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Lee J, Simpson L, Li Y, Becker S, Zou F, Zhang X, Bai L. Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579062. [PMID: 38370634 PMCID: PMC10871269 DOI: 10.1101/2024.02.06.579062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3D genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes are clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.
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Affiliation(s)
- James Lee
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Leman Simpson
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yi Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Samuel Becker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Fan Zou
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA
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2
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Zhao H, Li D, Xiao X, Liu C, Chen G, Su X, Yan Z, Gu S, Wang Y, Li G, Feng J, Li W, Chen P, Yang J, Li Q. Pluripotency state transition of embryonic stem cells requires the turnover of histone chaperone FACT on chromatin. iScience 2024; 27:108537. [PMID: 38213626 PMCID: PMC10783625 DOI: 10.1016/j.isci.2023.108537] [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: 05/30/2023] [Revised: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 01/13/2024] Open
Abstract
The differentiation of embryonic stem cells (ESCs) begins with the transition from the naive to the primed state. The formative state was recently established as a critical intermediate between the two states. Here, we demonstrate the role of the histone chaperone FACT in regulating the naive-to-formative transition. We found that the Q265K mutation in the FACT subunit SSRP1 increased the binding of FACT to histone H3-H4, impaired nucleosome disassembly in vitro, and reduced the turnover of FACT on chromatin in vivo. Strikingly, mouse ESCs harboring this mutation showed elevated naive-to-formative transition. Mechanistically, the SSRP1-Q265K mutation enriched FACT at the enhancers of formative-specific genes to increase targeted gene expression. Together, these findings suggest that the turnover of FACT on chromatin is crucial for regulating the enhancers of formative-specific genes, thereby mediating the naive-to-formative transition. This study highlights the significance of FACT in fine-tuning cell fate transition during early development.
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Affiliation(s)
- Hang Zhao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Di Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xue Xiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guifang Chen
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Xiaoyu Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhenxin Yan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shijia Gu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yizhou Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jiayi Yang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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3
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Wang X, McKillop WM, Dlugi TA, Faber ML, Alvarez-Argote J, Chambers CB, Wilber A, Medin JA. A mass spectrometry assay for detection of endogenous and lentiviral engineered hemoglobin in cultured cells and sickle cell disease mice. J Gene Med 2024; 26:e3567. [PMID: 37455676 DOI: 10.1002/jgm.3567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
Sickle cell disease (SCD) results from a sequence defect in the β-globin chain of adult hemoglobin (HbA) leading to expression of sickle hemoglobin (HbS). It is traditionally diagnosed by cellulose-acetate hemoglobin electrophoresis or high-performance liquid chromatography. While clinically useful, these methods have both sensitivity and specificity limitations. We developed a novel mass spectrometry (MS) method for the rapid, sensitive and highly quantitative detection of endogenous human β-globin and sickle hβ-globin, as well as lentiviral-encoded therapeutic hβAS3-globin in cultured cells and small quantities of mouse peripheral blood. The MS methods were used to phenotype homozygous HbA (AA), heterozygous HbA-HbS (AS) and homozygous HbS (SS) Townes SCD mice and detect lentiviral vector-encoded hβAS3-globin in transduced mouse erythroid cell cultures and transduced human CD34+ cells after erythroid differentiation. hβAS3-globin was also detected in peripheral blood 6 weeks post-transplant of transduced Townes SS bone marrow cells into syngeneic Townes SS mice and persisted for over 20 weeks post-transplant. As several genome-editing and gene therapy approaches for severe hemoglobin disorders are currently in clinical trials, this MS method will be useful for patient assessment before treatment and during follow-up.
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Affiliation(s)
- Xuejun Wang
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - William M McKillop
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Theresa A Dlugi
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mary L Faber
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Juliana Alvarez-Argote
- Department of Medicine, Division of Hematology-Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Christopher B Chambers
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Andrew Wilber
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Jeffrey A Medin
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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4
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Martell DJ, Merens HE, Caulier A, Fiorini C, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NBA, Babbs C, Higgs DR, Sankaran VG, Churchman LS. RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. Dev Cell 2023; 58:2112-2127.e4. [PMID: 37586368 PMCID: PMC10615711 DOI: 10.1016/j.devcel.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/23/2023] [Accepted: 07/25/2023] [Indexed: 08/18/2023]
Abstract
Controlled release of promoter-proximal paused RNA polymerase II (RNA Pol II) is crucial for gene regulation. However, studying RNA Pol II pausing is challenging, as pause-release factors are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H, which encodes SPT5, in individuals with β-thalassemia. During erythropoiesis in healthy human cells, cell cycle genes were highly paused as cells transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, RNA Pol II pause release was globally disrupted, and as cells began transitioning from progenitors to precursors, differentiation was delayed, accompanied by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, identifying a role for RNA Pol II pausing in temporally coordinating the cell cycle and erythroid differentiation.
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Affiliation(s)
- Danya J Martell
- Department of Genetics, Harvard University, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hope E Merens
- Department of Genetics, Harvard University, Boston, MA, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Karine Choquet
- Department of Genetics, Harvard University, Boston, MA, USA
| | - Giovanna Graziadei
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Brancaleoni
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Noémi B A Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Papaioannou I, Owen JS, Yáñez‐Muñoz RJ. Clinical applications of gene therapy for rare diseases: A review. Int J Exp Pathol 2023; 104:154-176. [PMID: 37177842 PMCID: PMC10349259 DOI: 10.1111/iep.12478] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 03/08/2023] [Accepted: 04/16/2023] [Indexed: 05/15/2023] Open
Abstract
Rare diseases collectively exact a high toll on society due to their sheer number and overall prevalence. Their heterogeneity, diversity, and nature pose daunting clinical challenges for both management and treatment. In this review, we discuss recent advances in clinical applications of gene therapy for rare diseases, focusing on a variety of viral and non-viral strategies. The use of adeno-associated virus (AAV) vectors is discussed in the context of Luxturna, licenced for the treatment of RPE65 deficiency in the retinal epithelium. Imlygic, a herpes virus vector licenced for the treatment of refractory metastatic melanoma, will be an example of oncolytic vectors developed against rare cancers. Yescarta and Kymriah will showcase the use of retrovirus and lentivirus vectors in the autologous ex vivo production of chimeric antigen receptor T cells (CAR-T), licenced for the treatment of refractory leukaemias and lymphomas. Similar retroviral and lentiviral technology can be applied to autologous haematopoietic stem cells, exemplified by Strimvelis and Zynteglo, licenced treatments for adenosine deaminase-severe combined immunodeficiency (ADA-SCID) and β-thalassaemia respectively. Antisense oligonucleotide technologies will be highlighted through Onpattro and Tegsedi, RNA interference drugs licenced for familial transthyretin (TTR) amyloidosis, and Spinraza, a splice-switching treatment for spinal muscular atrophy (SMA). An initial comparison of the effectiveness of AAV and oligonucleotide therapies in SMA is possible with Zolgensma, an AAV serotype 9 vector, and Spinraza. Through these examples of marketed gene therapies and gene cell therapies, we will discuss the expanding applications of such novel technologies to previously intractable rare diseases.
