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Hoareau M, Gerges E, Crémazy FGE. Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches. Methods Mol Biol 2024; 2819:3-26. [PMID: 39028499 DOI: 10.1007/978-1-0716-3930-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The complex architecture of DNA within living organisms is essential for maintaining the genetic information that dictates their functions and characteristics. Among the many complexities of genetic material organization, the folding and arrangement of DNA into chromosomes play a critical role in regulating gene expression, replication, and other essential cellular processes. Bacteria, despite their apparently simple cellular structure, exhibit a remarkable level of chromosomal organization that influences their adaptability and survival in diverse environments. Understanding the three-dimensional arrangement of bacterial chromosomes has long been a challenge due to technical limitations, but the development of Chromosome Conformation Capture (3C) methods revolutionized our ability to explore the hierarchical structure and the dynamics of bacterial genomes. Here, we review the major advances in the field of bacterial chromosome structure using 3C technology over the past decade.
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Affiliation(s)
- Marion Hoareau
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Elias Gerges
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France
| | - Frédéric G E Crémazy
- Université Paris-Saclay, UVSQ, Inserm, Infection et inflammation, Montigny-Le-Bretonneux, France.
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2
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Pandupuspitasari NS, Khan FA, Huang C, Ali A, Yousaf MR, Shakeel F, Putri EM, Negara W, Muktiani A, Prasetiyono BWHE, Kustiawan L, Wahyuni DS. Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease. Funct Integr Genomics 2023; 23:214. [PMID: 37386239 DOI: 10.1007/s10142-023-01146-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.
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Affiliation(s)
- Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Azhar Ali
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Rizwan Yousaf
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Farwa Shakeel
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Anis Muktiani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Bambang Waluyo Hadi Eko Prasetiyono
- Laboratory of Feed Technology, Animal Science Department, Faculty of Animal and Agricultural Sciences Universitas Diponegoro, Semarang, Indonesia
| | - Limbang Kustiawan
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
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3
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A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes. Nat Commun 2022; 13:1039. [PMID: 35210422 PMCID: PMC8873246 DOI: 10.1038/s41467-022-28666-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 02/04/2022] [Indexed: 12/15/2022] Open
Abstract
The contractile properties of adult myofibers are shaped by their Myosin heavy chain isoform content. Here, we identify by snATAC-seq a 42 kb super-enhancer at the locus regrouping the fast Myosin genes. By 4C-seq we show that active fast Myosin promoters interact with this super-enhancer by DNA looping, leading to the activation of a single promoter per nucleus. A rainbow mouse transgenic model of the locus including the super-enhancer recapitulates the endogenous spatio-temporal expression of adult fast Myosin genes. In situ deletion of the super-enhancer by CRISPR/Cas9 editing demonstrates its major role in the control of associated fast Myosin genes, and deletion of two fast Myosin genes at the locus reveals an active competition of the promoters for the shared super-enhancer. Last, by disrupting the organization of fast Myosin, we uncover positional heterogeneity within limb skeletal muscles that may underlie selective muscle susceptibility to damage in certain myopathies. The contractile properties of adult myofibers are shaped by their Myosin heavy chain isoform content. Here the authors show that a super enhancer controls the spatiotemporal expression of the genes at the fast myosin heavy chain locus by DNA looping and that this expression profile is recapitulated in a rainbow transgenic mouse model of the locus.
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Erlandsson L, Masoumi Z, Hansson LR, Hansson SR. The roles of free iron, heme, haemoglobin, and the scavenger proteins haemopexin and alpha-1-microglobulin in preeclampsia and fetal growth restriction. J Intern Med 2021; 290:952-968. [PMID: 34146434 DOI: 10.1111/joim.13349] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Preeclampsia (PE) is a complex pregnancy syndrome characterised by maternal hypertension and organ damage after 20 weeks of gestation and is associated with an increased risk of cardiovascular disease later in life. Extracellular haemoglobin (Hb) and its metabolites heme and iron are highly toxic molecules and several defence mechanisms have evolved to protect the tissue. OBJECTIVES We will discuss the roles of free iron, heme, Hb, and the scavenger proteins haemopexin and alpha-1-microglobulin in pregnancies complicated by PE and fetal growth restriction (FGR). CONCLUSION In PE, oxidative stress causes syncytiotrophoblast (STB) stress and increased shedding of placental STB-derived extracellular vesicles (STBEV). The level in maternal circulation correlates with the severity of hypertension and supports the involvement of STBEVs in causing maternal symptoms in PE. In PE and FGR, iron homeostasis is changed, and iron levels significantly correlate with the severity of the disease. The normal increase in plasma volume taking place during pregnancy is less for PE and FGR and therefore have a different impact on, for example, iron concentration, compared to normal pregnancy. Excess iron promotes ferroptosis is suggested to play a role in trophoblast stress and lipotoxicity. Non-erythroid α-globin regulates vasodilation through the endothelial nitric oxide synthase pathway, and hypoxia-induced α-globin expression in STBs in PE placentas is suggested to contribute to hypertension in PE. Underlying placental pathology in PE with and without FGR might be amplified by iron and heme overload causing oxidative stress and ferroptosis. As the placenta becomes stressed, the release of STBEVs increases and affects the maternal vasculature.
