpressed and characterized by an additive effect imposed by the absence of IKAROS and NOTCH induction; and (ii) those ‘desensitized’ and no more activated by NOTCH. At genes of both groups, IKAROS controls the timely recruitment of the chromatin remodelers CHD4 and BRG1. IKAROS then influences the activation of these genes through the organization of chromatin and poised transcription or through transcriptional elongation control. The importance of the IKAROS controlled and measured activation of genes is not limited to NOTCH signaling as it also characterizes Cdkn1a expression upon genotoxic stress. Thus, these results provide a new perspective on the importance of IKAROS for the adequate cellular response to stress, whether imposed by NOTCH or genotoxic insults.
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Affiliation(s)
- Maud Lemarié
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
| | - Lionel Mavoungou
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
| | - Helen Pak
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
| | - Eric Milot
- Maisonneuve-Rosemont Hospital Research Center; CIUSSS de l’est de l’Île de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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6
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Bottardi S, Milot E. An early start of Coup-TFII promotes γ-globin gene expression in adult erythroid cells. Haematologica 2021; 106:335-336. [PMID: 33522785 PMCID: PMC7849336 DOI: 10.3324/haematol.2020.266791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Indexed: 11/27/2022] Open
Affiliation(s)
- Stefania Bottardi
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l'Île de Montréal, Montréal
| | - Eric Milot
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l'Île de Montréal, Montréal; Department of Medicine, University of Montreal, Montréal, Québec.
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Kim YW, Yun WJ, Kim A. Erythroid activator NF-E2, TAL1 and KLF1 play roles in forming the LCR HSs in the human adult β-globin locus. Int J Biochem Cell Biol 2016; 75:45-52. [PMID: 27026582 DOI: 10.1016/j.biocel.2016.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/16/2016] [Accepted: 03/25/2016] [Indexed: 01/12/2023]
Abstract
The β-like globin genes are developmental stage specifically transcribed in erythroid cells. The transcription of the β-like globin genes requires erythroid specific activators such as GATA-1, NF-E2, TAL1 and KLF1. However, the roles of these activators have not fully elucidated in transcription of the human adult β-globin gene. Here we employed hybrid MEL cells (MEL/ch11) where a human chromosome containing the β-globin locus is present and the adult β-globin gene is highly transcribed by induction. The roles of erythroid specific activators were analyzed by inhibiting the expression of NF-E2, TAL1 or KLF1 in MEL/ch11 cells. The loss of each activator decreased the transcription of human β-globin gene, locus wide histone hyperacetylation and the binding of other erythroid specific activators including GATA-1, even though not affecting the expression of other activators. Notably, sensitivity to DNase I was reduced in the locus control region (LCR) hypersensitive sites (HSs) with the depletion of activators. These results indicate that NF-E2, TAL1 and KLF1, all activators play a primary role in HSs formation in the LCR. It might contribute to the transcription of human adult β-globin gene by allowing the access of activators and cofactors. The roles of activators in the adult β-globin locus appear to be different from the roles in the early fetal locus.
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Affiliation(s)
- Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Won Ju Yun
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea.
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Gasiorek JJ, Blank V. Regulation and function of the NFE2 transcription factor in hematopoietic and non-hematopoietic cells. Cell Mol Life Sci 2015; 72:2323-35. [PMID: 25721735 PMCID: PMC11114048 DOI: 10.1007/s00018-015-1866-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 01/01/2023]
Abstract
The NFE2 transcription factor was identified over 25 years ago. The NFE2 protein forms heterodimers with small MAF proteins, and the resulting complex binds to regulatory elements in a large number of target genes. In contrast to other CNC transcription family members including NFE2L1 (NRF1), NFE2L2 (NRF2) and NFE2L3 (NRF3), which are widely expressed, earlier studies had suggested that the major sites of NFE2 expression are hematopoietic cells. Based on cell culture studies it was proposed that this protein acts as a critical regulator of globin gene expression. However, the knockout mouse model displayed only mild erythroid abnormalities, while the major phenotype was a defect in megakaryocyte biogenesis. Indeed, absence of NFE2 led to severely impaired platelet production. A series of recent data, also summarized here, shed new light on the various functional roles of NFE2 and the regulation of its activity. NFE2 is part of a complex regulatory network, including transcription factors such as GATA1 and RUNX1, controlling megakaryocytic and/or erythroid cell function. Surprisingly, it was recently found that NFE2 also has a role in non-hematopoietic tissues, such as the trophoblast, in which it is also expressed, as well as the bone, opening the door to new research areas for this transcription factor. Additional data showed that NFE2 function is controlled by a series of posttranslational modifications. Important strides have been made with respect to the clinical significance of NFE2, linking this transcription factor to hematological disorders such as polycythemias.
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Affiliation(s)
- Jadwiga J. Gasiorek
- Lady Davis Institute for Medical Research, McGill University, 3755 Chemin de la Côte Sainte-Catherine, Montreal, QC H3T 1E2 Canada
- Department of Medicine, McGill University, Montreal, QC Canada
| | - Volker Blank
- Lady Davis Institute for Medical Research, McGill University, 3755 Chemin de la Côte Sainte-Catherine, Montreal, QC H3T 1E2 Canada
- Department of Medicine, McGill University, Montreal, QC Canada
- Department of Physiology, McGill University, Montreal, QC Canada
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Kang Y, Kim YW, Yun J, Shin J, Kim A. KLF1 stabilizes GATA-1 and TAL1 occupancy in the human β-globin locus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:282-9. [PMID: 25528728 DOI: 10.1016/j.bbagrm.2014.12.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 12/09/2014] [Accepted: 12/10/2014] [Indexed: 02/05/2023]
Abstract
KLF1 is an erythroid specific transcription factor that binds to regulatory regions of erythroid genes. Binding sites of KLF1 are often found near binding sites of GATA-1 and TAL1. In the β-globin locus, KLF1 is required for forming active chromatin structure, although its role is unclear. To explore the role of KLF1 in transcribing the human γ-globin genes, we stably reduced the expression of KLF1 in erythroid K562 cells, compromising its association in the β-globin locus. The γ-globin transcription was reduced with disappearance of active chromatin structure of the locus in the KLF1 knockdown cells. Interestingly, GATA-1 and TAL1 binding was reduced in the β-globin locus, even though their expressions were not affected by KLF1 knockdown. The KLF1-dependent GATA-1 and TAL1 binding was observed in the adult locus transcribing the β-globin gene and in several erythroid genes, where GATA-1 occupancy is independent from TAL1. These results indicate that KLF1 plays a role in facilitating and/or stabilizing GATA-1 and TAL1 occupancy in the erythroid genes, contributing to the generation of active chromatin structure such as histone acetylation and chromatin looping.