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Affiliation(s)
| | - James S. Owen
- Division of MedicineUniversity College LondonLondonUK
| | - Rafael J. Yáñez‐Muñoz
- AGCTlab.orgCentre of Gene and Cell TherapyCentre for Biomedical SciencesDepartment of Biological SciencesSchool of Life Sciences and the EnvironmentRoyal Holloway University of LondonEghamUK
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6
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Martell DJ, Merens HE, Fiorini C, Caulier A, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NB, Babbs C, Higgs DR, Sankaran VG, Churchman LS. RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.03.23286760. [PMID: 36945604 PMCID: PMC10029049 DOI: 10.1101/2023.03.03.23286760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The controlled release of promoter-proximal paused RNA polymerase II (Pol II) into productive elongation is a major step in gene regulation. However, functional analysis of Pol II pausing is difficult because factors that regulate pause release are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H , which encodes SPT5, in individuals with β-thalassemia unlinked to HBB mutations. During erythropoiesis in healthy human cells, cell cycle genes were highly paused at the transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, Pol II pause release was globally disrupted, and the transition from progenitors to precursors was delayed, marked by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, revealing a role for Pol II pausing in the temporal coordination between the cell cycle and differentiation.
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Affiliation(s)
- Danya J Martell
- Harvard University, Department of Genetics, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Hope E Merens
- Harvard University, Department of Genetics, Boston, MA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Giovanna Graziadei
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Brancaleoni
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Noémi Ba Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
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7
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Garg H, Tatiossian KJ, Peppel K, Kato GJ, Herzog E. Gene therapy as the new frontier for Sickle Cell Disease. Curr Med Chem 2021; 29:453-466. [PMID: 34047257 DOI: 10.2174/0929867328666210527092456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/28/2021] [Accepted: 04/11/2021] [Indexed: 11/22/2022]
Abstract
Sickle Cell Disease (SCD) is one of the most common monogenic disorders caused by a point mutation in the β-globin gene. This mutation results in polymerization of hemoglobin (Hb) under reduced oxygenation conditions, causing rigid sickle-shaped RBCs and hemolytic anemia. This clearly defined fundamental molecular mechanism makes SCD a prototypical target for precision therapy. Both the mutant β-globin protein and its downstream pathophysiology are pharmacological targets of intensive research. SCD also is a disease well-suited for biological interventions like gene therapy. Recent advances in hematopoietic stem cell (HSC) transplantation and gene therapy platforms, like Lentiviral vectors and gene editing strategies, expand the potentially curative options for patients with SCD. This review discusses the recent advances in precision therapy for SCD and the preclinical and clinical advances in autologous HSC gene therapy for SCD.
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Affiliation(s)
- Himanshu Garg
- CSL Behring, 1020 1St Ave, King of Prussia, PA 19406, United States
| | | | - Karsten Peppel
- CSL Behring, 1020 1St Ave, King of Prussia, PA 19406, United States
| | - Gregory J Kato
- CSL Behring, 1020 1St Ave, King of Prussia, PA 19406, United States
| | - Eva Herzog
- CSL Behring, 1020 1St Ave, King of Prussia, PA 19406, United States
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8
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Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021; 22:108. [PMID: 33858480 PMCID: PMC8051032 DOI: 10.1186/s13059-021-02322-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.
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Affiliation(s)
- Anil Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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9
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Choi J, Lysakovskaia K, Stik G, Demel C, Söding J, Tian TV, Graf T, Cramer P. Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 2021; 10:e65381. [PMID: 33770473 PMCID: PMC8004103 DOI: 10.7554/elife.65381] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/14/2021] [Indexed: 12/18/2022] Open
Abstract
Enhancer activity drives cell differentiation and cell fate determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human leukemia B-cells to macrophages. Putative enhancers are established by binding of the pioneer factor C/EBPα followed by chromatin opening and enhancer RNA (eRNA) synthesis from H3K4-monomethylated regions. Using eRNA synthesis as a proxy for enhancer activity, we find that most putative enhancers cooperate in an additive way to regulate transcription of assigned target genes. However, transcription from 136 target genes depends exponentially on the summed activity of its putative paired enhancers, indicating that these enhancers cooperate synergistically. The target genes are cell type-specific, suggesting that enhancer synergy can contribute to cell fate determination. Enhancer synergy appears to depend on cell type-specific transcription factors, and such interacting enhancers are not predicted from occupancy or accessibility data that are used to detect superenhancers.
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Affiliation(s)
- Jinmi Choi
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Kseniia Lysakovskaia
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Gregoire Stik
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Carina Demel
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Johannes Söding
- Max Planck Institute for Biophysical Chemistry, Quantitative Biology and BioinformaticsGöttingenGermany
| | - Tian V Tian
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
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10
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Larke MSC, Schwessinger R, Nojima T, Telenius J, Beagrie RA, Downes DJ, Oudelaar AM, Truch J, Graham B, Bender MA, Proudfoot NJ, Higgs DR, Hughes JR. Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Mol Cell 2021; 81:983-997.e7. [PMID: 33539786 PMCID: PMC7612206 DOI: 10.1016/j.molcel.2021.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 09/25/2020] [Accepted: 01/02/2021] [Indexed: 12/16/2022]
Abstract
Gene transcription occurs via a cycle of linked events, including initiation, promoter-proximal pausing, and elongation of RNA polymerase II (Pol II). A key question is how transcriptional enhancers influence these events to control gene expression. Here, we present an approach that evaluates the level and change in promoter-proximal transcription (initiation and pausing) in the context of differential gene expression, genome-wide. This combinatorial approach shows that in primary cells, control of gene expression during differentiation is achieved predominantly via changes in transcription initiation rather than via release of Pol II pausing. Using genetically engineered mouse models, deleted for functionally validated enhancers of the α- and β-globin loci, we confirm that these elements regulate Pol II recruitment and/or initiation to modulate gene expression. Together, our data show that gene expression during differentiation is regulated predominantly at the level of initiation and that enhancers are key effectors of this process.
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Affiliation(s)
- Martin S C Larke
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Julia Truch
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - M A Bender
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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11
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Gurumurthy A, Yu DT, Stees JR, Chamales P, Gavrilova E, Wassel P, Li L, Stribling D, Chen J, Brackett M, Ishov AM, Xie M, Bungert J. Super-enhancer mediated regulation of adult β-globin gene expression: the role of eRNA and Integrator. Nucleic Acids Res 2021; 49:1383-1396. [PMID: 33476375 PMCID: PMC7897481 DOI: 10.1093/nar/gkab002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 01/05/2023] Open
Abstract
Super-enhancers (SEs) mediate high transcription levels of target genes. Previous studies have shown that SEs recruit transcription complexes and generate enhancer RNAs (eRNAs). We characterized transcription at the human and murine β-globin locus control region (LCR) SE. We found that the human LCR is capable of recruiting transcription complexes independently from linked globin genes in transgenic mice. Furthermore, LCR hypersensitive site 2 (HS2) initiates the formation of bidirectional transcripts in transgenic mice and in the endogenous β-globin gene locus in murine erythroleukemia (MEL) cells. HS2 3′eRNA is relatively unstable and remains in close proximity to the globin gene locus. Reducing the abundance of HS2 3′eRNA leads to a reduction in β-globin gene transcription and compromises RNA polymerase II (Pol II) recruitment at the promoter. The Integrator complex has been shown to terminate eRNA transcription. We demonstrate that Integrator interacts downstream of LCR HS2. Inducible ablation of Integrator function in MEL or differentiating primary human CD34+ cells causes a decrease in expression of the adult β-globin gene and accumulation of Pol II and eRNA at the LCR. The data suggest that transcription complexes are assembled at the LCR and transferred to the globin genes by mechanisms that involve Integrator mediated release of Pol II and eRNA from the LCR.