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Affiliation(s)
- Lena Erlandsson
- Division of Obstetrics and Gynecology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Zahra Masoumi
- Division of Obstetrics and Gynecology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Lucas R Hansson
- Division of Obstetrics and Gynecology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Stefan R Hansson
- Division of Obstetrics and Gynecology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Obstetrics and Gynecology, Skåne University Hospital, Lund/Malmö, Sweden
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5
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Liu N, Low WY, Alinejad-Rokny H, Pederson S, Sadlon T, Barry S, Breen J. Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics Chromatin 2021; 14:41. [PMID: 34454581 PMCID: PMC8399707 DOI: 10.1186/s13072-021-00417-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Eukaryotic genomes are highly organised within the nucleus of a cell, allowing widely dispersed regulatory elements such as enhancers to interact with gene promoters through physical contacts in three-dimensional space. Recent chromosome conformation capture methodologies such as Hi-C have enabled the analysis of interacting regions of the genome providing a valuable insight into the three-dimensional organisation of the chromatin in the nucleus, including chromosome compartmentalisation and gene expression. Complicating the analysis of Hi-C data, however, is the massive amount of identified interactions, many of which do not directly drive gene function, thus hindering the identification of potentially biologically functional 3D interactions. In this review, we collate and examine the downstream analysis of Hi-C data with particular focus on methods that prioritise potentially functional interactions. We classify three groups of approaches: structural-based discovery methods, e.g. A/B compartments and topologically associated domains, detection of statistically significant chromatin interactions, and the use of epigenomic data integration to narrow down useful interaction information. Careful use of these three approaches is crucial to successfully identifying potentially functional interactions within the genome.
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Affiliation(s)
- Ning Liu
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, The Graduate School of Biomedical Engineering, The University of New South Wales, NSW, 2052, Sydney, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
| | - Stephen Pederson
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
- Dame Roma Mitchell Cancer Research Laboratories (DRMCRL), Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - Simon Barry
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - James Breen
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia.
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia.
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia.
- South Australian Genomics Centre (SAGC), South Australian Health & Medical Research Institute (SAHMRI), SA, 5000, Adelaide, Australia.
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6
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Boltsis I, Grosveld F, Giraud G, Kolovos P. Chromatin Conformation in Development and Disease. Front Cell Dev Biol 2021; 9:723859. [PMID: 34422840 PMCID: PMC8371409 DOI: 10.3389/fcell.2021.723859] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
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Affiliation(s)
- Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
- Cancer Research Center of Lyon – INSERM U1052, Lyon, France
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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7
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Zittersteijn HA, Harteveld CL, Klaver-Flores S, Lankester AC, Hoeben RC, Staal FJT, Gonçalves MAFV. A Small Key for a Heavy Door: Genetic Therapies for the Treatment of Hemoglobinopathies. Front Genome Ed 2021; 2:617780. [PMID: 34713239 PMCID: PMC8525365 DOI: 10.3389/fgeed.2020.617780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Throughout the past decades, the search for a treatment for severe hemoglobinopathies has gained increased interest within the scientific community. The discovery that ɤ-globin expression from intact HBG alleles complements defective HBB alleles underlying β-thalassemia and sickle cell disease, has provided a promising opening for research directed at relieving ɤ-globin repression mechanisms and, thereby, improve clinical outcomes for patients. Various gene editing strategies aim to reverse the fetal-to-adult hemoglobin switch to up-regulate ɤ-globin expression through disabling either HBG repressor genes or repressor binding sites in the HBG promoter regions. In addition to these HBB mutation-independent strategies involving fetal hemoglobin (HbF) synthesis de-repression, the expanding genome editing toolkit is providing increased accuracy to HBB mutation-specific strategies encompassing adult hemoglobin (HbA) restoration for a personalized treatment of hemoglobinopathies. Moreover, besides genome editing, more conventional gene addition strategies continue under investigation to restore HbA expression. Together, this research makes hemoglobinopathies a fertile ground for testing various innovative genetic therapies with high translational potential. Indeed, the progressive understanding of the molecular clockwork underlying the hemoglobin switch together with the ongoing optimization of genome editing tools heightens the prospect for the development of effective and safe treatments for hemoglobinopathies. In this context, clinical genetics plays an equally crucial role by shedding light on the complexity of the disease and the role of ameliorating genetic modifiers. Here, we cover the most recent insights on the molecular mechanisms underlying hemoglobin biology and hemoglobinopathies while providing an overview of state-of-the-art gene editing platforms. Additionally, current genetic therapies under development, are equally discussed.