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Affiliation(s)
- Yujin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Jangmi Yun
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Jongo Shin
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea.
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Bottardi S, Mavoungou L, Pak H, Daou S, Bourgoin V, Lakehal YA, Affar EB, Milot E. The IKAROS interaction with a complex including chromatin remodeling and transcription elongation activities is required for hematopoiesis. PLoS Genet 2014; 10:e1004827. [PMID: 25474253 PMCID: PMC4256266 DOI: 10.1371/journal.pgen.1004827] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/14/2014] [Indexed: 12/15/2022] Open
Abstract
IKAROS is a critical regulator of hematopoietic cell fate and its dynamic expression pattern is required for proper hematopoiesis. In collaboration with the Nucleosome Remodeling and Deacetylase (NuRD) complex, it promotes gene repression and activation. It remains to be clarified how IKAROS can support transcription activation while being associated with the HDAC-containing complex NuRD. IKAROS also binds to the Positive-Transcription Elongation Factor b (P-TEFb) at gene promoters. Here, we demonstrate that NuRD and P-TEFb are assembled in a complex that can be recruited to specific genes by IKAROS. The expression level of IKAROS influences the recruitment of the NuRD-P-TEFb complex to gene regulatory regions and facilitates transcription elongation by transferring the Protein Phosphatase 1α (PP1α), an IKAROS-binding protein and P-TEFb activator, to CDK9. We show that an IKAROS mutant that is unable to bind PP1α cannot sustain gene expression and impedes normal differentiation of IkNULL hematopoietic progenitors. Finally, the knock-down of the NuRD subunit Mi2 reveals that the occupancy of the NuRD complex at transcribed regions of genes favors the relief of POL II promoter-proximal pausing and thereby, promotes transcription elongation. Perturbation of the expression level of IKAROS, a transcription factor critical during hematopoiesis, is associated with malignant transformation in mice and humans. The importance of IKAROS expression levels for the control of target-gene regulation was addressed in hematopoietic progenitor cells. The collaboration between IKAROS and the Nucleosome Remodeling and Deacetylase (NuRD) complex can promote gene activation or repression. IKAROS can also interact with the Positive-Transcription Elongation Factor b (P-TEFb) and the Protein Phosphatase 1 (PP1), an important P-TEFb regulator. Immunoaffinity purification of IKAROS interacting proteins and Fast Protein Liquid Chromatography analysis revealed a dynamic interaction between IKAROS, PP1 and the newly defined NuRD-P-TEFb complex. This complex can be targeted to specific genes in cells expressing high levels of IKAROS to promote productive transcription elongation. Based on our results we suggest that, in addition to P-TEFb, the NuRD complex and PP1 are required to facilitate transcription elongation of IKAROS-target genes and normal differentiation of hematopoietic progenitor cells.
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Affiliation(s)
- Stefania Bottardi
- Maisonneuve Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Lionel Mavoungou
- Maisonneuve Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Helen Pak
- Maisonneuve Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Salima Daou
- Maisonneuve Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Vincent Bourgoin
- Maisonneuve Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Yahia A. Lakehal
- Maisonneuve Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - El Bachir Affar
- Maisonneuve Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Eric Milot
- Maisonneuve Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
- * E-mail:
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11
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Transcription factor EKLF (KLF1) recruitment of the histone chaperone HIRA is essential for β-globin gene expression. Proc Natl Acad Sci U S A 2014; 111:13337-42. [PMID: 25197097 DOI: 10.1073/pnas.1405422111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The binding of chromatin-associated proteins and incorporation of histone variants correlates with alterations in gene expression. These changes have been particularly well analyzed at the mammalian β-globin locus, where transcription factors such as erythroid Krüppel-like factor (EKLF), which is also known as Krüppel-like factor 1 (KLF1), play a coordinating role in establishing the proper chromatin structure and inducing high-level expression of adult β-globin. We had previously shown that EKLF preferentially interacts with histone H3 and that the H3.3 variant is differentially recruited to the β-globin promoter. We now find that a novel interaction between EKLF and the histone cell cycle regulation defective homolog A (HIRA) histone chaperone accounts for these effects. HIRA is not only critical for β-globin expression but is also required for activation of the erythropoietic regulators EKLF and GATA binding protein 1 (GATA1). Our results provide a mechanism by which transcription factor-directed recruitment of a generally expressed histone chaperone can lead to tissue-restricted changes in chromatin components, structure, and transcription at specific genomic sites during differentiation.
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12
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Deho' L, Leoni C, Brodie TM, Montagner S, De Simone M, Polletti S, Barozzi I, Natoli G, Monticelli S. Two functionally distinct subsets of mast cells discriminated By IL-2-independent CD25 activities. THE JOURNAL OF IMMUNOLOGY 2014; 193:2196-206. [PMID: 25063866 DOI: 10.4049/jimmunol.1400516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We identified two mast cell subsets characterized by the differential expression of surface CD25 (IL-2Rα) and by different abilities to produce cytokines and to proliferate, both in vitro and in vivo. CD25 can be expressed on the surface of immune cells in the absence of the other chains of the IL-2R, which are indispensable for IL-2 signaling. We show that functional differences between the two mast cell populations were dependent on CD25 itself, which directly modulated proliferation and cytokine responses. These effects were completely independent from IL-2 or the expression of the other chains of the high-affinity IL-2R, indicating an autonomous and previously unappreciated role for CD25 in regulating cell functions. Cells genetically ablated for CD25 completely recapitulated the CD25-negative phenotype and never acquired the properties characteristic of CD25-positive mast cells. Finally, adoptive transfer experiments in the mouse demonstrated a different impact of these populations in models of anaphylaxis and contact sensitivity. Our findings indicate a general role for CD25 in contexts where IL-2 signaling is not involved, and may have important implications for all mast cell-related diseases, as well as in all cell types expressing CD25 independently of its IL-2-related functions.
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Affiliation(s)
- Lorenzo Deho'
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Cristina Leoni
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Tess M Brodie
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Sara Montagner
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Marco De Simone
- National Institute for Molecular Genetics, 20122 Milan, Italy; and
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy
| | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milan, Italy
| | - Silvia Monticelli
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland;
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13
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Maksimenko O, Georgiev P. Mechanisms and proteins involved in long-distance interactions. Front Genet 2014; 5:28. [PMID: 24600469 PMCID: PMC3927085 DOI: 10.3389/fgene.2014.00028] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/25/2014] [Indexed: 12/28/2022] Open
Abstract
Due to advances in genome-wide technologies, consistent distant interactions within chromosomes of higher eukaryotes have been revealed. In particular, it has been shown that enhancers can specifically and directly interact with promoters by looping out intervening sequences, which can be up to several hundred kilobases long. This review is focused on transcription factors that are supposed to be involved in long-range interactions. Available data are in agreement with the model that several known transcription factors and insulator proteins belong to an abundant but poorly studied class of proteins that are responsible for chromosomal architecture.