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Affiliation(s)
- Aishwarya Gurumurthy
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - David T Yu
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Jared R Stees
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Pamela Chamales
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Ekaterina Gavrilova
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Paul Wassel
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Lu Li
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Daniel Stribling
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, Gainesville, FL 32610, USA
| | - Jinyang Chen
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Marissa Brackett
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
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12
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Perreault AA, Brown JD, Venters BJ. Erythropoietin Regulates Transcription and YY1 Dynamics in a Pre-established Chromatin Architecture. iScience 2020; 23:101583. [PMID: 33089097 PMCID: PMC7559257 DOI: 10.1016/j.isci.2020.101583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/07/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
The three-dimensional architecture of the genome plays an essential role in establishing and maintaining cell identity. However, the magnitude and temporal kinetics of changes in chromatin structure that arise during cell differentiation remain poorly understood. Here, we leverage a murine model of erythropoiesis to study the relationship between chromatin conformation, the epigenome, and transcription in erythroid cells. We discover that acute transcriptional responses induced by erythropoietin (EPO), the hormone necessary for erythroid differentiation, occur within an invariant chromatin topology. Within this pre-established landscape, Yin Yang 1 (YY1) occupancy dynamically redistributes to sites in proximity of EPO-regulated genes. Using HiChIP, we identify chromatin contacts mediated by H3K27ac and YY1 that are enriched for enhancer-promoter interactions of EPO-responsive genes. Taken together, these data are consistent with an emerging model that rapid, signal-dependent transcription occurs in the context of a pre-established chromatin architecture. EPO induces rapid RNA Pol II response at a key subset of genes YY1 is redistributed in the genome following 1 h EPO stimulation CTCF and YY1 bind different locations pre and post 1 h EPO stimulation E-P loops mediated by H3K27ac are largely invariant in response to EPO
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Affiliation(s)
- Andrea A Perreault
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37232, USA.,Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Jonathan D Brown
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Bryan J Venters
- Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
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13
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Enhancer RNAs are an important regulatory layer of the epigenome. Nat Struct Mol Biol 2020; 27:521-528. [PMID: 32514177 DOI: 10.1038/s41594-020-0446-0] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 05/07/2020] [Indexed: 12/20/2022]
Abstract
Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development and disease through their regulation of transcription, RNA processing and translation. Leading the charge in the RNA revolution is a class of ncRNAs that are synthesized at active enhancers, called enhancer RNAs (eRNAs). Here, we review recent insights into the biogenesis of eRNAs and the mechanisms underlying their multifaceted functions and consider how these findings could inform future investigations into enhancer transcription and eRNA function.
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14
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Milevskiy MJG, Gujral U, Del Lama Marques C, Stone A, Northwood K, Burke LJ, Gee JMW, Nephew K, Clark S, Brown MA. MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ breast cancer. Br J Cancer 2019; 120:621-632. [PMID: 30783203 PMCID: PMC6461839 DOI: 10.1038/s41416-019-0395-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/16/2018] [Accepted: 01/15/2019] [Indexed: 12/18/2022] Open
Abstract
Background MicroRNAs are potent post-transcriptional regulators involved in all hallmarks of cancer. Mir-196a is transcribed from two loci and has been implicated in a wide range of developmental and pathogenic processes, with targets including Hox, Fox, Cdk inhibitors and annexins. Genetic variants and altered expression of MIR196A are associated with risk and progression of multiple cancers including breast cancer, however little is known about the regulation of the genes encoding this miRNA, nor the impact of variants therein. Methods Genomic data and chromatin interaction analysis were used to discover functional promoter and enhancer elements for MIR196A. Expression data were used to associate MIR196A with mechanisms of resistance, breast cancer subtypes and prognosis. Results Here we demonstrate that MIR196A displays complex and dynamic expression patterns, in part controlled by long-range transcriptional regulation between promoter and enhancer elements bound by ERα. Expression of this miRNA is significantly increased in drug-resistant models of hormone-receptor positive disease. The expression of MIR196A also proves to be a robust prognostic factor for patients with advanced and post-menopausal ER+ disease. Conclusion This work sheds light on the normal and abnormal regulation of MIR196A and provides a novel stratification method for therapeutically resistant breast cancer.
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Affiliation(s)
- Michael J G Milevskiy
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia. .,ACRF Stem Cells and Cancer, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
| | - Udai Gujral
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | | | - Andrew Stone
- Division of Genomics and Epigenetics, Epigenetics Research Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Korinne Northwood
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.,UQ Centre for Clinical Research, The University of Queensland, Herston, QLD, Australia
| | - Lez J Burke
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Julia M W Gee
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Kenneth Nephew
- School of Medicine, Indiana University, Bloomington, IN, USA
| | - Susan Clark
- Division of Genomics and Epigenetics, Epigenetics Research Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
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15
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Gurumurthy A, Shen Y, Gunn E, Bungert J. Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly? Bioessays 2019; 41:e1800164. [PMID: 30500078 PMCID: PMC6484441 DOI: 10.1002/bies.201800164] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/31/2018] [Indexed: 01/10/2023]
Abstract
It is proposed that the multiple enhancer elements associated with locus control regions and super-enhancers recruit RNA polymerase II and efficiently assemble elongation competent transcription complexes that are transferred to target genes by transcription termination and transient looping mechanisms. It is well established that transcription complexes are recruited not only to promoters but also to enhancers, where they generate enhancer RNAs. Transcription at enhancers is unstable and frequently aborted. Furthermore, the Integrator and WD-domain containing protein 82 mediate transcription termination at enhancers. Abortion and termination of transcription at the multiple enhancers of locus control regions and super-enhancers provide a large pool of elongation competent transcription complexes. These are efficiently captured by strong basal promoter elements at target genes during transient looping interactions.
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Affiliation(s)
- Aishwarya Gurumurthy
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Eliot Gunn
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine,
UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center,
University of Florida, Gainesville, Florida, 32610, U.S.A., Phone: 352-273-8098,
Fax: 352-3f92-2953
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16
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Agrawal P, Heimbruch KE, Rao S. Genome-Wide Maps of Transcription Regulatory Elements and Transcription Enhancers in Development and Disease. Compr Physiol 2018; 9:439-455. [PMID: 30549021 DOI: 10.1002/cphy.c180028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gene expression is regulated by numerous elements including enhancers, insulators, transcription factors, and architectural proteins. Regions of DNA distal to the transcriptional start site, called enhancers, play a central role in the temporal and tissue-specific regulation of gene expression through RNA polymerase II. The identification of enhancers and other cis regulatory elements has largely been possible due to advances in next generation sequencing technologies. Enhancers regulate gene expression through chromatin loops mediated by architectural proteins such as YY1, CTCF, the cohesin complex, and LDB1. Additionally, enhancers can be transcribed to produce noncoding RNAs termed enhancer RNAs that likely participate in transcriptional regulation. The central role of enhancers in regulating gene expression implicates them in both normal physiology but also many disease states. The importance of enhancers is evident by the suggested role of SNPs, duplications, and other alterations of enhancer function in many diseases, ranging from cancer to atherosclerosis to chronic kidney disease. Although much progress has been made in recent years, the field of enhancer biology and our knowledge of the cis regulome remains a work in progress. This review will highlight recent seminal studies which demonstrate the role of enhancers in normal physiology and disease pathogenesis. © 2019 American Physiological Society. Compr Physiol 9:439-455, 2019.
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Affiliation(s)
- Puja Agrawal
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Katelyn E Heimbruch
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sridhar Rao
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow Transplantation, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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17
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Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol 2018; 19:621-637. [PMID: 29946135 PMCID: PMC6205604 DOI: 10.1038/s41580-018-0028-8] [Citation(s) in RCA: 357] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA polymerase II (Pol II) core promoters are specialized DNA sequences at transcription start sites of protein-coding and non-coding genes that support the assembly of the transcription machinery and transcription initiation. They enable the highly regulated transcription of genes by selectively integrating regulatory cues from distal enhancers and their associated regulatory proteins. In this Review, we discuss the defining properties of gene core promoters, including their sequence features, chromatin architecture and transcription initiation patterns. We provide an overview of molecular mechanisms underlying the function and regulation of core promoters and their emerging functional diversity, which defines distinct transcription programmes. On the basis of the established properties of gene core promoters, we discuss transcription start sites within enhancers and integrate recent results obtained from dedicated functional assays to propose a functional model of transcription initiation. This model can explain the nature and function of transcription initiation at gene starts and at enhancers and can explain the different roles of core promoters, of Pol II and its associated factors and of the activating cues provided by enhancers and the transcription factors and cofactors they recruit.
