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Morgan RA, Ma F, Unti MJ, Brown D, Ayoub PG, Tam C, Lathrop L, Aleshe B, Kurita R, Nakamura Y, Senadheera S, Wong RL, Hollis RP, Pellegrini M, Kohn DB. Creating New β-Globin-Expressing Lentiviral Vectors by High-Resolution Mapping of Locus Control Region Enhancer Sequences. Mol Ther Methods Clin Dev 2020; 17:999-1013. [PMID: 32426415 PMCID: PMC7225380 DOI: 10.1016/j.omtm.2020.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/18/2022]
Abstract
Hematopoietic stem cell gene therapy is a promising approach for treating disorders of the hematopoietic system. Identifying combinations of cis-regulatory elements that do not impede packaging or transduction efficiency when included in lentiviral vectors has proven challenging. In this study, we deploy LV-MPRA (lentiviral vector-based, massively parallel reporter assay), an approach that simultaneously analyzes thousands of synthetic DNA fragments in parallel to identify sequence-intrinsic and lineage-specific enhancer function at near-base-pair resolution. We demonstrate the power of LV-MPRA in elucidating the boundaries of previously unknown intrinsic enhancer sequences of the human β-globin locus control region. Our approach facilitated the rapid assembly of novel therapeutic βAS3-globin lentiviral vectors harboring strong lineage-specific recombinant control elements capable of correcting a mouse model of sickle cell disease. LV-MPRA can be used to map any genomic locus for enhancer activity and facilitates the rapid development of therapeutic vectors for treating disorders of the hematopoietic system or other specific tissues and cell types.
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Affiliation(s)
- Richard A. Morgan
- Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feiyang Ma
- Molecular Biology Institute Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mildred J. Unti
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Devin Brown
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Paul George Ayoub
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Curtis Tam
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lindsay Lathrop
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bamidele Aleshe
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Shantha Senadheera
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ryan L. Wong
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Roger P. Hollis
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Molecular Biology Institute Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donald B. Kohn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- The Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
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2
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Morgan RA, Unti MJ, Aleshe B, Brown D, Osborne KS, Koziol C, Ayoub PG, Smith OB, O'Brien R, Tam C, Miyahira E, Ruiz M, Quintos JP, Senadheera S, Hollis RP, Kohn DB. Improved Titer and Gene Transfer by Lentiviral Vectors Using Novel, Small β-Globin Locus Control Region Elements. Mol Ther 2019; 28:328-340. [PMID: 31628051 DOI: 10.1016/j.ymthe.2019.09.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/11/2019] [Accepted: 09/19/2019] [Indexed: 01/11/2023] Open
Abstract
β-globin lentiviral vectors (β-LV) have faced challenges in clinical translation for gene therapy of sickle cell disease (SCD) due to low titer and sub-optimal gene transfer to hematopoietic stem and progenitor cells (HSPCs). To overcome the challenge of preserving efficacious expression while increasing vector performance, we used published genomic and epigenomic data available through ENCODE to redefine enhancer element boundaries of the β-globin locus control region (LCR) to construct novel ENCODE core sequences. These novel LCR elements were used to design a β-LV of reduced proviral length, termed CoreGA-AS3-FB, produced at higher titers and possessing superior gene transfer to HSPCs when compared to the full-length parental β-LV at equal MOI. At low vector copy number, vectors containing the ENCODE core sequences were capable of reversing the sickle phenotype in a mouse model of SCD. These studies provide a β-LV that will be beneficial for gene therapy of SCD by significantly reducing the cost of vector production and extending the vector supply.