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Affiliation(s)
- Oksana Maksimenko
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences Moscow, Russia
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14
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Barrow JJ, Li Y, Hossain M, Huang S, Bungert J. Dissecting the function of the adult β-globin downstream promoter region using an artificial zinc finger DNA-binding domain. Nucleic Acids Res 2014; 42:4363-74. [PMID: 24497190 PMCID: PMC3985677 DOI: 10.1093/nar/gku107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Developmental stage-specific expression of the β-type globin genes is regulated by many cis- and trans-acting components. The adult β-globin gene contains an E-box located 60 bp downstream of the transcription start site that has been shown to bind transcription factor upstream stimulatory factor (USF) and to contribute to efficient in vitro transcription. We expressed an artificial zinc finger DNA-binding domain (ZF-DBD) targeting this site (+60 ZF-DBD) in murine erythroleukemia cells. Expression of the +60 ZF-DBD reduced the recruitment and elongation of RNA polymerase II (Pol II) at the adult β-globin gene and at the same time increased the binding of Pol II at locus control region (LCR) element HS2, suggesting that Pol II is transferred from the LCR to the globin gene promoters. Expression of the +60 ZF-DBD also reduced the frequency of interactions between the LCR and the adult β-globin promoter. ChIP-exonuclease-sequencing revealed that the +60ZF-DBD was targeted to the adult β-globin downstream promoter and that the binding of the ZF-DBD caused alterations in the association of USF2 containing protein complexes. The data demonstrate that targeting a ZF-DBD to the adult β-globin downstream promoter region interferes with the LCR-mediated recruitment and activity of Pol II.
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Affiliation(s)
- Joeva J Barrow
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Shands Cancer Center, Powell-Gene Therapy Center, University of Florida, Gainesville, 32610, FL, USA
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15
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Lahiji A, Kucerová-Levisohn M, Lovett J, Holmes R, Zúñiga-Pflücker JC, Ortiz BD. Complete TCR-α gene locus control region activity in T cells derived in vitro from embryonic stem cells. THE JOURNAL OF IMMUNOLOGY 2013; 191:472-9. [PMID: 23720809 DOI: 10.4049/jimmunol.1300521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Locus control regions (LCRs) are cis-acting gene regulatory elements with the unique, integration site-independent ability to transfer the characteristics of their locus-of-origin's gene expression pattern to a linked transgene in mice. LCR activities have been discovered in numerous T cell lineage-expressed gene loci. These elements can be adapted to the design of stem cell gene therapy vectors that direct robust therapeutic gene expression to the T cell progeny of engineered stem cells. Currently, transgenic mice provide the only experimental approach that wholly supports all the critical aspects of LCR activity. In this study, we report the manifestation of all key features of mouse TCR-α gene LCR function in T cells derived in vitro from mouse embryonic stem cells. High-level, copy number-related TCR-α LCR-linked reporter gene expression levels are cell type restricted in this system, and upregulated during the expected stage transition of T cell development. We also report that de novo introduction of TCR-α LCR-linked transgenes into existing T cell lines yields incomplete LCR activity. These data indicate that establishing full TCR-α LCR activity requires critical molecular events occurring prior to final T lineage determination. This study also validates a novel, tractable, and more rapid approach for the study of LCR activity in T cells, and its translation to therapeutic genetic engineering.
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Affiliation(s)
- Armin Lahiji
- Department of Biological Sciences, City University of New York, Hunter College, New York, NY 10065, USA
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16
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Yien YY, Bieker JJ. EKLF/KLF1, a tissue-restricted integrator of transcriptional control, chromatin remodeling, and lineage determination. Mol Cell Biol 2013; 33:4-13. [PMID: 23090966 PMCID: PMC3536305 DOI: 10.1128/mcb.01058-12] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Erythroid Krüppel-like factor (EKLF or KLF1) is a transcriptional regulator that plays a critical role in lineage-restricted control of gene expression. KLF1 expression and activity are tightly controlled in a temporal and differentiation stage-specific manner. The mechanisms by which KLF1 is regulated encompass a range of biological processes, including control of KLF1 RNA transcription, protein stability, localization, and posttranslational modifications. Intact KLF1 regulation is essential to correctly regulate erythroid function by gene transcription and to maintain hematopoietic lineage homeostasis by ensuring a proper balance of erythroid/megakaryocytic differentiation. In turn, KLF1 regulates erythroid biology by a wide variety of mechanisms, including gene activation and repression by regulation of chromatin configuration, transcriptional initiation and elongation, and localization of gene loci to transcription factories in the nucleus. An extensive series of biochemical, molecular, and genetic analyses has uncovered some of the secrets of its success, and recent studies are highlighted here. These reveal a multilayered set of control mechanisms that enable efficient and specific integration of transcriptional and epigenetic controls and that pave the way for proper lineage commitment and differentiation.
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Affiliation(s)
- Yvette Y. Yien
- Department of Developmental and Regenerative Biology
- Graduate School of Biological Sciences
| | - James J. Bieker
- Department of Developmental and Regenerative Biology
- Black Family Stem Cell Institute
- Tisch Cancer Institute, Mount Sinai School of Medicine, New York, New York, USA
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17
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GATA-1 utilizes Ikaros and polycomb repressive complex 2 to suppress Hes1 and to promote erythropoiesis. Mol Cell Biol 2012; 32:3624-38. [PMID: 22778136 DOI: 10.1128/mcb.00163-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription factor Hairy Enhancer of Split 1 (HES1), a downstream effector of the Notch signaling pathway, is an important regulator of hematopoiesis. Here, we demonstrate that in primary erythroid cells, Hes1 gene expression is transiently repressed around proerythroblast stage of differentiation. Using mouse erythroleukemia cells, we found that the RNA interference (RNAi)-mediated depletion of HES1 enhances erythroid cell differentiation, suggesting that this protein opposes terminal erythroid differentiation. This is also supported by the decreased primary erythroid cell differentiation upon HES1 upregulation in Ikaros-deficient mice. A comprehensive analysis led us to determine that Ikaros favors Hes1 repression in erythroid cells by facilitating recruitment of the master regulator of erythropoiesis GATA-1 alongside FOG-1, which mediates Hes1 repression. GATA-1 is then necessary for the chromatin binding of the NuRD remodeling complex ATPase MI-2, the transcription factor GFI1B, and the histone H3K27 methyltransferase EZH2 along with Polycomb repressive complex 2. We show that EZH2 is required for the transient repression of Hes1 in erythroid cells. In aggregate, our results describe a mechanism whereby GATA-1 utilizes Ikaros and Polycomb repressive complex 2 to promote Hes1 repression as an important step in erythroid cell differentiation.