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Affiliation(s)
- Vanja Haberle
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
- Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
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18
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Sun Y, Dai H, Chen S, Xu M, Wang X, Zhang Y, Xu S, Xu A, Weng J, Liu S, Wu L. Graphene oxide regulates cox2 in human embryonic kidney 293T cells via epigenetic mechanisms: dynamic chromosomal interactions. Nanotoxicology 2018; 12:117-137. [PMID: 29338479 DOI: 10.1080/17435390.2018.1425498] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To extend the applications of engineered nanomaterials, such as graphene oxide (GO), it is necessary to minimize cytotoxicity. However, the mechanisms underlying this cytotoxicity are unclear. Dynamic chromosomal interactions have been used to illustrate the molecular bases of gene expression, which offers a more sensitive and cutting-edge technology to elucidate complex biological processes associated with epigenetic regulations. In this study, the role of GO-triggered chromatin interactions in the activation of cox2, a hallmark of inflammation, was investigated in normal human cells. Using chromosome conformation capture technology, we showed that GO triggers physical interactions between the downstream enhancer and the cox2 promoter in human embryonic kidney 293T (293T) via p65 and p300 complex-mediated dynamic chromatin looping, which was required for high cox2 expression. Moreover, tumor necrosis factor-α (TNF-α), located upstream of the p65 signaling pathway, contributed to the regulation of cox2 activation through dynamic chromatin architecture. Compared with pristine GO and aminated GO (GO-NH2), poly (acrylic acid)-functionalized GO (GO-PAA) induced a weaker inflammatory response and a weaker effect on chromatin architecture. Our results mechanistically link GO-mediated chromatin interactions with the regulation of cox2 and suggest that GO derivatives may minimize toxicity in practical applications.
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Affiliation(s)
- Yuxiang Sun
- a Key Laboratory of High Magnetic Field and Ion Beam Physical Biology , Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei , Anhui , People's Republic of China.,c Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province , Hefei , Anhui , People's Republic of China
| | - Hui Dai
- a Key Laboratory of High Magnetic Field and Ion Beam Physical Biology , Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei , Anhui , People's Republic of China.,b University of Science and Technology of China , Hefei , Anhui , People's Republic of China.,c Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province , Hefei , Anhui , People's Republic of China
| | - Shaopeng Chen
- a Key Laboratory of High Magnetic Field and Ion Beam Physical Biology , Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei , Anhui , People's Republic of China.,c Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province , Hefei , Anhui , People's Republic of China
| | - Ming Xu
- d State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Xuanyu Wang
- a Key Laboratory of High Magnetic Field and Ion Beam Physical Biology , Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei , Anhui , People's Republic of China.,c Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province , Hefei , Anhui , People's Republic of China
| | - Yajun Zhang
- a Key Laboratory of High Magnetic Field and Ion Beam Physical Biology , Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei , Anhui , People's Republic of China.,c Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province , Hefei , Anhui , People's Republic of China
| | - Shengmin Xu
- a Key Laboratory of High Magnetic Field and Ion Beam Physical Biology , Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei , Anhui , People's Republic of China.,c Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province , Hefei , Anhui , People's Republic of China
| | - An Xu
- a Key Laboratory of High Magnetic Field and Ion Beam Physical Biology , Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei , Anhui , People's Republic of China.,c Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province , Hefei , Anhui , People's Republic of China
| | - Jian Weng
- e Research Center of Biomedical Engineering, Department of Biomaterials, College of Materials , Xiamen University , Xiamen , People's Republic of China
| | - Sijin Liu
- d State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Lijun Wu
- a Key Laboratory of High Magnetic Field and Ion Beam Physical Biology , Hefei Institutes of Physical Science, Chinese Academy of Sciences , Hefei , Anhui , People's Republic of China.,b University of Science and Technology of China , Hefei , Anhui , People's Republic of China.,c Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province , Hefei , Anhui , People's Republic of China
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19
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Cavazzana M, Antoniani C, Miccio A. Gene Therapy for β-Hemoglobinopathies. Mol Ther 2017; 25:1142-1154. [PMID: 28377044 DOI: 10.1016/j.ymthe.2017.03.024] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 01/09/2023] Open
Abstract
β-Thalassemia and sickle cell disease (SCD) are the world's two most widely disseminated hereditary hemoglobinopathies. β-Thalassemia originated in the Mediterranean, Middle Eastern, and Asian regions, and SCD originated in central Africa. However, subsequent population migration means that these two diseases are now global and thus constitute a growing health problem in many countries. Despite remarkable improvements in medical care for patients with β-hemoglobinopathies, there is still only one definitive treatment option: allogeneic hematopoietic stem cell (HSC) transplantation. The development of gene therapy for β-hemoglobinopathies has been justified by (1) the limited availability of human leukocyte antigen (HLA)-identical donors, (2) the narrow window of application of HSC transplantation to the youngest patients, and (3) recent advances in HSC-based gene therapy. The huge ongoing efforts in translational medicine and the high number of related publications show that gene therapy has the potential to become the treatment of choice for patients who lack either an HLA genoidentical sibling or an alternative, medically acceptable donor. In this dynamic scientific context, we first summarize the main steps toward clinical translation of this therapeutic approach and then discuss novel lentiviral- and genome editing-based treatment strategies for β-hemoglobinopathies.
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Affiliation(s)
- Marina Cavazzana
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France; Biotherapy Clinical Investigation Center, Assistance Publique-Hôpitaux de Paris, INSERM, Groupe Hospitalier Universitaire Ouest, 75015 Paris, France; INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis, 75015 Paris, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France.
| | - Chiara Antoniani
- Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; INSERM UMR 1163, Laboratory of Chromatin and Gene Regulation, 75015 Paris, France
| | - Annarita Miccio
- Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; INSERM UMR 1163, Laboratory of Chromatin and Gene Regulation, 75015 Paris, France.