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Affiliation(s)
- Hidde A. Zittersteijn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Cornelis L. Harteveld
- Department of Human and Clinical Genetics, The Hemoglobinopathies Laboratory, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arjan C. Lankester
- Department of Pediatrics, Stem Cell Transplantation Program, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Rob C. Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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8
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Bottardi S, Milot E. An early start of Coup-TFII promotes γ-globin gene expression in adult erythroid cells. Haematologica 2021; 106:335-336. [PMID: 33522785 PMCID: PMC7849336 DOI: 10.3324/haematol.2020.266791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Indexed: 11/27/2022] Open
Affiliation(s)
- Stefania Bottardi
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l'Île de Montréal, Montréal
| | - Eric Milot
- Maisonneuve Rosemont Hospital Research Center, CIUSSS Est de l'Île de Montréal, Montréal; Department of Medicine, University of Montreal, Montréal, Québec.
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9
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Domcke S, Hill AJ, Daza RM, Cao J, O'Day DR, Pliner HA, Aldinger KA, Pokholok D, Zhang F, Milbank JH, Zager MA, Glass IA, Steemers FJ, Doherty D, Trapnell C, Cusanovich DA, Shendure J. A human cell atlas of fetal chromatin accessibility. Science 2020; 370:eaba7612. [PMID: 33184180 PMCID: PMC7785298 DOI: 10.1126/science.aba7612] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022]
Abstract
The chromatin landscape underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of chromatin accessibility and gene expression in fetal tissues. For chromatin accessibility, we devised a three-level combinatorial indexing assay and applied it to 53 samples representing 15 organs, profiling ~800,000 single cells. We leveraged cell types defined by gene expression to annotate these data and cataloged hundreds of thousands of candidate regulatory elements that exhibit cell type-specific chromatin accessibility. We investigated the properties of lineage-specific transcription factors (such as POU2F1 in neurons), organ-specific specializations of broadly distributed cell types (such as blood and endothelial), and cell type-specific enrichments of complex trait heritability. These data represent a rich resource for the exploration of in vivo human gene regulation in diverse tissues and cell types.
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Affiliation(s)
- Silvia Domcke
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew J Hill
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Junyue Cao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah A Pliner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Kimberly A Aldinger
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Jennifer H Milbank
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael A Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Darren A Cusanovich
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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10
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Siwek W, Tehrani SSH, Mata JF, Jansen LET. Activation of Clustered IFNγ Target Genes Drives Cohesin-Controlled Transcriptional Memory. Mol Cell 2020; 80:396-409.e6. [PMID: 33108759 PMCID: PMC7657446 DOI: 10.1016/j.molcel.2020.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/31/2020] [Accepted: 10/01/2020] [Indexed: 12/15/2022]
Abstract
Cytokine activation of cells induces gene networks involved in inflammation and immunity. Transient gene activation can have a lasting effect even in the absence of ongoing transcription, known as long-term transcriptional memory. Here we explore the nature of the establishment and maintenance of interferon γ (IFNγ)-induced priming of human cells. We find that, although ongoing transcription and local chromatin signatures are short-lived, the IFNγ-primed state stably propagates through at least 14 cell division cycles. Single-cell analysis reveals that memory is manifested by an increased probability of primed cells to engage in target gene expression, correlating with the strength of initial gene activation. Further, we find that strongly memorized genes tend to reside in genomic clusters and that long-term memory of these genes is locally restricted by cohesin. We define the duration, stochastic nature, and molecular mechanisms of IFNγ-induced transcriptional memory, relevant to understanding enhanced innate immune signaling.
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Affiliation(s)
- Wojciech Siwek
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
| | - Sahar S H Tehrani
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - João F Mata
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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11
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Papadopoulos P, Kafasi A, De Cuyper IM, Barroca V, Lewandowski D, Kadri Z, Veldthuis M, Berghuis J, Gillemans N, Benavente Cuesta CM, Grosveld FG, van Zwieten R, Philipsen S, Vernet M, Gutiérrez L, Patrinos GP. Mild dyserythropoiesis and β-like globin gene expression imbalance due to the loss of histone chaperone ASF1B. Hum Genomics 2020; 14:39. [PMID: 33066815 PMCID: PMC7566067 DOI: 10.1186/s40246-020-00283-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/10/2020] [Indexed: 01/09/2023] Open
Abstract
The expression of the human β-like globin genes follows a well-orchestrated developmental pattern, undergoing two essential switches, the first one during the first weeks of gestation (ε to γ), and the second one during the perinatal period (γ to β). The γ- to β-globin gene switching mechanism includes suppression of fetal (γ-globin, HbF) and activation of adult (β-globin, HbA) globin gene transcription. In hereditary persistence of fetal hemoglobin (HPFH), the γ-globin suppression mechanism is impaired leaving these individuals with unusual elevated levels of fetal hemoglobin (HbF) in adulthood. Recently, the transcription factors KLF1 and BCL11A have been established as master regulators of the γ- to β-globin switch. Previously, a genomic variant in the KLF1 gene, identified by linkage analysis performed on twenty-seven members of a Maltese family, was found to be associated with HPFH. However, variation in the levels of HbF among family members, and those from other reported families carrying genetic variants in KLF1, suggests additional contributors to globin switching. ASF1B was downregulated in the family members with HPFH. Here, we investigate the role of ASF1B in γ- to β-globin switching and erythropoiesis in vivo. Mouse-human interspecies ASF1B protein identity is 91.6%. By means of knockdown functional assays in human primary erythroid cultures and analysis of the erythroid lineage in Asf1b knockout mice, we provide evidence that ASF1B is a novel contributor to steady-state erythroid differentiation, and while its loss affects the balance of globin expression, it has no major role in hemoglobin switching.