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18
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Abstract
The cellular events that lead to terminal erythroid differentiation rely on the controlled interplay of extra- and intracellular regulatory factors. Their downstream effects are highly coordinated and result in the structural/morphologic and metabolic changes that uniquely characterize a maturing red blood cell. Erythroid Krüppel-like factor (EKLF/KLF1) is one of a very small number of intrinsic transcription factors that play a major role in regulating these events. This review covers 3 major aspects of erythropoiesis in which EKLF plays crucial functions: (1) at the megakaryocyte-erythroid progenitor stage, where it is involved in erythroid lineage commitment; (2) during the global expansion of erythroid gene expression in primitive and definitive lineages, where it plays a direct role in globin switching; and (3) during the terminal maturation of red cells, where it helps control exit from the cell cycle. We conclude by describing recent studies of mammalian EKLF/KLF1 mutations that lead to altered red cell phenotypes and disease.
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Affiliation(s)
- Miroslawa Siatecka
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, NY, USA
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19
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Structural and functional characterization of an atypical activation domain in erythroid Kruppel-like factor (EKLF). Proc Natl Acad Sci U S A 2011; 108:10484-9. [PMID: 21670263 DOI: 10.1073/pnas.1017029108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Erythroid Krüppel-like factor (EKLF) plays an important role in erythroid development by stimulating β-globin gene expression. We have examined the details by which the minimal transactivation domain (TAD) of EKLF (EKLFTAD) interacts with several transcriptional regulatory factors. We report that EKLFTAD displays homology to the p53TAD and, like the p53TAD, can be divided into two functional subdomains (EKLFTAD1 and EKLFTAD2). Based on sequence analysis, we found that EKLFTAD2 is conserved in KLF2, KLF4, KLF5, and KLF15. In addition, we demonstrate that EKLFTAD2 binds the amino-terminal PH domain of the Tfb1/p62 subunit of TFIIH (Tfb1PH/p62PH) and four domains of CREB-binding protein/p300. The solution structure of the EKLFTAD2/Tfb1PH complex indicates that EKLFTAD2 binds Tfb1PH in an extended conformation, which is in contrast to the α-helical conformation seen for p53TAD2 in complex with Tfb1PH. These studies provide detailed mechanistic information into EKLFTAD functions as well as insights into potential interactions of the TADs of other KLF proteins. In addition, they suggest that not only have acidic TADs evolved so that they bind using different conformations on a common target, but that transitioning from a disordered to a more ordered state is not a requirement for their ability to bind multiple partners.
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20
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Alhashem YN, Vinjamur DS, Basu M, Klingmüller U, Gaensler KML, Lloyd JA. Transcription factors KLF1 and KLF2 positively regulate embryonic and fetal beta-globin genes through direct promoter binding. J Biol Chem 2011; 286:24819-27. [PMID: 21610079 DOI: 10.1074/jbc.m111.247536] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Krüppel-like factors (KLFs) control cell differentiation and embryonic development. KLF1 (erythroid Krüppel-like factor) plays essential roles in embryonic and adult erythropoiesis. KLF2 is a positive regulator of the mouse and human embryonic β-globin genes. KLF1 and KLF2 have highly homologous zinc finger DNA-binding domains. They have overlapping roles in embryonic erythropoiesis, as demonstrated using single and double KO mouse models. Ablation of the KLF1 or KLF2 gene causes embryonic lethality, but double KO embryos are more anemic and die sooner than either single KO. In this work, a dual human β-globin locus transgenic and KLF knockout mouse model was used. The results demonstrate that the human ε- (embryonic) and γ-globin (fetal) genes are positively regulated by KLF1 and KLF2 in embryos. Conditional KO mouse experiments indicate that the effect of KLF2 on embryonic globin gene regulation is at least partly erythroid cell-autonomous. KLF1 and KLF2 bind directly to the promoters of the human ε- and γ-globin genes, the mouse embryonic Ey- and βh1-globin genes, and also to the β-globin locus control region, as demonstrated by ChIP assays with mouse embryonic blood cells. H3K9Ac and H3K4me3 marks indicate open chromatin and active transcription, respectively. These marks are diminished at the Ey-, βh1-, ε- and γ-globin genes and locus control region in KLF1(-/-) embryos, correlating with reduced gene expression. Therefore, KLF1 and KLF2 positively regulate the embryonic and fetal β-globin genes through direct promoter binding. KLF1 is required for normal histone modifications in the β-globin locus in mouse embryos.
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Affiliation(s)
- Yousef N Alhashem
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298-0035, USA
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21
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Role of helix-loop-helix proteins during differentiation of erythroid cells. Mol Cell Biol 2011; 31:1332-43. [PMID: 21282467 DOI: 10.1128/mcb.01186-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Helix-loop-helix (HLH) proteins play a profound role in the process of development and cellular differentiation. Among the HLH proteins expressed in differentiating erythroid cells are the ubiquitous proteins Myc, USF1, USF2, and TFII-I, as well as the hematopoiesis-specific transcription factor Tal1/SCL. All of these HLH proteins exhibit distinct functions during the differentiation of erythroid cells. For example, Myc stimulates the proliferation of erythroid progenitor cells, while the USF proteins and Tal1 regulate genes that specify the differentiated phenotype. This minireview summarizes the known activities of Myc, USF, TFII-I, and Tal11/SCL and discusses how they may function sequentially, cooperatively, or antagonistically in regulating expression programs during the differentiation of erythroid cells.
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22
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Bottardi S, Zmiri FA, Bourgoin V, Ross J, Mavoungou L, Milot E. Ikaros interacts with P-TEFb and cooperates with GATA-1 to enhance transcription elongation. Nucleic Acids Res 2011; 39:3505-19. [PMID: 21245044 PMCID: PMC3089448 DOI: 10.1093/nar/gkq1271] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Ikaros is associated with both gene transcriptional activation and repression in lymphocytes. Ikaros acts also as repressor of human γ-globin (huγ-) gene transcription in fetal and adult erythroid cells. Whether and eventually, how Ikaros can function as a transcriptional activator in erythroid cells remains poorly understood. Results presented herein demonstrate that Ikaros is a developmental-specific activator of huγ-gene expression in yolk sac erythroid cells. Molecular analysis in primary cells revealed that Ikaros interacts with Gata-1 and favors Brg1 recruitment to the human β-globin Locus Control Region and the huγ-promoters, supporting long-range chromatin interactions between these regions. Additionally, we demonstrate that Ikaros contributes to transcription initiation and elongation of the huγ-genes, since it is not only required for TBP and RNA Polymerase II (Pol II) assembly at the huγ-promoters but also for conversion of Pol II into the elongation-competent phosphorylated form. In agreement with the latter, we show that Ikaros interacts with Cyclin-dependent kinase 9 (Cdk9), which contributes to efficient transcription elongation by phosphorylating the C-terminal domain of the large subunit of Pol II on Serine 2, and favours Cdk9 recruitment to huγ-promoters. Our results show that Ikaros exerts dual functionality during gene activation, by promoting efficient transcription initiation and elongation.