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20
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Reading NS, Shooter C, Song J, Miller R, Agarwal A, Lanikova L, Clark B, Thein SL, Divoky V, Prchal JT. Loss of Major DNase I Hypersensitive Sites in Duplicatedβ-globinGene Cluster Incompletely SilencesHBBGene Expression. Hum Mutat 2016; 37:1153-1156. [DOI: 10.1002/humu.23061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/21/2016] [Accepted: 07/27/2016] [Indexed: 11/06/2022]
Affiliation(s)
- N. Scott Reading
- Institute for Clinical and Experimental Pathology; ARUP Laboratories; Salt Lake City Utah
- Division of Hematology, Department of Internal Medicine, School of Medicine; University of Utah; Salt Lake City Utah
- Department of Pathology, School of Medicine; University of Utah; Salt Lake City Utah
| | - Claire Shooter
- Molecular Haematology, Division of Cancer Studies; King's College London Faculty of Life Sciences & Medicine; London UK
| | - Jihyun Song
- Division of Hematology, Department of Internal Medicine, School of Medicine; University of Utah; Salt Lake City Utah
| | - Robin Miller
- Center for Cancer and Blood Disorders; Nemours/El Dupont Hospital for Children; Wilmington Delaware
| | - Archana Agarwal
- Institute for Clinical and Experimental Pathology; ARUP Laboratories; Salt Lake City Utah
- Department of Pathology, School of Medicine; University of Utah; Salt Lake City Utah
| | - Lucie Lanikova
- Division of Hematology, Department of Internal Medicine, School of Medicine; University of Utah; Salt Lake City Utah
- Department of Cell and Developmental Biology, Institute of Molecular Genetics; Academy of Sciences of the Czech Republic; Prague Czech Republic
| | - Barnaby Clark
- Molecular Haematology, Division of Cancer Studies; King's College London Faculty of Life Sciences & Medicine; London UK
- Department of Molecular Pathology; Viapath at King's College Hospital NHS Foundation Trust; London UK
| | - Swee Lay Thein
- Molecular Haematology, Division of Cancer Studies; King's College London Faculty of Life Sciences & Medicine; London UK
- National Heart, Lung and Blood Institute, Sickle Cell Branch; National Institutes of Health; Bethesda Maryland
| | - Vladimir Divoky
- Department of Biology, Faculty of Medicine and Dentistry; Palacky University; Olomouc Czech Republic
- Department of Biology, Faculty of Medicine; Masaryk University; Brno Czech Republic
| | - Josef T. Prchal
- Institute for Clinical and Experimental Pathology; ARUP Laboratories; Salt Lake City Utah
- Division of Hematology, Department of Internal Medicine, School of Medicine; University of Utah; Salt Lake City Utah
- Department of Pathology, School of Medicine; University of Utah; Salt Lake City Utah
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21
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Vernimmen D, Bickmore WA. The Hierarchy of Transcriptional Activation: From Enhancer to Promoter. Trends Genet 2016; 31:696-708. [PMID: 26599498 DOI: 10.1016/j.tig.2015.10.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/18/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Regulatory elements (enhancers) that are remote from promoters play a critical role in the spatial, temporal, and physiological control of gene expression. Studies on specific loci, together with genome-wide approaches, suggest that there may be many common mechanisms involved in enhancer-promoter communication. Here, we discuss the multiprotein complexes that are recruited to enhancers and the hierarchy of events taking place between regulatory elements and promoters.
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Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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22
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Liu T, Zhang J, Zhou T. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression. PLoS Comput Biol 2016; 12:e1004917. [PMID: 27153118 PMCID: PMC4859557 DOI: 10.1371/journal.pcbi.1004917] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/14/2016] [Indexed: 01/09/2023] Open
Abstract
According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.
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Affiliation(s)
- Tuoqi Liu
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiajun Zhang
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Tianshou Zhou
- School of Mathematics and Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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23
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Bartman CR, Hsu SC, Hsiung CCS, Raj A, Blobel GA. Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. Mol Cell 2016; 62:237-247. [PMID: 27067601 DOI: 10.1016/j.molcel.2016.03.007] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/21/2015] [Accepted: 03/04/2016] [Indexed: 01/05/2023]
Abstract
Mammalian genes transcribe RNA not continuously, but in bursts. Transcriptional output can be modulated by altering burst fraction or burst size, but how regulatory elements control bursting parameters remains unclear. Single-molecule RNA FISH experiments revealed that the β-globin enhancer (LCR) predominantly augments transcriptional burst fraction of the β-globin gene with modest stimulation of burst size. To specifically measure the impact of long-range chromatin contacts on transcriptional bursting, we forced an LCR-β-globin promoter chromatin loop. We observed that raising contact frequencies increases burst fraction but not burst size. In cells in which two developmentally distinct LCR-regulated globin genes are cotranscribed in cis, burst sizes of both genes are comparable. However, allelic co-transcription of both genes is statistically disfavored, suggesting mutually exclusive LCR-gene contacts. These results are consistent with competition between the β-type globin genes for LCR contacts and suggest that LCR-promoter loops are formed and released with rapid kinetics.
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Affiliation(s)
- Caroline R Bartman
- Division of Hematology, Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah C Hsu
- Division of Hematology, Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chris C-S Hsiung
- Division of Hematology, Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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24
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Lee K, Hsiung CCS, Huang P, Raj A, Blobel GA. Dynamic enhancer-gene body contacts during transcription elongation. Genes Dev 2016; 29:1992-7. [PMID: 26443845 PMCID: PMC4604340 DOI: 10.1101/gad.255265.114] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Enhancers govern transcription through multiple mechanisms, including the regulation of elongation by RNA polymerase II (RNAPII). We characterized the dynamics of looped enhancer contacts during synchronous transcription elongation. We found that many distal enhancers form stable contacts with their target promoters during the entire interval of elongation. Notably, we detected additional dynamic enhancer contacts throughout the gene bodies that track with elongating RNAPII and the leading edge of RNA synthesis. These results support a model in which the gene body changes its position relative to a stable enhancer-promoter complex, which has broad ramifications for enhancer function and architectural models of transcriptional elongation.
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Affiliation(s)
- Kiwon Lee
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chris C-S Hsiung
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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25
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Abstract
Gerasimova et al. describe a three-step pathway that establishes the structure of the 2.8-Mb immunoglobulin heavy chain gene (IgH) locus in pro-B cells. Each step uses a different transcription factor and leads to increasing levels of structural organization. Conformation of antigen receptor gene loci spatially juxtaposes rearranging gene segments in the appropriate cell lineage and developmental stage. We describe a three-step pathway that establishes the structure of the 2.8-Mb immunoglobulin heavy chain gene (IgH) locus in pro-B cells. Each step uses a different transcription factor and leads to increasing levels of structural organization. CTCF mediates one level of compaction that folds the locus into several 250- to 400-kb subdomains, and Pax5 further compacts the 2-Mb region that encodes variable (VH) gene segments. The 5′ and 3′ domains are brought together by the transcription factor YY1 to establish the configuration within which gene recombination initiates. Such stepwise mechanisms may apply more generally to establish regulatory fine structure within megabase-sized topologically associated domains.
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26
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High Fractional Occupancy of a Tandem Maf Recognition Element and Its Role in Long-Range β-Globin Gene Regulation. Mol Cell Biol 2015; 36:238-50. [PMID: 26503787 DOI: 10.1128/mcb.00723-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/20/2015] [Indexed: 12/11/2022] Open
Abstract
Enhancers and promoters assemble protein complexes that ultimately regulate the recruitment and activity of RNA polymerases. Previous work has shown that at least some enhancers form stable protein complexes, leading to the formation of enhanceosomes. We analyzed protein-DNA interactions in the murine β-globin gene locus using the methyltransferase accessibility protocol for individual templates (MAPit). The data show that a tandem Maf recognition element (MARE) in locus control region (LCR) hypersensitive site 2 (HS2) reveals a remarkably high degree of occupancy during differentiation of mouse erythroleukemia cells. Most of the other transcription factor binding sites in LCR HS2 or in the adult β-globin gene promoter regions exhibit low fractional occupancy, suggesting highly dynamic protein-DNA interactions. Targeting of an artificial zinc finger DNA-binding domain (ZF-DBD) to the HS2 tandem MARE caused a reduction in the association of MARE-binding proteins and transcription complexes at LCR HS2 and the adult βmajor-globin gene promoter but did not affect expression of the βminor-globin gene. The data demonstrate that a stable MARE-associated footprint in LCR HS2 is important for the recruitment of transcription complexes to the adult βmajor-globin gene promoter during erythroid cell differentiation.
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27
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Abstract
To accommodate genomes in the limited space of the cell nucleus and ensure the correct execution of gene expression programs, genomes are packaged in complex fashion in the three-dimensional cell nucleus. As a consequence of the extensive higher-order organization of chromosomes, distantly located genomic regions on the same or distinct chromosomes undergo long-range interactions. This article discusses the nature of long interactions, mechanisms of their formation, and their emerging functional roles in gene regulation and genome maintenance.