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Affiliation(s)
- Petros Papadopoulos
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain.
| | - Athanassia Kafasi
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
| | - Iris M De Cuyper
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
| | - Vilma Barroca
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
- U1274, Inserm, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Daniel Lewandowski
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
- U1274, Inserm, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Zahra Kadri
- Division of Innovative Therapies, UMR1184, Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - Martijn Veldthuis
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Jeffrey Berghuis
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Nynke Gillemans
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Celina María Benavente Cuesta
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Rob van Zwieten
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
- Laboratory of Red Blood Cell Diagnostics, Sanquin Diagnostics, Amsterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Muriel Vernet
- UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université de Paris-Saclay, CEA, 18 route du Panorama, 92260, Fontenay-aux-Roses, France
| | - Laura Gutiérrez
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
- Department of Hematology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, UvA, Amsterdam, The Netherlands
- Platelet Research Lab -Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-, Department of Medicine -University of Oviedo-, Oviedo, Spain
| | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
- Department of Pathology, College of Medicine and Health Sciences and Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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12
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Tsujimura T. Mechanistic insights into the evolution of the differential expression of tandemly arrayed cone opsin genes in zebrafish. Dev Growth Differ 2020; 62:465-475. [PMID: 32712957 DOI: 10.1111/dgd.12690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/10/2020] [Accepted: 07/18/2020] [Indexed: 12/21/2022]
Abstract
The genome of many organisms contains several loci consisting of duplicated genes that are arrayed in tandem. The daughter genes produced by duplication typically exhibit differential expression patterns with each other or otherwise experience pseudogenization. Remarkably, opsin genes in fish are preserved after many duplications in different lineages. This fact indicates that fish opsin genes are characterized by a regulatory mechanism that could intrinsically facilitate the differentiation of the expression patterns. However, little is known about the mechanisms that underlie the differential expression patterns or how they were established during evolution. The loci of green (RH2)- and red (LWS)-sensitive cone opsin genes in zebrafish have been used as model systems to study the differential regulation of tandemly arrayed opsin genes. Over a decade of studies have uncovered several mechanistic features that might have assisted the differentiation and preservation of duplicated genes. Furthermore, recent progress in the understanding of the transcriptional process in general has added essential insights. In this article, the current understanding of the transcriptional regulation of differentially expressed tandemly arrayed cone opsin genes in zebrafish is summarized and a possible evolutionary scenario that could achieve this differentiation is discussed.
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Affiliation(s)
- Taro Tsujimura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
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13
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Endothelial Cell-Selective Adhesion Molecule Contributes to the Development of Definitive Hematopoiesis in the Fetal Liver. Stem Cell Reports 2020; 13:992-1005. [PMID: 31813828 PMCID: PMC6915804 DOI: 10.1016/j.stemcr.2019.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 02/06/2023] Open
Abstract
Endothelial cell-selective adhesion molecule (ESAM) is a lifelong marker of hematopoietic stem cells (HSCs). Although we previously elucidated the functional importance of ESAM in HSCs in stress-induced hematopoiesis in adults, it is unclear how ESAM affects hematopoietic development during fetal life. To address this issue, we analyzed fetuses from conventional or conditional ESAM-knockout mice. Approximately half of ESAM-null fetuses died after mid-gestation due to anemia. RNA sequencing analyses revealed downregulation of adult-type globins and Alas2, a heme biosynthesis enzyme, in ESAM-null fetal livers. These abnormalities were attributed to malfunction of ESAM-null HSCs, which was demonstrated in culture and transplantation experiments. Although crosslinking ESAM directly influenced gene transcription in HSCs, observations in conditional ESAM-knockout fetuses revealed the critical involvement of ESAM expressed in endothelial cells in fetal lethality. Thus, we showed that ESAM had important roles in developing definitive hematopoiesis. Furthermore, we unveiled the importance of endothelial ESAM in this process.