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Affiliation(s)
- Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital and Faculty of Medicine, University of Montreal, 5415 boulevard l'Assomption, Montreal, Quebec, Canada H1T 2M4
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23
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Heruth DP, Hawkins T, Logsdon DP, Gibson MI, Sokolovsky IV, Nsumu NN, Major SL, Fegley B, Woods GM, Lewing KB, Neville KA, Cornetta K, Peterson KR, White RA. Mutation in erythroid specific transcription factor KLF1 causes Hereditary Spherocytosis in the Nan hemolytic anemia mouse model. Genomics 2010; 96:303-7. [PMID: 20691777 PMCID: PMC6390478 DOI: 10.1016/j.ygeno.2010.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 07/28/2010] [Accepted: 07/28/2010] [Indexed: 12/17/2022]
Abstract
KLF1 regulates definitive erythropoiesis of red blood cells by facilitating transcription through high affinity binding to CACCC elements within its erythroid specific target genes including those encoding erythrocyte membrane skeleton (EMS) proteins. Deficiencies of EMS proteins in humans lead to the hemolytic anemia Hereditary Spherocytosis (HS) which includes a subpopulation with no known genetic defect. Here we report that a mutation, E339D, in the second zinc finger domain of KLF1 is responsible for HS in the mouse model Nan. The causative nature of this mutation was verified with an allelic test cross between Nan/+ and heterozygous Klf1(+/-) knockout mice. Homology modeling predicted Nan KLF1 binds CACCC elements more tightly, suggesting that Nan KLF1 is a competitive inhibitor of wild-type KLF1. This is the first association of a KLF1 mutation with a disease state in adult mammals and also presents the possibility of being another causative gene for HS in humans.
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Affiliation(s)
- Daniel P. Heruth
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, 2411 Holmes Street, Kansas City, MO 64108
| | - Troy Hawkins
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, 980 W. Walnut Street, Indianapolis, IN 46202
| | - Derek P. Logsdon
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
| | - Margaret I. Gibson
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
| | - Inna V. Sokolovsky
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
| | - Ndona N. Nsumu
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
| | - Stephanie L. Major
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
| | - Barbara Fegley
- Electron Microscopy Research Laboratory, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160
| | - Gerald M. Woods
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, 2411 Holmes Street, Kansas City, MO 64108
| | - Karen B. Lewing
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, 2411 Holmes Street, Kansas City, MO 64108
| | - Kathleen A. Neville
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, 2411 Holmes Street, Kansas City, MO 64108
| | - Kenneth Cornetta
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, 980 W. Walnut Street, Indianapolis, IN 46202
| | - Kenneth R. Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160
| | - Robert A. White
- Department of Pediatrics, Children’s Mercy Hospitals & Clinics, 2401 Gillham Road, Kansas City, MO 64108
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, 2411 Holmes Street, Kansas City, MO 64108
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24
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Severe anemia in the Nan mutant mouse caused by sequence-selective disruption of erythroid Kruppel-like factor. Proc Natl Acad Sci U S A 2010; 107:15151-6. [PMID: 20696915 DOI: 10.1073/pnas.1004996107] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Studies of mouse models of anemia have long provided fundamental insights into red blood cell formation and function. Here we show that the semidominant mouse mutation Nan ("neonatal anemia") carries a single amino acid change (E339D) within the second zinc finger of the erythroid Krüppel-like factor (EKLF), a critical erythroid regulatory transcription factor. The mutation alters the DNA-binding specificity of EKLF so that it no longer binds promoters of a subset of its DNA targets. Remarkably, even when mutant Nan and wild-type EKLF alleles are expressed at equivalent levels, the mutant form selectively interferes with expression of EKLF target genes whose promoter elements it no longer binds. This interference yields a distorted genetic output and selective protein deficiencies that differ from those seen in EKLF-heterozygous and EKLF-null red blood cells and presents a unique and unexpected mechanism of inherited disease.
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Haploinsufficiency for the erythroid transcription factor KLF1 causes hereditary persistence of fetal hemoglobin. Nat Genet 2010; 42:801-5. [PMID: 20676099 PMCID: PMC2930131 DOI: 10.1038/ng.630] [Citation(s) in RCA: 304] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 06/23/2010] [Indexed: 01/04/2023]
Abstract
Hereditary Persistence of Fetal Hemoglobin (HPFH) is characterized by
persistent high levels of fetal hemoglobin (HbF) in adults. Several contributory
factors, both genetic and environmental, have been identified 1, but others remain elusive. Ten of twenty-seven
members from a Maltese family presented with HPFH. A genome-wide SNP scan
followed by linkage analysis revealed a candidate region on chromosome
19p13.12–13. Sequencing identified a nonsense mutation in the
KLF1 gene, p.K288X, ablating the DNA binding domain of this
key erythroid transcriptional regulator 2.
Only HPFH family members were heterozygote carriers of this mutation. Expression
profiling on primary erythroid progenitors revealed down-regulation of KLF1
target genes in HPFH samples. Functional assays demonstrated that, in addition
to its established role in adult globin expression, KLF1 is a critical activator
of the BCL11A gene, encoding a suppressor of HbF expression
3. These observations provide a
rationale for the effects of KLF1 haploinsufficiency on HbF
levels.
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EKLF directly activates the p21WAF1/CIP1 gene by proximal promoter and novel intronic regulatory regions during erythroid differentiation. Mol Cell Biol 2010; 30:2811-22. [PMID: 20368355 DOI: 10.1128/mcb.01016-09] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The switch from proliferation to differentiation during the terminal stages of erythropoiesis is a tightly controlled process that relies in part on transcription factor-mediated activation of cell cycle components. EKLF is a key transcription factor that is necessary for the initial establishment of the red cell phenotype. Here, we find that EKLF also plays a role during the subsequent differentiation process, as it induces p21(WAF1/CIP1) expression independent of p53 to regulate the changes in the cell cycle underlying erythroid maturation. EKLF activates p21 not only by directly binding to an EKLF site within a previously characterized GC-rich region in the p21 proximal promoter but also by occupancy at a novel, phylogenetically conserved region that contains consensus CACCC core motifs located downstream from the p21 TATA box. Our findings demonstrate that EKLF, likely in coordination with other transcription factors, directly contributes to the complex set of events that occur at the final erythroid cell divisions and accentuates terminal differentiation directly by activation of CDK inhibitors such as p21.