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Affiliation(s)
- Job Dekker
- University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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28
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Razin SV, Gavrilov AA, Ulyanov SV. Transcription-controlling regulatory elements of the eukaryotic genome. Mol Biol 2015. [DOI: 10.1134/s0026893315020119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Abstract
Over the last three decades, studies of the α- and β-globin genes clusters have led to elucidation of the general principles of mammalian gene regulation, such as RNA stability, termination of transcription, and, more importantly, the identification of remote regulatory elements. More recently, detailed studies of α-globin regulation, using both mouse and human loci, allowed the dissection of the sequential order in which transcription factors are recruited to the locus during lineage specification. These studies demonstrated the importance of the remote regulatory elements in the recruitment of RNA polymerase II (PolII) together with their role in the generation of intrachromosomal loops within the locus and the removal of polycomb complexes during differentiation. The multiple roles attributed to remote regulatory elements that have emerged from these studies will be discussed.
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Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- * E-mail:
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30
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Abstract
Enhancers establish spatial or temporal patterns of gene expression that are critical for development, yet our understanding of how these DNA cis-regulatory elements function from a distance to increase transcription of their target genes and shape the cellular transcriptome has been gleaned primarily from studies of individual genes or gene families. High-throughput sequencing studies place enhancer-gene interactions within the 3D context of chromosome folding, inviting a new look at enhancer function and stimulating provocative new questions. Here, we integrate these whole-genome studies with recent mechanistic studies to illuminate how enhancers physically interact with target genes, how enhancer activity is regulated during development, and the role of noncoding RNAs transcribed from enhancers in their function.
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Affiliation(s)
- Jennifer L Plank
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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31
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Krivega I, Dale RK, Dean A. Role of LDB1 in the transition from chromatin looping to transcription activation. Genes Dev 2014; 28:1278-90. [PMID: 24874989 PMCID: PMC4066399 DOI: 10.1101/gad.239749.114] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Many questions remain about the relationship between chromatin loop formation and transcription. In erythroid cells, LDB1 is required for looping of the β-globin locus control region (LCR) to the active β-globin promoter. Dean and colleagues show that the LDB1 dimerization domain (DD) is necessary to restore LCR-promoter looping and transcription in LDB1-depleted cells. Deletion analysis reveals a conserved region of the LDB1 DD dispensable for dimerization and chromatin looping but necessary for transcription activation. The results thus uncouple enhancer–promoter looping from transcription at the β-globin locus. Many questions remain about how close association of genes and distant enhancers occurs and how this is linked to transcription activation. In erythroid cells, lim domain binding 1 (LDB1) protein is recruited to the β-globin locus via LMO2 and is required for looping of the β-globin locus control region (LCR) to the active β-globin promoter. We show that the LDB1 dimerization domain (DD) is necessary and, when fused to LMO2, sufficient to completely restore LCR–promoter looping and transcription in LDB1-depleted cells. The looping function of the DD is unique and irreplaceable by heterologous DDs. Dissection of the DD revealed distinct functional properties of conserved subdomains. Notably, a conserved helical region (DD4/5) is dispensable for LDB1 dimerization and chromatin looping but essential for transcriptional activation. DD4/5 is required for the recruitment of the coregulators FOG1 and the nucleosome remodeling and deacetylating (NuRD) complex. Lack of DD4/5 alters histone acetylation and RNA polymerase II recruitment and results in failure of the locus to migrate to the nuclear interior, as normally occurs during erythroid maturation. These results uncouple enhancer–promoter looping from nuclear migration and transcription activation and reveal new roles for LDB1 in these processes.
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Affiliation(s)
- Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ryan K Dale
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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32
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Abstract
Enhancer elements regulate the tissue- and developmental-stage-specific expression of genes. Recent estimates suggest that there are more than 50,000 enhancers in mammalian cells. At least a subset of enhancers has been shown to recruit RNA polymerase II transcription complexes and to generate enhancer transcripts. Here, we provide an overview of enhancer function and discuss how transcription of enhancers or enhancer-generated transcripts could contribute to the regulation of gene expression during development and differentiation.
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33
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Cadiz-Rivera B, Fromm G, de Vries C, Fields J, McGrath KE, Fiering S, Bulger M. The chromatin "landscape" of a murine adult β-globin gene is unaffected by deletion of either the gene promoter or a downstream enhancer. PLoS One 2014; 9:e92947. [PMID: 24817273 PMCID: PMC4015891 DOI: 10.1371/journal.pone.0092947] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 02/27/2014] [Indexed: 01/11/2023] Open
Abstract
In mammals, the complex tissue- and developmental-specific expression of genes within the β-globin cluster is known to be subject to control by the gene promoters, by a locus control region (LCR) located upstream of the cluster, and by sequence elements located across the intergenic regions. Despite extensive investigation, however, the complement of sequences that is required for normal regulation of chromatin structure and gene expression within the cluster is not fully defined. To further elucidate regulation of the adult β-globin genes, we investigate the effects of two deletions engineered within the endogenous murine β-globin locus. First, we find that deletion of the β2-globin gene promoter, while eliminating β2-globin gene expression, results in no additional effects on chromatin structure or gene expression within the cluster. Notably, our observations are not consistent with competition among the β-globin genes for LCR activity. Second, we characterize a novel enhancer located 3′ of the β2-globin gene, but find that deletion of this sequence has no effect whatsoever on gene expression or chromatin structure. This observation highlights the difficulty in assigning function to enhancer sequences identified by the chromatin “landscape” or even by functional assays.
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Affiliation(s)
- Brenda Cadiz-Rivera
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
| | - George Fromm
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
- National Institute for Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, United States of America
| | - Christina de Vries
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
| | - Jennifer Fields
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Kathleen E. McGrath
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
| | - Steven Fiering
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Michael Bulger
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
- * E-mail:
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34
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Wendt KS, Grosveld FG. Transcription in the context of the 3D nucleus. Curr Opin Genet Dev 2014; 25:62-7. [DOI: 10.1016/j.gde.2013.11.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/29/2013] [Indexed: 11/27/2022]
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35
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Wang W, Yao X, Huang Y, Hu X, Liu R, Hou D, Chen R, Wang G. Mediator MED23 regulates basal transcription in vivo via an interaction with P-TEFb. Transcription 2013; 4:39-51. [PMID: 23340209 DOI: 10.4161/trns.22874] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Mediator is a multi-subunit complex that transduces regulatory information from transcription regulators to the RNA polymerase II apparatus. Growing evidence suggests that Mediator plays roles in multiple stages of eukaryotic transcription, including elongation. However, the detailed mechanism by which Mediator regulates elongation remains elusive. In this study, we demonstrate that Mediator MED23 subunit controls a basal level of transcription by recruiting elongation factor P-TEFb, via an interaction with its CDK9 subunit. The mRNA level of Egr1, a MED23-controlled model gene, is reduced 4-5 fold in Med23 (-/-) ES cells under an unstimulated condition, but Med23-deficiency does not alter the occupancies of RNAP II, GTFs, Mediator complex, or activator ELK1 at the Egr1 promoter. Instead, Med23 depletion results in a significant decrease in P-TEFb and RNAP II (Ser2P) binding at the coding region, but no changes for several other elongation regulators, such as DSIF and NELF. ChIP-seq revealed that Med23-deficiency partially reduced the P-TEFb occupancy at a set of MED23-regulated gene promoters. Further, we demonstrate that MED23 interacts with CDK9 in vivo and in vitro. Collectively, these results provide the mechanistic insight into how Mediator promotes RNAP II into transcription elongation.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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36
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Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nat Rev Genet 2013; 14:288-95. [PMID: 23503198 DOI: 10.1038/nrg3458] [Citation(s) in RCA: 339] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
It is estimated that the human genome contains hundreds of thousands of enhancers, so understanding these gene-regulatory elements is a crucial goal. Several fundamental questions need to be addressed about enhancers, such as how do we identify them all, how do they work, and how do they contribute to disease and evolution? Five prominent researchers in this field look at how much we know already and what needs to be done to answer these questions.