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14
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Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers. Nat Commun 2019; 10:2626. [PMID: 31201308 PMCID: PMC6572804 DOI: 10.1038/s41467-019-10402-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Chromatin of mammalian nucleus folds into discrete contact enriched regions such as Topologically Associating Domains (TADs). Folding hierarchy and internal organization of TADs is highly dynamic throughout cellular differentiation, and are correlated with gene activation and silencing. To account for multiple interacting TADs, we developed a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency Hi-C encounters within and between TADs into direct loci interactions using cross-links at a given base-pair resolution. We reconstruct three TADs of the mammalian X chromosome for three stages of differentiation. We compute the radius of gyration of TADs and the encounter probability between genomic segments. We found 1) a synchronous compaction and decompaction of TADs throughout differentiation and 2) high order organization into meta-TADs resulting from weak inter-TAD interactions. Finally, the present framework allows to infer transient properties of the chromatin from steady-state statistics embedded in the Hi-C/5C data. Chromatin is folded into Topologically Associating domains (TADs), with the organization and folding hierarchy of the TADs being highly dynamic. Here the authors develop a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency encounters present in Hi-C data within and between TADs and reconstruct TADs across cell differentiation, revealing local chromatin re-organization.
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15
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Zheng H, Xie W. The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol 2019; 20:535-550. [DOI: 10.1038/s41580-019-0132-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Barbarani G, Fugazza C, Strouboulis J, Ronchi AE. The Pleiotropic Effects of GATA1 and KLF1 in Physiological Erythropoiesis and in Dyserythropoietic Disorders. Front Physiol 2019; 10:91. [PMID: 30809156 PMCID: PMC6379452 DOI: 10.3389/fphys.2019.00091] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/25/2019] [Indexed: 01/19/2023] Open
Abstract
In the last few years, the advent of new technological approaches has led to a better knowledge of the ontogeny of erythropoiesis during development and of the journey leading from hematopoietic stem cells (HSCs) to mature red blood cells (RBCs). Our view of a well-defined hierarchical model of hematopoiesis with a near-homogeneous HSC population residing at the apex has been progressively challenged in favor of a landscape where HSCs themselves are highly heterogeneous and lineages separate earlier than previously thought. The coordination of these events is orchestrated by transcription factors (TFs) that work in a combinatorial manner to activate and/or repress their target genes. The development of next generation sequencing (NGS) has facilitated the identification of pathological mutations involving TFs underlying hematological defects. The examples of GATA1 and KLF1 presented in this review suggest that in the next few years the number of TF mutations associated with dyserythropoietic disorders will further increase.
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Affiliation(s)
- Gloria Barbarani
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi Milano-Bicocca, Milan, Italy
| | - Cristina Fugazza
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi Milano-Bicocca, Milan, Italy
| | - John Strouboulis
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Antonella E Ronchi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi Milano-Bicocca, Milan, Italy
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17
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Khan NM, Rehman SU, Shakeel M, Khan S, Ahmed U, Rehman H, Yaseen T, Javid A. Molecular Characterization of β-Thalassemia Mutations Via the Amplification Refractory Mutation System-Polymerase Chain Reaction Method at the North Waziristan Agency, Pakistan. Hemoglobin 2018; 42:91-95. [PMID: 30200837 DOI: 10.1080/03630269.2018.1487308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
β-Thalassemia (β-thal) is a monogenic disease characterized by mutations on the HBB gene, affecting the production of globin that results in hypochromic and microcytic anemia. The aim of this study was to determine the prevalence of six common β-thal mutations, and their frequency and inheritance pattern in affected populations of North Waziristan Agency, Pakistan. In this study, 130 blood samples from 37 unrelated β-thalassemic families having a minimum of one transfusion-dependent child with β-thal major (β-TM), were retrieved either from the Thalassaemia Centre for Women and Children Hospital Bannu or their home towns situated in Noth Waziristan Agency. All samples were analyzed by the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) using six allele-specific primers for the presence of the six β-thal mutations common in the Pakistani population. Of the six common mutations, our study demonstrated five HBB mutations comprising HBB: c.27_28insG, HBB: c.92+5G>C, HBB: c.126_129delCTTT, HBB: c.92+1G>T and HBB: c.17_18delCT from the families studied, while mutation HBB: c.47G>A [codon 15 (G>A)] was not detected in any of the studied families. Furthermore, the HBB: c.27_28insG and HBB: c.92+5G>C were noted to be the most common with frequencies of 42.85 and 31.42%, respectively. The findings of the present study may be useful in launching carrier screening and prenatal diagnosis (PND) programs by screening analyzed and other unanalyzed affected families for the possible presence of common mutations through the ARMS-PCR technique that will help to control the disease.