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Affiliation(s)
- Richard A Morgan
- Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mildred J Unti
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bamidele Aleshe
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Devin Brown
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kyle S Osborne
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Colin Koziol
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Paul G Ayoub
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Oliver B Smith
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rachel O'Brien
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Curtis Tam
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Miyahira
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marlene Ruiz
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason P Quintos
- CSUN-UCLA Stem Cell Scientist Training Program, California State University, Northridge, Northridge, CA 91330, USA
| | - Shantha Senadheera
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Roger P Hollis
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donald B Kohn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; The Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
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3
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Weber L, Poletti V, Magrin E, Antoniani C, Martin S, Bayard C, Sadek H, Felix T, Meneghini V, Antoniou MN, El-Nemer W, Mavilio F, Cavazzana M, Andre-Schmutz I, Miccio A. An Optimized Lentiviral Vector Efficiently Corrects the Human Sickle Cell Disease Phenotype. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 10:268-280. [PMID: 30140714 PMCID: PMC6105766 DOI: 10.1016/j.omtm.2018.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/29/2018] [Indexed: 12/17/2022]
Abstract
Autologous transplantation of hematopoietic stem cells transduced with a lentiviral vector (LV) expressing an anti-sickling HBB variant is a potential treatment for sickle cell disease (SCD). With a clinical trial as our ultimate goal, we generated LV constructs containing an anti-sickling HBB transgene (HBBAS3), a minimal HBB promoter, and different combinations of DNase I hypersensitive sites (HSs) from the locus control region (LCR). Hematopoietic stem progenitor cells (HSPCs) from SCD patients were transduced with LVs containing either HS2 and HS3 (β-AS3) or HS2, HS3, and HS4 (β-AS3 HS4). The inclusion of the HS4 element drastically reduced vector titer and infectivity in HSPCs, with negligible improvement of transgene expression. Conversely, the LV containing only HS2 and HS3 was able to efficiently transduce SCD bone marrow and Plerixafor-mobilized HSPCs, with anti-sickling HBB representing up to ∼60% of the total HBB-like chains. The expression of the anti-sickling HBB and the reduced incorporation of the βS-chain in hemoglobin tetramers allowed up to 50% reduction in the frequency of RBC sickling under hypoxic conditions. Together, these results demonstrate the ability of a high-titer LV to express elevated levels of a potent anti-sickling HBB transgene ameliorating the SCD cell phenotype.
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Affiliation(s)
- Leslie Weber
- Laboratory of Human Lymphohematopoiesis, INSERM UMR_S1163, 75015 Paris, France.,Paris Diderot University - Sorbonne Paris Cité, 75015 Paris, France
| | | | - Elisa Magrin
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Chiara Antoniani
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.,Laboratory of chromatin and gene regulation during development, INSERM UMR_S1163, 75015 Paris, France
| | | | - Charles Bayard
- Laboratory of Human Lymphohematopoiesis, INSERM UMR_S1163, 75015 Paris, France
| | - Hanem Sadek
- Laboratory of Human Lymphohematopoiesis, INSERM UMR_S1163, 75015 Paris, France
| | - Tristan Felix
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.,Laboratory of chromatin and gene regulation during development, INSERM UMR_S1163, 75015 Paris, France
| | - Vasco Meneghini
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.,Laboratory of chromatin and gene regulation during development, INSERM UMR_S1163, 75015 Paris, France
| | | | - Wassim El-Nemer
- Biologie Intégrée du Globule Rouge, INSERM UMR_S1134, Paris Diderot University, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles, 75015 Paris, France.,Institut National de la Transfusion Sanguine, 75015 Paris, France.,Laboratoire d'Excellence GR-Ex, 75015 Paris, France
| | - Fulvio Mavilio
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.,Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Marina Cavazzana
- Laboratory of Human Lymphohematopoiesis, INSERM UMR_S1163, 75015 Paris, France.,Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Isabelle Andre-Schmutz
- Laboratory of Human Lymphohematopoiesis, INSERM UMR_S1163, 75015 Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Annarita Miccio
- Genethon, INSERM UMR951, 91000 Evry, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.,Laboratory of chromatin and gene regulation during development, INSERM UMR_S1163, 75015 Paris, France
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4
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Iarovaia OV, Kovina AP, Petrova NV, Razin SV, Ioudinkova ES, Vassetzky YS, Ulianov SV. Genetic and Epigenetic Mechanisms of β-Globin Gene Switching. BIOCHEMISTRY (MOSCOW) 2018; 83:381-392. [PMID: 29626925 DOI: 10.1134/s0006297918040090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vertebrates have multiple forms of hemoglobin that differ in the composition of their polypeptide chains. During ontogenesis, the composition of these subunits changes. Genes encoding different α- and β-polypeptide chains are located in two multigene clusters on different chromosomes. Each cluster contains several genes that are expressed at different stages of ontogenesis. The phenomenon of stage-specific transcription of globin genes is referred to as globin gene switching. Mechanisms of expression switching, stage-specific activation, and repression of transcription of α- and β-globin genes are of interest from both theoretical and practical points of view. Alteration of balanced expression of globin genes, which usually occurs due to damage to adult β-globin genes, leads to development of severe diseases - hemoglobinopathies. In most cases, reactivation of the fetal hemoglobin gene in patients with β-thalassemia and sickle cell disease can reduce negative consequences of irreversible alterations of expression of the β-globin genes. This review focuses on the current state of research on genetic and epigenetic mechanisms underlying stage-specific switching of β-globin genes.