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Zhou Z, Li X, Deng C, Ney PA, Huang S, Bungert J. USF and NF-E2 cooperate to regulate the recruitment and activity of RNA polymerase II in the beta-globin gene locus. J Biol Chem 2010; 285:15894-905. [PMID: 20236933 DOI: 10.1074/jbc.m109.098376] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The human beta-globin gene is expressed at high levels in erythroid cells and regulated by proximal and distal cis-acting DNA elements, including promoter, enhancer, and a locus control region (LCR). Transcription complexes are recruited not only to the globin gene promoters but also to the LCR. Previous studies have implicated the ubiquitously expressed transcription factor USF and the tissue-restricted activator NF-E2 in the recruitment of transcription complexes to the beta-globin gene locus. Here we demonstrate that although USF is required for the efficient association of RNA polymerase II (Pol II) with immobilized LCR templates, USF and NF-E2 together regulate the association of Pol II with the adult beta-globin gene promoter. Recruitment of Pol II to the LCR occurs in undifferentiated murine erythroleukemia cells, but phosphorylation of LCR-associated Pol II at serine 5 of the C-terminal domain is mediated by erythroid differentiation and requires the activity of NF-E2. Furthermore, we provide evidence showing that USF interacts with NF-E2 in erythroid cells. The data provide mechanistic insight into how ubiquitous and tissue-restricted transcription factors cooperate to regulate the recruitment and activity of transcription complexes in a tissue-specific chromatin domain.
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Affiliation(s)
- Zhuo Zhou
- Department of Biochemistry and Molecular Biology, Powell Gene Therapy Center, Center for Epigenetics, and Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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A zinc-finger transcriptional activator designed to interact with the gamma-globin gene promoters enhances fetal hemoglobin production in primary human adult erythroblasts. Blood 2010; 115:3033-41. [PMID: 20190190 DOI: 10.1182/blood-2009-08-240556] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Fetal hemoglobin (HbF) is a potent genetic modifier of the severity of beta-thalassemia and sickle cell anemia. We used an in vitro culture model of human erythropoiesis in which late-stage erythroblasts are derived directly from human CD34(+) hematopoietic cells to evaluate HbF production. This system recapitulates expression of globin genes according to the developmental stage of the originating cell source. When cytokine-mobilized peripheral blood CD34(+) cells from adults were cultured, background levels of HbF were 2% or less. Cultured cells were readily transduced with lentiviral vectors when exposed to vector particles between 48 and 72 hours. Among the genetic elements that may enhance fetal hemoglobin production is an artificial zinc-finger transcription factor, GG1-VP64, designed to interact with the proximal gamma-globin gene promoters. Our data show that lentiviral-mediated, enforced expression of GG1-VP64 under the control of relatively weak erythroid-specific promoters induced significant amounts of HbF (up to 20%) in erythroblasts derived from adult CD34(+) cells without altering their capacity for erythroid maturation and only modestly reducing the total numbers of cells that accumulate in culture after transduction. These observations demonstrate the potential for sequence-specific enhancement of HbF in patients with beta-thalassemia or sickle cell anemia.
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Fromm G, Bulger M. A spectrum of gene regulatory phenomena at mammalian beta-globin gene loci. Biochem Cell Biol 2010; 87:781-90. [PMID: 19898527 DOI: 10.1139/o09-048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The beta-globin gene cluster in mammals, consisting of a set of erythroid-specific, developmentally activated, and (or) silenced genes, has long presented a model system for the investigation of gene regulation. As the number and complexity of models of gene activation and repression have expanded, so too has the complexity of phenomena associated with the regulation of the beta-globin genes. Models for expression from within the locus must account for local (promoter-proximal), distal (enhancer-mediated), and domain-wide components of the regulatory pathways that proceed through mammalian development and erythroid differentiation. In this review, we provide an overview of transcriptional activation, silencing, chromatin structure, and the function of distal regulatory elements involved in the normal developmental regulation of beta-globin gene expression.
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Affiliation(s)
- George Fromm
- Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, NY 14642, USA
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Kim SI, Bresnick EH, Bultman SJ. BRG1 directly regulates nucleosome structure and chromatin looping of the alpha globin locus to activate transcription. Nucleic Acids Res 2009; 37:6019-27. [PMID: 19696073 PMCID: PMC2764439 DOI: 10.1093/nar/gkp677] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
α globin expression must be regulated properly to prevent the occurrence of α-thalassemias, yet many questions remain unanswered regarding the mechanism of transcriptional activation. Identifying factors that regulate chromatin structure of the endogenous α globin locus in developing erythroblasts will provide important mechanistic insight. Here, we demonstrate that the BRG1 catalytic subunit of SWI/SNF-related complexes co-immunoprecipitates with GATA-1 and EKLF in murine fetal liver cells in vivo and is recruited to the far-upstream major-regulatory element (MRE) and α2 promoter. Furthermore, based on our analysis of Brg1null/ENU1 mutant mice, BRG1 regulates DNase I sensitivity, H3ac, and H3K4me2 but not CpG methylation at both sites. Most importantly, BRG1 is required for chromatin loop formation between the MRE and α2 promoter and for maximal RNA Polymerase II occupancy at the α2 promoter. Consequently, Brg1 mutants express α globin mRNA at only 5–10% of wild-type levels and die at mid-gestation. These data identify BRG1 as a chromatin-modifying factor required for nucleosome remodeling and transcriptional activation of the α globin locus. These data also demonstrate that chromatin looping between the MRE and α2 promoter is required as part of the transcriptional activation mechanism.
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Affiliation(s)
- Shin-Il Kim
- Department of Pharmacology, University of Wisconsin School of Medicine and Public Health, Medical Sciences Center, Madison, WI, USA
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31
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Ross J, Bottardi S, Bourgoin V, Wollenschlaeger A, Drobetsky E, Trudel M, Milot E. Differential requirement of a distal regulatory region for pre-initiation complex formation at globin gene promoters. Nucleic Acids Res 2009; 37:5295-308. [PMID: 19567738 PMCID: PMC2760785 DOI: 10.1093/nar/gkp545] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although distal regulatory regions are frequent throughout the genome, the molecular mechanisms by which they act in a promoter-specific manner remain to be elucidated. The human β-globin locus constitutes an extremely well-established multigenic model to investigate this issue. In erythroid cells, the β-globin locus control region (LCR) exerts distal regulatory function by influencing local chromatin organization and inducing high-level expression of individual β-like globin genes. Moreover, in transgenic mice expressing the entire human β-globin locus, deletion of LCR-hypersensitive site 2 (HS2) can alter β-like globin gene expression. Here, we show that abnormal expression of human β-like globin genes in the absence of HS2 is associated with decreased efficacy of pre-initiation complex formation at the human ɛ- and γ-promoters, but not at the β-promoter. This promoter-specific phenomenon is associated with reduced long-range interactions between the HS2-deleted LCR and human γ-promoters. We also find that HS2 is dispensable for high-level human β-gene transcription, whereas deletion of this hypersensitive site can alter locus chromatin organization; therefore the functions exerted by HS2 in transcriptional enhancement and locus chromatin organization are distinct. Overall, our data delineate one mechanism whereby a distal regulatory region provides promoter-specific transcriptional enhancement.