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Affiliation(s)
- Noor M Khan
- a Department of Biotechnology , University of Science and Technology Bannu (USTB) , Bannu , Khyber Pakhtunkhwa Province , Pakistan
| | - Shoaib Ur Rehman
- a Department of Biotechnology , University of Science and Technology Bannu (USTB) , Bannu , Khyber Pakhtunkhwa Province , Pakistan
| | - Muhammad Shakeel
- b Department of Biotechnology , Bacha Khan University Charsadda , Charsadda , Khyber Pakhtunkhwa Province , Pakistan
| | - Saadullah Khan
- c Department of Biotechnology and Genetic Engineering , Kohat University of Science and Technology , Kohat , Khyber Pakhtunkhwa Province , Pakistan
| | - Usman Ahmed
- a Department of Biotechnology , University of Science and Technology Bannu (USTB) , Bannu , Khyber Pakhtunkhwa Province , Pakistan
| | - Hazir Rehman
- d Department of Microbiology , Kohat University of Science and Technology , Kohat , Khyber Pakhtunkhwa Province , Pakistan
| | - Tabassum Yaseen
- e Department of Botany , Bacha Khan University Charsadda , Charsadda , Khyber Pakhtunkhwa Province , Pakistan
| | - Asad Javid
- a Department of Biotechnology , University of Science and Technology Bannu (USTB) , Bannu , Khyber Pakhtunkhwa Province , Pakistan
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18
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Abstract
In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.
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Affiliation(s)
- Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom; .,Current affiliation: Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; .,Institute for Integrative Biology of the Cell, 91190 Gif-sur-Yvette, France
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom;
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19
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Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cell 2018; 174:1309-1324.e18. [PMID: 30078704 PMCID: PMC6158300 DOI: 10.1016/j.cell.2018.06.052] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/08/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023]
Abstract
We applied a combinatorial indexing assay, sci-ATAC-seq, to profile genome-wide chromatin accessibility in ∼100,000 single cells from 13 adult mouse tissues. We identify 85 distinct patterns of chromatin accessibility, most of which can be assigned to cell types, and ∼400,000 differentially accessible elements. We use these data to link regulatory elements to their target genes, to define the transcription factor grammar specifying each cell type, and to discover in vivo correlates of heterogeneity in accessibility within cell types. We develop a technique for mapping single cell gene expression data to single-cell chromatin accessibility data, facilitating the comparison of atlases. By intersecting mouse chromatin accessibility with human genome-wide association summary statistics, we identify cell-type-specific enrichments of the heritability signal for hundreds of complex traits. These data define the in vivo landscape of the regulatory genome for common mammalian cell types at single-cell resolution.
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Affiliation(s)
- Darren A Cusanovich
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Andrew J Hill
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Delasa Aghamirzaie
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Hannah A Pliner
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joel B Berletch
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Galina N Filippova
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Computer Science, University of Washington, Seattle, WA 98195, USA
| | | | - William S DeWitt
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Samuel G Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David F Read
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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20
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Diepstraten ST, Hart AH. Modelling human haemoglobin switching. Blood Rev 2018; 33:11-23. [PMID: 30616747 DOI: 10.1016/j.blre.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
Genetic lesions of the β-globin gene result in haemoglobinopathies such as β-thalassemia and sickle cell disease. To discover and test new molecular medicines for β-haemoglobinopathies, cell-based and animal models are now being widely utilised. However, multiple in vitro and in vivo models are required due to the complex structure and regulatory mechanisms of the human globin gene locus, subtle species-specific differences in blood cell development, and the influence of epigenetic factors. Advances in genome sequencing, gene editing, and precision medicine have enabled the first generation of molecular therapies aimed at reactivating, repairing, or replacing silenced or damaged globin genes. Here we compare and contrast current animal and cell-based models, highlighting their complementary strengths, reflecting on how they have informed the scope and direction of the field, and describing some of the novel molecular and precision medicines currently under development or in clinical trial.
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Affiliation(s)
- Sarah T Diepstraten
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Adam H Hart
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
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21
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Iarovaia OV, Kovina AP, Petrova NV, Razin SV, Ioudinkova ES, Vassetzky YS, Ulianov SV. Genetic and Epigenetic Mechanisms of β-Globin Gene Switching. BIOCHEMISTRY (MOSCOW) 2018; 83:381-392. [PMID: 29626925 DOI: 10.1134/s0006297918040090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vertebrates have multiple forms of hemoglobin that differ in the composition of their polypeptide chains. During ontogenesis, the composition of these subunits changes. Genes encoding different α- and β-polypeptide chains are located in two multigene clusters on different chromosomes. Each cluster contains several genes that are expressed at different stages of ontogenesis. The phenomenon of stage-specific transcription of globin genes is referred to as globin gene switching. Mechanisms of expression switching, stage-specific activation, and repression of transcription of α- and β-globin genes are of interest from both theoretical and practical points of view. Alteration of balanced expression of globin genes, which usually occurs due to damage to adult β-globin genes, leads to development of severe diseases - hemoglobinopathies. In most cases, reactivation of the fetal hemoglobin gene in patients with β-thalassemia and sickle cell disease can reduce negative consequences of irreversible alterations of expression of the β-globin genes. This review focuses on the current state of research on genetic and epigenetic mechanisms underlying stage-specific switching of β-globin genes.