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Affiliation(s)
- Len A Pennacchio
- Genomics Division, One Cyclotron Road, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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37
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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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38
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Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R, Martin O, Harshman K, Delorenzi M, Desvergne B, Herr W, Deplancke B, Schibler U, Rougemont J, Guex N, Hernandez N, Naef F. Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol 2012; 10:e1001442. [PMID: 23209382 PMCID: PMC3507959 DOI: 10.1371/journal.pbio.1001442] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 10/25/2012] [Indexed: 01/01/2023] Open
Abstract
Genome-wide rhythms in RNA polymerase II loading and dynamic chromatin remodeling underlie periodic gene expression during diurnal cycles in the mouse liver. Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we generated temporal DNA occupancy profiles by RNA polymerase II (Pol II) as well as profiles of the histone modifications H3K4me3 and H3K36me3. We used these data to quantify the relationships of phases and amplitudes between different marks. We found that rhythmic Pol II recruitment at promoters rather than rhythmic transition from paused to productive elongation underlies diurnal gene transcription, a conclusion further supported by modeling. Moreover, Pol II occupancy preceded mRNA accumulation by 3 hours, consistent with mRNA half-lives. Both methylation marks showed that the epigenetic landscape is highly dynamic and globally remodeled during the 24-hour cycle. While promoters of transcribed genes had tri-methylated H3K4 even at their trough activity times, tri-methylation levels reached their peak, on average, 1 hour after Pol II. Meanwhile, rhythms in tri-methylation of H3K36 lagged transcription by 3 hours. Finally, modeling profiles of Pol II occupancy and mRNA accumulation identified three classes of genes: one showing rhythmicity both in transcriptional and mRNA accumulation, a second class with rhythmic transcription but flat mRNA levels, and a third with constant transcription but rhythmic mRNAs. The latter class emphasizes widespread temporally gated posttranscriptional regulation in the mouse liver. In mammalian organs such as the liver, many metabolic and physiological processes occur preferentially at specific times during the 24-hour daily cycle. The timing of these rhythmic functions depends on a complex interplay between the endogenous circadian clock and environmental timing cues relayed through the master circadian clock in the suprachiasmatic nucleus, or via feeding rhythms. These rhythms can be implemented on several regulatory levels, and here we aimed at a better understanding of the transcriptional and epigenetic changes that regulate diurnal rhythms. We performed genome-wide analysis of the locations of RNA polymerase II (Pol II) and the epigenetic histone modifications H3K4me3 and H3K36me3 at specific times of day, relating these data to mRNA expression levels. Our analyses show that Pol II transcriptional rhythms are biphasic in mouse liver, having predominant peak activities in the morning and evening. Moreover, dynamic changes in histone marks lag transcription rhythms genome-wide, indicating that the epigenetic landscape can be remodeled during the 24-hour cycle. Finally, a quantitative analysis of temporal Pol II and mRNA accumulation profiles indicates that posttranscriptional regulation significantly contributes to the amplitude and phase of mRNA accumulation profiles. While many studies have analyzed how transcription and chromatin states are modified during irreversible cell differentiation processes, our work highlights how these states can evolve reversibly in a system exhibiting periodicity in time.
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Affiliation(s)
| | - Donatella Canella
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Laura Symul
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Eugenia Migliavacca
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Federica Gilardi
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Robin Liechti
- Vital IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Martin
- Vital IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Keith Harshman
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Mauro Delorenzi
- Département de Formation et de Recherche, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Béatrice Desvergne
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Winship Herr
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Bart Deplancke
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ueli Schibler
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Jacques Rougemont
- Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Vital IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- * E-mail: (NH); (FN)
| | - Felix Naef
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail: (NH); (FN)
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39
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Palstra RJ, Grosveld F. Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux. Front Genet 2012; 3:195. [PMID: 23060900 PMCID: PMC3460357 DOI: 10.3389/fgene.2012.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/12/2012] [Indexed: 12/26/2022] Open
Abstract
The mammalian genome is packed tightly in the nucleus of the cell. This packing is primarily facilitated by histone proteins and results in an ordered organization of the genome in chromosome territories that can be roughly divided in heterochromatic and euchromatic domains. On top of this organization several distinct gene regulatory elements on the same chromosome or other chromosomes are thought to dynamically communicate via chromatin looping. Advances in genome-wide technologies have revealed the existence of a plethora of these regulatory elements in various eukaryotic genomes. These regulatory elements are defined by particular in vitro assays as promoters, enhancers, insulators, and boundary elements. However, recent studies indicate that the in vivo distinction between these elements is often less strict. Regulatory elements are bound by a mixture of common and lineage-specific transcription factors which mediate the long-range interactions between these elements. Inappropriate modulation of the binding of these transcription factors can alter the interactions between regulatory elements, which in turn leads to aberrant gene expression with disease as an ultimate consequence. Here we discuss the bi-modal behavior of regulatory elements that act in cis (with a focus on enhancers), how their activity is modulated by transcription factor binding and the effect this has on gene regulation.
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Affiliation(s)
- Robert-Jan Palstra
- Department of Cell Biology, Erasmus MC University Medical Center Rotterdam, Netherlands
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40
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Abstract
RNA polymerase is a ratchet machine that oscillates between productive and backtracked states at numerous DNA positions. Since its first description 15 years ago, backtracking--the reversible sliding of RNA polymerase along DNA and RNA--has been implicated in many critical processes in bacteria and eukaryotes, including the control of transcription elongation, pausing, termination, fidelity, and genome instability.
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41
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Natoli G, Andrau JC. Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet 2012; 46:1-19. [PMID: 22905871 DOI: 10.1146/annurev-genet-110711-155459] [Citation(s) in RCA: 288] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mammalian genomes are extensively transcribed outside the borders of protein-coding genes. Genome-wide studies recently demonstrated that cis-regulatory genomic elements implicated in transcriptional control, such as enhancers and locus-control regions, represent major sites of extragenic noncoding transcription. Enhancer-templated transcripts provide a quantitatively small contribution to the total amount of cellular nonribosomal RNA; nevertheless, the possibility that enhancer transcription and the resulting enhancer RNAs may, in some cases, have functional roles, rather than represent mere transcriptional noise at accessible genomic regions, is supported by an increasing amount of experimental data. In this article we review the current knowledge on enhancer transcription and its functional implications.
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Affiliation(s)
- Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), I-20139 Milan, Italy.
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42
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Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 2012; 149:1233-44. [PMID: 22682246 DOI: 10.1016/j.cell.2012.03.051] [Citation(s) in RCA: 491] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/05/2012] [Accepted: 03/30/2012] [Indexed: 11/19/2022]
Abstract
Chromatin loops juxtapose distal enhancers with active promoters, but their molecular architecture and relationship with transcription remain unclear. In erythroid cells, the locus control region (LCR) and β-globin promoter form a chromatin loop that requires transcription factor GATA1 and the associated molecule Ldb1. We employed artificial zinc fingers (ZF) to tether Ldb1 to the β-globin promoter in GATA1 null erythroblasts, in which the β-globin locus is relaxed and inactive. Remarkably, targeting Ldb1 or only its self-association domain to the β-globin promoter substantially activated β-globin transcription in the absence of GATA1. Promoter-tethered Ldb1 interacted with endogenous Ldb1 complexes at the LCR to form a chromatin loop, causing recruitment and phosphorylation of RNA polymerase II. ZF-Ldb1 proteins were inactive at alleles lacking the LCR, demonstrating that their activities depend on long-range interactions. Our findings establish Ldb1 as a critical effector of GATA1-mediated loop formation and indicate that chromatin looping causally underlies gene regulation.