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Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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5
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Xie S, Duan J, Li B, Zhou P, Hon GC. Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells. Mol Cell 2017; 66:285-299.e5. [PMID: 28416141 DOI: 10.1016/j.molcel.2017.03.007] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 01/18/2017] [Accepted: 03/07/2017] [Indexed: 12/25/2022]
Abstract
The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure their endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors of target gene expression. Binding of p300 and RNAPII are key features of these constituents. We determine two key parameters of enhancer activity in single cells: their penetrance in a population and their contribution to expression in these cells. Through combinatorial interrogation, we find that simultaneous repression of multiple weak constituents can alter super-enhancer activity in a manner greatly exceeding repression of individual constituents.
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Affiliation(s)
- Shiqi Xie
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pei Zhou
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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6
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Peterson KR, Fedosyuk H, Harju-Baker S. LCR 5' hypersensitive site specificity for globin gene activation within the active chromatin hub. Nucleic Acids Res 2012; 40:11256-69. [PMID: 23042246 PMCID: PMC3526258 DOI: 10.1093/nar/gks900] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The DNaseI hypersensitive sites (HSs) of the human β-globin locus control region (LCR) may function as part of an LCR holocomplex within a larger active chromatin hub (ACH). Differential activation of the globin genes during development may be controlled in part by preferential interaction of each gene with specific individual HSs during globin gene switching, a change in conformation of the LCR holocomplex, or both. To distinguish between these possibilities, human β-globin locus yeast artificial chromosome (β-YAC) lines were produced in which the ε-globin gene was replaced with a second marked β-globin gene (βm), coupled to an intact LCR, a 5′HS3 complete deletion (5′ΔHS3) or a 5′HS3 core deletion (5′ΔHS3c). The 5′ΔHS3c mice expressed βm-globin throughout development; γ-globin was co-expressed in the embryonic yolk sac, but not in the fetal liver; and wild-type β-globin was co-expressed in adult mice. Although the 5′HS3 core was not required for βm-globin expression, previous work showed that the 5′HS3 core is necessary for ε-globin expression during embryonic erythropoiesis. A similar phenotype was observed in 5′HS complete deletion mice, except βm-globin expression was higher during primitive erythropoiesis and γ-globin expression continued into fetal definitive erythropoiesis. These data support a site specificity model of LCR HS-globin gene interaction.