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Affiliation(s)
- Julie Ross
- Faculty of Medicine, University of Montreal, Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec, Canada
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32
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Distinct modes of gene regulation by a cell-specific transcriptional activator. Proc Natl Acad Sci U S A 2009; 106:4213-8. [PMID: 19251649 DOI: 10.1073/pnas.0808347106] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The architectural layout of a eukaryotic RNA polymerase II core promoter plays a role in general transcriptional activation. However, its role in tissue-specific expression is not known. For example, differing modes of its recognition by general transcription machinery can provide an additional layer of control within which a single tissue-restricted transcription factor may operate. Erythroid Kruppel-like factor (EKLF) is a hematopoietic-specific transcription factor that is critical for the activation of subset of erythroid genes. We find that EKLF interacts with TATA binding protein-associated factor 9 (TAF9), which leads to important consequences for expression of adult beta-globin. First, TAF9 functionally supports EKLF activity by enhancing its ability to activate the beta-globin gene. Second, TAF9 interacts with a conserved beta-globin downstream promoter element, and ablation of this interaction by beta-thalassemia-causing mutations decreases its promoter activity and disables superactivation. Third, depletion of EKLF prevents recruitment of TAF9 to the beta-globin promoter, whereas depletion of TAF9 drastically impairs beta-promoter activity. However, a TAF9-independent mode of EKLF transcriptional activation is exhibited by the alpha-hemoglobin-stabilizing protein (AHSP) gene, which does not contain a discernable downstream promoter element. In this case, TAF9 does not enhance EKLF activity and depletion of TAF9 has no effect on AHSP promoter activation. These studies demonstrate that EKLF directs different modes of tissue-specific transcriptional activation depending on the architecture of its target core promoter.
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33
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Perrine SP, Mankidy R, Boosalis MS, Bieker JJ, Faller DV. Erythroid Kruppel-like factor (EKLF) is recruited to the gamma-globin gene promoter as a co-activator and is required for gamma-globin gene induction by short-chain fatty acid derivatives. Eur J Haematol 2009; 82:466-76. [PMID: 19220418 DOI: 10.1111/j.1600-0609.2009.01234.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVES The erythroid Kruppel-like factor (EKLF) is an essential transcription factor for beta-type globin gene switching, and specifically activates transcription of the adult beta-globin gene promoter. We sought to determine if EKLF is also required for activation of the gamma-globin gene by short-chain fatty acid (SCFA) derivatives, which are now entering clinical trials. METHODS The functional and physical interaction of EKLF and co-regulatory molecules with the endogenous human globin gene promoters was studied in primary human erythroid progenitors and cell lines, using chromatin immunoprecipitation (ChIP) assays and genetic manipulation of the levels of EKLF and co-regulators. RESULTS AND CONCLUSIONS Knockdown of EKLF prevents SCFA-induced expression of the gamma-globin promoter in a stably expressed microLCRbeta(pr)R(luc) (A)gamma(pr)F(luc) cassette, and prevents induction of the endogenous gamma-globin gene in primary human erythroid progenitors. EKLF is actively recruited to endogenous gamma-globin gene promoters after exposure of primary human erythroid progenitors, and murine hematopoietic cell lines, to SCFA derivatives. The core ATPase BRG1 subunit of the human SWI/WNF complex, a ubiquitous multimeric complex that regulates gene expression by remodeling nucleosomal structure, is also required for gamma-globin gene induction by SCFA derivatives. BRG1 is actively recruited to the endogenous gamma-globin promoter of primary human erythroid progenitors by exposure to SCFA derivatives, and this recruitment is dependent upon the presence of EKLF. These findings demonstrate that EKLF, and the co-activator BRG1, previously demonstrated to be required for definitive or adult erythropoietic patterns of globin gene expression, are co-opted by SCFA derivatives to activate the fetal globin genes.
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Affiliation(s)
- Susan P Perrine
- Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
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Liang S, Moghimi B, Yang TP, Strouboulis J, Bungert J. Locus control region mediated regulation of adult beta-globin gene expression. J Cell Biochem 2008; 105:9-16. [PMID: 18500726 DOI: 10.1002/jcb.21820] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Many genes residing in gene clusters and expressed in a differentiation or developmental-stage specific manner are regulated by locus control regions (LCRs). These complex genetic regulatory elements are often composed of several DNAse I hypersensitive sites (HS sites) that function together to regulate the expression of several cis-linked genes. Particularly well characterized is the LCR associated with the beta-globin gene locus. The beta-globin LCR consists of five HS sites that are located upstream of the beta-like globin genes. Recent data demonstrate that the LCR is required for the association of the beta-globin gene locus with transcription foci or factories. The observation that RNA polymerase II associates with the LCR in erythroid progenitor or hematopoietic stem cells which do not express the globin genes suggests that the LCR is always in an accessible chromatin configuration during differentiation of erythroid cells. We propose that erythroid specific factors together with ubiquitous proteins mediate a change in chromatin configuration that juxtaposes the globin genes and the LCR. The proximity then facilitates the transfer of activities from the LCR to the globin genes. In this article we will discuss recent observations regarding beta-globin locus activation with a particular emphasis on LCR mediated activation of adult beta-globin gene expression.
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Affiliation(s)
- Shermi Liang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Center for Mammalian Genetics, Genetics Institute, Shands Cancer Center, Gainesville, Florida 32610, USA
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35
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Stem cell–specific epigenetic priming and B cell–specific transcriptional activation at the mouse Cd19 locus. Blood 2008; 112:1673-82. [DOI: 10.1182/blood-2008-02-142786] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Low-level expression of multiple lineage-specific genes is a hallmark of hematopoietic stem cells (HSCs). HSCs predominantly express genes specific for the myeloid or megakaryocytic-erythroid lineages, whereas the transcription of lymphoid specific genes appears to begin after lymphoid specification. It has been demonstrated for a number of genes that epigenetic priming occurs before gene expression and lineage specification; however, little is known about how epigenetic priming of lymphoid genes is regulated. To address the question of how B cell–restricted expression is established, we studied activation of the Cd19 gene during hematopoietic development. We identified a B cell–specific upstream enhancer and showed that the developmental regulation of Cd19 expression involves precisely coordinated alterations in transcription factor binding and chromatin remodeling at Cd19 cis-regulatory elements. In multipotent progenitor cells, Cd19 chromatin is first remodeled at the upstream enhancer, and this remodeling is associated with binding of E2A. This is followed by the binding of EBF and PAX5 during B-cell differentiation. The Cd19 promoter is transcriptionally activated only after PAX5 binding. Our experiments give important mechanistic insights into how widely expressed and B lineage–specific transcription factors cooperate to mediate the developmental regulation of lymphoid genes during hematopoiesis.