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Affiliation(s)
- Wulan Deng
- Division of Hematology, The Children's Hospital of Philadelphia, PA 19104, USA
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43
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Stadhouders R, van den Heuvel A, Kolovos P, Jorna R, Leslie K, Grosveld F, Soler E. Transcription regulation by distal enhancers: who's in the loop? Transcription 2012; 3:181-6. [PMID: 22771987 DOI: 10.4161/trns.20720] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome-wide chromatin profiling efforts have shown that enhancers are often located at large distances from gene promoters within the noncoding genome. Whereas enhancers can stimulate transcription initiation by communicating with promoters via chromatin looping mechanisms, we propose that enhancers may also stimulate transcription elongation by physical interactions with intronic elements. We review here recent findings derived from the study of the hematopoietic system.
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Affiliation(s)
- Ralph Stadhouders
- Department of Cell Biology; Erasmus Medical Center, Rotterdam, The Netherlands
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44
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Knuesel MT, Taatjes DJ. Mediator and post-recruitment regulation of RNA polymerase II. Transcription 2012; 2:28-31. [PMID: 21326907 DOI: 10.4161/trns.2.1.13950] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 10/10/2010] [Accepted: 10/17/2010] [Indexed: 11/19/2022] Open
Abstract
The human Mediator complex interacts extensively with the RNA polymerase II (Pol II) enzyme and recent data from our lab suggest activator-induced structural shifts within Mediator trigger activation of stalled Pol II. These results are discussed together with other recent findings regarding post-recruitment regulation of Pol II.
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Affiliation(s)
- Matthew T Knuesel
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, USA
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45
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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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46
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Hasanali Z, Sharma K, Epner E. Flipping the cyclin D1 switch in mantle cell lymphoma. Best Pract Res Clin Haematol 2012; 25:143-52. [PMID: 22687450 DOI: 10.1016/j.beha.2012.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Mantle cell lymphoma (MCL) is a rare, aggressive subtype of B cell NHL for which there is no standard of care. It is characterized by the t(11;14) translocation, implicating cyclin D1 (CCND1) in its pathogenesis. Cyclin D1 is one of a family of 3 unlinked D type cyclin genes, CCND1, 2, 3. CCND1 is not expressed in normal B cells. Deregulated expression occurs as a result of juxtaposition of cis IgH enhancer elements, Eμ and 3' Cα, to the cyclin D1 gene. These enhancer elements and regions upstream of the CCND1 gene are hypomethylated on the translocated allele. Histones surrounding the translocation have shown hyperacetylation as well, a hallmark of transcriptionally active chromatin. The t(11;14) translocation is an epigenetic event, leading to cyclin D1 deregulated transcription. These findings provide the rationale for the use of epigenetic and targeted cyclin D1 therapies to overcome resistance and induce durable remissions in MCL.
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Affiliation(s)
- Zainul Hasanali
- Penn State Hershey Cancer Institute, Experimental Therapeutics A - CH74, Room T3319, 500 University Drive, Hershey, PA 17033-0850, USA
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47
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The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation. Blood 2012; 119:3820-7. [PMID: 22378846 DOI: 10.1182/blood-2011-09-380485] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The β-globin locus control region (LCR) is necessary for high-level β-globin gene transcription and differentiation-dependent relocation of the β-globin locus from the nuclear periphery to the central nucleoplasm and to foci of hyperphosphorylated Pol II "transcription factories" (TFys). To determine the contribution of individual LCR DNaseI hypersensitive sites (HSs) to transcription and nuclear location, in the present study, we compared β-globin gene activity and location in erythroid cells derived from mice with deletions of individual HSs, deletions of 2 HSs, and deletion of the whole LCR and found all of the HSs had a similar spectrum of activities, albeit to different degrees. Each HS acts as an independent module to activate expression in an additive manner, and this is correlated with relocation away from the nuclear periphery. In contrast, HSs have redundant activities with respect to association with TFys and the probability that an allele is actively transcribed, as measured by primary RNA transcript FISH. The limiting effect on RNA levels occurs after β-globin genes associate with TFys, at which time HSs contribute to the amount of RNA arising from each burst of transcription by stimulating transcriptional elongation.
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48
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Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development. EMBO J 2011; 31:986-99. [PMID: 22157820 PMCID: PMC3280550 DOI: 10.1038/emboj.2011.450] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 11/16/2011] [Indexed: 12/31/2022] Open
Abstract
The key haematopoietic regulator Myb is essential for coordinating proliferation and differentiation. ChIP-Sequencing and Chromosome Conformation Capture (3C)-Sequencing were used to characterize the structural and protein-binding dynamics of the Myb locus during erythroid differentiation. In proliferating cells expressing Myb, enhancers within the Myb-Hbs1l intergenic region were shown to form an active chromatin hub (ACH) containing the Myb promoter and first intron. This first intron was found to harbour the transition site from transcription initiation to elongation, which takes place around a conserved CTCF site. Upon erythroid differentiation, Myb expression is downregulated and the ACH destabilized. We propose a model for Myb activation by distal enhancers dynamically bound by KLF1 and the GATA1/TAL1/LDB1 complex, which primarily function as a transcription elongation element through chromatin looping.
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49
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From stem cell to red cell: regulation of erythropoiesis at multiple levels by multiple proteins, RNAs, and chromatin modifications. Blood 2011; 118:6258-68. [PMID: 21998215 DOI: 10.1182/blood-2011-07-356006] [Citation(s) in RCA: 304] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This article reviews the regulation of production of RBCs at several levels. We focus on the regulated expansion of burst-forming unit-erythroid erythroid progenitors by glucocorticoids and other factors that occur during chronic anemia, inflammation, and other conditions of stress. We also highlight the rapid production of RBCs by the coordinated regulation of terminal proliferation and differentiation of committed erythroid colony-forming unit-erythroid progenitors by external signals, such as erythropoietin and adhesion to a fibronectin matrix. We discuss the complex intracellular networks of coordinated gene regulation by transcription factors, chromatin modifiers, and miRNAs that regulate the different stages of erythropoiesis.
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50
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Haddad D, Puget N, Laviolette-Malirat N, Conte C, Khamlichi AA. Seeking sense of antisense switch transcripts. Transcription 2011; 2:183-188. [PMID: 21922061 DOI: 10.4161/trns.2.4.16784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/03/2011] [Accepted: 06/03/2011] [Indexed: 11/19/2022] Open
Abstract
In B lymphocytes, class switch recombination (CSR) machinery targets highly repetitive sequences, called switch (S) sequences, in the constant domain of the immunoglobulin heavy chain (IgH) locus. Cotranscriptional generation of R loops at S sequences provides the substrate for the mutagenic enzyme AID (Activation-Induced cytidine Deaminase), which initiates the DNA breaks at the transcribed sequences. Both sense and antisense transcripts across the S regions have been reported. Our recent work shows that, unlike its sense counterpart, antisense transcription of S sequences is dispensable for CSR in vivo.
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Affiliation(s)
- Dania Haddad
- CNRS UMR 5089-IPBS (Institut de Pharmacologie et de Biologie Structurale) and Université Paul Sabatier III; Equipe "Instabilité Génétique et Régulation Transcriptionnelle"; Université de Toulouse; Toulouse, France
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