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Affiliation(s)
- Kenneth R Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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7
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Fleetwood MR, Ho Y, Cooke NE, Liebhaber SA. DNase I hypersensitive site II of the human growth hormone locus control region mediates an essential and distinct long-range enhancer function. J Biol Chem 2012; 287:25454-65. [PMID: 22669946 DOI: 10.1074/jbc.m112.365825] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Locus control regions (LCRs) comprise sets of DNA elements capable of establishing autonomous chromatin domains that support robust and physiologically appropriate expression of target genes, often working over extensive distances. Human growth hormone (hGH-N) expression in the pituitary is under the regulation of a well characterized LCR containing four DNase I hypersensitive sites (HSs). The two pituitary-specific HS, HSI and HSII, are located 14.5 and 15.5 kb 5' to the hGH-N promoter. HSI is essential for activation of hGH-N during pituitary development and for sustaining robust activity in the adult. To determine whether the closely linked HSII has a role in hGH-N expression, it was deleted from a previously validated hGH/P1 transgene. Analysis of three independent hGH/P1(ΔHSII) transgenic mouse lines revealed that this deletion had no adverse effect on the formation of HSI, yet resulted in a substantial loss (70%) in hGH-N mRNA expression. This loss of expression was accompanied by a corresponding reduction in recruitment of the pituitary-specific transcription factor Pit-1 to the hGH-N promoter and a selective decrease in promoter occupancy of the elongation-linked isoform of RNA polymerase II. Sufficiency of HSI and HSII in LCR activity was explored by establishing two additional sets of mouse transgenic lines in which DNA segments containing these HS were positioned within the λ phage genome. In this "neutral" DNA context, HSII was required for the recruitment of HAT activity. These data establish HSII as a nonredundant component of the hGH LCR essential for establishment of robust levels of hGH-N gene expression.
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Affiliation(s)
- Margaret R Fleetwood
- Department of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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8
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Kim S, Kim YW, Shim SH, Kim CG, Kim A. Chromatin structure of the LCR in the human β-globin locus transcribing the adult δ- and β-globin genes. Int J Biochem Cell Biol 2011; 44:505-13. [PMID: 22178075 DOI: 10.1016/j.biocel.2011.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 11/21/2011] [Accepted: 12/01/2011] [Indexed: 11/15/2022]
Abstract
The β-like globin genes are transcribed in a developmental stage specific fashion in erythroid cells. The specific transcription of globin genes is conferred by the locus control region (LCR), but the chromatin structure of the LCR in the human adult β-globin locus transcribing the δ- and β-globin genes is not clear. Here, we employed hybrid MEL cells that contain a human chromosome 11. The δ- and β-globin genes were highly transcribed in hybrid MEL/ch11 cells after transcriptional induction. LCR HS3 and HS2 were strongly occupied by erythroid specific transcriptional activators and co-factors in the induced locus. These HSs, but not HS4 and HS1, were in close proximity with the active globin genes as revealed by high resolution 3C experiments. The active features at HS3 were markedly established after transcriptional induction, while HS2 was in a relatively active conformation before the induction. Unexpectedly, HS1 did not show notable active features except histone hyperacetylation. Taken together, the LCR of the human β-globin locus transcribing the adult δ- and β-globin genes has HS specific chromatin structure. The structure at each HS, which is different from the locus transcribing the fetal globin genes, might relate to its role in transcribing the adult genes.
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Affiliation(s)
- Seoyeon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan 609-735, Republic of Korea
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9
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Karmakar S, Mahajan MC, Schulz V, Boyapaty G, Weissman SM. A multiprotein complex necessary for both transcription and DNA replication at the β-globin locus. EMBO J 2010; 29:3260-71. [PMID: 20808282 DOI: 10.1038/emboj.2010.204] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 07/29/2010] [Indexed: 12/17/2022] Open
Abstract
DNA replication, repair, transcription and chromatin structure are intricately associated nuclear processes, but the molecular links between these events are often obscure. In this study, we have surveyed the protein complexes that bind at β-globin locus control region, and purified and characterized the function of one such multiprotein complex from human erythroleukemic K562 cells. We further validated the existence of this complex in human CD34+ cell-derived normal erythroid cells. This complex contains ILF2/ILF3 transcription factors, p300 acetyltransferase and proteins associated with DNA replication, transcription and repair. RNAi knockdown of ILF2, a DNA-binding component of this complex, abrogates the recruitment of the complex to its cognate DNA sequence and inhibits transcription, histone acetylation and usage of the origin of DNA replication at the β-globin locus. These results imply a direct link between mammalian DNA replication, transcription and histone acetylation mediated by a single multiprotein complex.