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Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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22
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Vinjamur DS, Bauer DE, Orkin SH. Recent progress in understanding and manipulating haemoglobin switching for the haemoglobinopathies. Br J Haematol 2017; 180:630-643. [PMID: 29193029 DOI: 10.1111/bjh.15038] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The major β-haemoglobinopathies, sickle cell disease and β-thalassaemia, represent the most common monogenic disorders worldwide and a steadily increasing global disease burden. Allogeneic haematopoietic stem cell transplantation, the only curative therapy, is only applied to a small minority of patients. Common clinical management strategies act mainly downstream of the root causes of disease. The observation that elevated fetal haemoglobin expression ameliorates these disorders has motivated longstanding investigations into the mechanisms of haemoglobin switching. Landmark studies over the last decade have led to the identification of two potent transcriptional repressors of γ-globin, BCL11A and ZBTB7A. These regulators act with additional trans-acting epigenetic repressive complexes, lineage-defining factors and developmental programs to silence fetal haemoglobin by working on cis-acting sequences at the globin gene loci. Rapidly advancing genetic technology is enabling researchers to probe deeply the interplay between the molecular players required for γ-globin (HBG1/HBG2) silencing. Gene therapies may enable permanent cures with autologous modified haematopoietic stem cells that generate persistent fetal haemoglobin expression. Ultimately rational small molecule pharmacotherapies to reactivate HbF could extend benefits widely to patients.
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Affiliation(s)
- Divya S Vinjamur
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Stuart H Orkin
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
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23
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Oudelaar AM, Hanssen LL, Hardison RC, Kassouf MT, Hughes JR, Higgs DR. Between form and function: the complexity of genome folding. Hum Mol Genet 2017; 26:R208-R215. [PMID: 28977451 PMCID: PMC5886466 DOI: 10.1093/hmg/ddx306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 01/24/2023] Open
Abstract
It has been known for over a century that chromatin is not randomly distributed within the nucleus. However, the question of how DNA is folded and the influence of such folding on nuclear processes remain topics of intensive current research. A longstanding, unanswered question is whether nuclear organization is simply a reflection of nuclear processes such as transcription and replication, or whether chromatin is folded by independent mechanisms and this per se encodes function? Evidence is emerging that both may be true. Here, using the α-globin gene cluster as an illustrative model, we provide an overview of the most recent insights into the layers of genome organization across different scales and how this relates to gene activity.
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Affiliation(s)
- A. Marieke Oudelaar
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Lars L.P. Hanssen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mira T. Kassouf
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Douglas R. Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
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24
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Seguin A, Takahashi-Makise N, Yien YY, Huston NC, Whitman JC, Musso G, Wallace JA, Bradley T, Bergonia HA, Kafina MD, Matsumoto M, Igarashi K, Phillips JD, Paw BH, Kaplan J, Ward DM. Reductions in the mitochondrial ABC transporter Abcb10 affect the transcriptional profile of heme biosynthesis genes. J Biol Chem 2017; 292:16284-16299. [PMID: 28808058 DOI: 10.1074/jbc.m117.797415] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/09/2017] [Indexed: 11/06/2022] Open
Abstract
ATP-binding cassette subfamily B member 10 (Abcb10) is a mitochondrial ATP-binding cassette (ABC) transporter that complexes with mitoferrin1 and ferrochelatase to enhance heme biosynthesis in developing red blood cells. Reductions in Abcb10 levels have been shown to reduce mitoferrin1 protein levels and iron import into mitochondria, resulting in reduced heme biosynthesis. As an ABC transporter, Abcb10 binds and hydrolyzes ATP, but its transported substrate is unknown. Here, we determined that decreases in Abcb10 did not result in protoporphyrin IX accumulation in morphant-treated zebrafish embryos or in differentiated Abcb10-specific shRNA murine Friend erythroleukemia (MEL) cells in which Abcb10 was specifically silenced with shRNA. We also found that the ATPase activity of Abcb10 is necessary for hemoglobinization in MEL cells, suggesting that the substrate transported by Abcb10 is important in mediating increased heme biosynthesis during erythroid development. Inhibition of 5-aminolevulinic acid dehydratase (EC 4.2.1.24) with succinylacetone resulted in both 5-aminolevulinic acid (ALA) accumulation in control and Abcb10-specific shRNA MEL cells, demonstrating that reductions in Abcb10 do not affect ALA export from mitochondria and indicating that Abcb10 does not transport ALA. Abcb10 silencing resulted in an alteration in the heme biosynthesis transcriptional profile due to repression by the transcriptional regulator Bach1, which could be partially rescued by overexpression of Alas2 or Gata1, providing a mechanistic explanation for why Abcb10 shRNA MEL cells exhibit reduced hemoglobinization. In conclusion, our findings rule out that Abcb10 transports ALA and indicate that Abcb10's ATP-hydrolysis activity is critical for hemoglobinization and that the substrate transported by Abcb10 provides a signal that optimizes hemoglobinization.