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36
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Acetylation of EKLF is essential for epigenetic modification and transcriptional activation of the beta-globin locus. Mol Cell Biol 2008; 28:6160-70. [PMID: 18710946 DOI: 10.1128/mcb.00919-08] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Posttranslational modifications of transcription factors provide alternate protein interaction platforms that lead to varied downstream effects. We have investigated how the acetylation of EKLF plays a role in its ability to alter the beta-like globin locus chromatin structure and activate transcription of the adult beta-globin gene. By establishing an EKLF-null erythroid line whose closed beta-locus chromatin structure and silent beta-globin gene status can be rescued by retroviral infection of EKLF, we demonstrate the importance of EKLF acetylation at lysine 288 in the recruitment of CBP to the locus, modification of histone H3, occupancy by EKLF, opening of the chromatin structure, and transcription of adult beta-globin. We also find that EKLF helps to coordinate this process by the specific association of its zinc finger domain with the histone H3 amino terminus. Although EKLF interacts equally well with H3.1 and H3.3, we find that only H3.3 is enriched at the adult beta-globin promoter. These data emphasize the critical nature of lysine acetylation in transcription factor activity and enable us to propose a model of how modified EKLF integrates coactivators, chromatin remodelers, and nucleosomal components to alter epigenetic chromatin structure and stimulate transcription.
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37
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Lohmann F, Bieker JJ. Activation of Eklf expression during hematopoiesis by Gata2 and Smad5 prior to erythroid commitment. Development 2008; 135:2071-82. [PMID: 18448565 DOI: 10.1242/dev.018200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The hierarchical progression of stem and progenitor cells to their more-committed progeny is mediated through cell-to-cell signaling pathways and intracellular transcription factor activity. However, the mechanisms that govern the genetic networks underlying lineage fate decisions and differentiation programs remain poorly understood. Here we show how integration of Bmp4 signaling and Gata factor activity controls the progression of hematopoiesis, as exemplified by the regulation of Eklf during establishment of the erythroid lineage. Utilizing transgenic reporter assays in differentiating mouse embryonic stem cells as well as in the murine fetal liver, we demonstrate that Eklf expression is initiated prior to erythroid commitment during hematopoiesis. Applying phylogenetic footprinting and in vivo binding studies in combination with newly developed loss-of-function technology in embryoid bodies, we find that Gata2 and Smad5 cooperate to induce Eklf in a progenitor population, followed by a switch to Gata1-controlled regulation of Eklf transcription upon erythroid commitment. This stage- and lineage-dependent control of Eklf expression defines a novel role for Eklf as a regulator of lineage fate decisions during hematopoiesis.
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Affiliation(s)
- Felix Lohmann
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, Box 1020, 1 Gustave Levy Place, New York, NY 10029, USA
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38
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Brown E, Malakar S, Krebs JE. How many remodelers does it take to make a brain? Diverse and cooperative roles of ATP-dependent chromatin-remodeling complexes in development. Biochem Cell Biol 2008; 85:444-62. [PMID: 17713580 DOI: 10.1139/o07-059] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The development of a metazoan from a single-celled zygote to a complex multicellular organism requires elaborate and carefully regulated programs of gene expression. However, the tight packaging of genomic DNA into chromatin makes genes inaccessible to the cellular machinery and must be overcome by the processes of chromatin remodeling; in addition, chromatin remodeling can preferentially silence genes when their expression is not required. One class of chromatin remodelers, ATP-dependent chromatin-remodeling enzymes, can slide nucleosomes along the DNA to make specific DNA sequences accessible or inaccessible to regulators at a particular stage of development. While all ATPases in the SWI2/SNF2 superfamily share the fundamental ability to alter DNA accessibility in chromatin, they do not act alone, but rather, are subunits of a large assortment of protein complexes. Recent studies illuminate common themes by which the subunit compositions of chromatin-remodeling complexes specify the developmental roles that chromatin remodelers play in specific tissues and at specific stages of development, in response to specific signaling pathways and transcription factors. In this review, we will discuss the known roles in metazoan development of 3 major subfamilies of chromatin-remodeling complexes: the SNF2, ISWI, and CHD subfamilies.
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Affiliation(s)
- Elvin Brown
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
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39
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Wozniak RJ, Bresnick EH. Chapter 3 Epigenetic Control of Complex Loci During Erythropoiesis. Curr Top Dev Biol 2008; 82:55-83. [DOI: 10.1016/s0070-2153(07)00003-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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Palstra R, de Laat W, Grosveld F. Chapter 4 β‐Globin Regulation and Long‐Range Interactions. LONG-RANGE CONTROL OF GENE EXPRESSION 2008; 61:107-42. [DOI: 10.1016/s0065-2660(07)00004-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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41
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Kooren J, Palstra RJ, Klous P, Splinter E, von Lindern M, Grosveld F, de Laat W. Beta-globin active chromatin Hub formation in differentiating erythroid cells and in p45 NF-E2 knock-out mice. J Biol Chem 2007; 282:16544-52. [PMID: 17428799 DOI: 10.1074/jbc.m701159200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of the beta-globin genes proceeds from basal to exceptionally high levels during erythroid differentiation in vivo. High expression is dependent on the locus control region (LCR) and coincides with more frequent LCR-gene contacts. These contacts are established in the context of an active chromatin hub (ACH), a spatial chromatin configuration in which the LCR, together with other regulatory sequences, loops toward the active beta-globin-like genes. Here, we used recently established I/11 cells as a model system that faithfully recapitulates the in vivo erythroid differentiation program to study the molecular events that accompany and underlie ACH formation. Upon I/11 cell induction, histone modifications changed, the ACH was formed, and the beta-globin-like genes were transcribed at rates similar to those observed in vivo. The establishment of frequent LCR-gene contacts coincided with a more efficient loading of polymerase onto the beta-globin promoter. Binding of the transcription factors GATA-1 and EKLF to the locus, although previously shown to be required, was not sufficient for ACH formation. Moreover, we used knock-out mice to show that the erythroid transcription factor p45 NF-E2, which has been implicated in beta-globin gene regulation, is dispensable for beta-globin ACH formation.
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Affiliation(s)
- Jurgen Kooren
- Department of Cell Biology, Erasmus Medical Center, P. O. Box 2040, 3000 CA Rotterdam, The Netherlands
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