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Affiliation(s)
- Subhradip Karmakar
- Department of Genetics, The Anlyan Center, Yale University School of Medicine, New Haven, CT, USA
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10
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Shimotsuma M, Okamura E, Matsuzaki H, Fukamizu A, Tanimoto K. DNase I hypersensitivity and epsilon-globin transcriptional enhancement are separable in locus control region (LCR) HS1 mutant human beta-globin YAC transgenic mice. J Biol Chem 2010; 285:14495-503. [PMID: 20231293 DOI: 10.1074/jbc.m110.116525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of the five beta-like globin genes (epsilon, Ggamma, Agamma, delta, beta) in the human beta-globin locus depends on enhancement by the locus control region, which consists of five DNase I hypersensitive sites (5'HS1 through 5'HS5). We report here a novel enhancer activity in 5'HS1 that appears to be potent in transfected K562 cells. Deletion analyses identified a core activating element that bound to GATA-1, and a two-nucleotide mutation that disrupted GATA-1 binding in vitro abrogated 5'HS1 enhancer activity in transfection experiments. To determine the in vivo role of this GATA site, we generated multiple lines of human beta-globin YAC transgenic mice bearing the same two-nucleotide mutation. In the mutant mice, epsilon-, but not gamma-globin, gene expression in primitive erythroid cells was severely attenuated, while adult beta-globin gene expression in definitive erythroid cells was unaffected. Interestingly, DNaseI hypersensitivity near the 5'HS1 mutant sequence was eliminated in definitive erythroid cells, whereas it was only mildly affected in primitive erythroid cells. We therefore conclude that, although the GATA site in 5'HS1 is critical for efficient epsilon-globin gene expression, hypersensitive site formation per se is independent of 5'HS1 function, if any, in definitive erythroid cells.
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Affiliation(s)
- Motoshi Shimotsuma
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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11
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Fang X, Yin W, Xiang P, Han H, Stamatoyannopoulos G, Li Q. The higher structure of chromatin in the LCR of the beta-globin locus changes during development. J Mol Biol 2009; 394:197-208. [PMID: 19781549 DOI: 10.1016/j.jmb.2009.09.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 09/14/2009] [Accepted: 09/17/2009] [Indexed: 11/17/2022]
Abstract
The beta-globin locus control region (LCR) is able to enhance the expression of all globin genes throughout the course of development. However, the chromatin structure of the LCR at the different developmental stages is not well defined. We report DNase I and micrococcal nuclease hypersensitivity, chromatin immunoprecipitation analyses for histones H2A, H2B, H3, and H4, and 3C (chromatin conformation capture) assays of the normal and mutant beta-globin loci, which demonstrate that nucleosomes at the DNase I hypersensitive sites of the LCR could be either depleted or retained depending on the stages of development. Furthermore, MNase sensitivity and 3C assays suggest that the LCR chromatin is more open in embryonic erythroblasts than in definitive erythroblasts at the primary- and secondary-structure levels; however, the LCR chromatin is packaged more tightly in embryonic erythroblasts than in definitive erythroblasts at the tertiary chromatin level. Our study provides the first evidence that the occupancy of nucleosomes at a DNase I hypersensitive site is a developmental stage-related event and that embryonic and adult cells possess distinct chromatin structures of the LCR.
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Affiliation(s)
- Xiangdong Fang
- Division of Medical Genetics, Department of Medicine, Box 357720, University of Washington, Seattle, WA 98195, USA
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Lisowski L, Sadelain M. Current status of globin gene therapy for the treatment of β-thalassaemia. Br J Haematol 2008; 141:335-45. [DOI: 10.1111/j.1365-2141.2008.07098.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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