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Affiliation(s)
- Alexandra Seguin
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | | | | | | | | | - Gabriel Musso
- the Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Jared A Wallace
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Thomas Bradley
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Hector A Bergonia
- the Division of Hematology-Oncology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | | | - Mitsuyo Matsumoto
- the Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - Kazuhiko Igarashi
- the Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - John D Phillips
- the Division of Hematology-Oncology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Barry H Paw
- the Division of Hematology and.,the Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, and.,the Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Jerry Kaplan
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Diane M Ward
- From the Division of Microbiology and Immunology, Department of Pathology, and
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25
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Du M, Zhang Q, Bai L. Three distinct mechanisms of long-distance modulation of gene expression in yeast. PLoS Genet 2017; 13:e1006736. [PMID: 28426659 PMCID: PMC5417705 DOI: 10.1371/journal.pgen.1006736] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/04/2017] [Accepted: 04/05/2017] [Indexed: 12/04/2022] Open
Abstract
Recent Hi-C measurements have revealed numerous intra- and inter-chromosomal interactions in various eukaryotic cells. To what extent these interactions regulate gene expression is not clear. This question is particularly intriguing in budding yeast because it has extensive long-distance chromosomal interactions but few cases of gene regulation over-a-distance. Here, we developed a medium-throughput assay to screen for functional long-distance interactions that affect the average expression level of a reporter gene as well as its cell-to-cell variability (noise). We ectopically inserted an insulated MET3 promoter (MET3pr) flanked by ~1kb invariable sequences into thousands of genomic loci, allowing it to make contacts with different parts of the genome, and assayed the MET3pr activity in single cells. Changes of MET3pr activity in this case necessarily involve mechanisms that function over a distance. MET3pr has similar activities at most locations. However, at some locations, they deviate from the norm and exhibit three distinct patterns including low expression / high noise, low expression / low noise, and high expression / low noise. We provided evidence that these three patterns of MET3pr expression are caused by Sir2-mediated silencing, transcriptional interference, and 3D clustering. The clustering also occurs in the native genome and enhances the transcription of endogenous Met4-targeted genes. Overall, our results demonstrate that a small fraction of long-distance chromosomal interactions can affect gene expression in yeast. Eukaryotic transcription occurs within the nucleus where DNA is packaged into high order chromosome structures. Some long-distance chromosomal interactions play an important role in gene regulation in higher eukaryotic species, such as mouse and human. In budding yeast, gene expression is traditionally thought to be regulated over short distances because the upstream regulatory sequences (URSs) are usually located close to the core promoters. However, recent chromosome conformation capture experiments have detected numerous long-distance chromosomal interactions in the yeast genome. The function of these interactions in gene regulation remains unclear. Here, we developed a new assay to screen for long-distance interactions that affect the activity of a reporter gene. We found three regulatory mechanisms that act from a distance: silencing, transcriptional interference, and 3D clustering, which alter expression level of the reporter gene as well as its cell-to-cell variability. Our results demonstrate that transcription in budding yeast, similar to transcription in higher eukaryotes, can be regulated over long distances. We anticipate our assay can be used as a general platform to screen for functional long-distance chromosomal interactions that affect gene expression.
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Affiliation(s)
- Manyu Du
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, State College, PA, United States of America
- Center for Eukaryotic Gene Regulation, the Pennsylvania State University, University Park, PA, State College, United States of America
| | - Qian Zhang
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, State College, PA, United States of America
- Center for Eukaryotic Gene Regulation, the Pennsylvania State University, University Park, PA, State College, United States of America
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, State College, PA, United States of America
- Center for Eukaryotic Gene Regulation, the Pennsylvania State University, University Park, PA, State College, United States of America
- Department of Physics, the Pennsylvania State University, University Park, State College, PA, United States of America
- * E-mail:
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26
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Lee WS, McColl B, Maksimovic J, Vadolas J. Epigenetic interplay at the β-globin locus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:393-404. [DOI: 10.1016/j.bbagrm.2017.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 02/02/2023]
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27
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Kang Y, Kim YW, Kang J, Yun WJ, Kim A. Erythroid specific activator GATA-1-dependent interactions between CTCF sites around the β-globin locus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:416-426. [PMID: 28161276 DOI: 10.1016/j.bbagrm.2017.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/22/2017] [Accepted: 01/30/2017] [Indexed: 11/24/2022]
Abstract
CTCF sites (binding motifs for CCCTC-binding factor, an insulator protein) are located considerable distances apart on genomes but are closely positioned in organized chromatin. The close positioning of CTCF sites is often cell type or tissue specific. Here we analyzed chromatin organization in eight CTCF sites around the β-globin locus by 3C assay and explored the roles of erythroid specific transcription activator GATA-1 and KLF1 in it. It was found five CTCF sites convergent to the locus interact with each other in erythroid K562 cells but not in non-erythroid 293 cells. The interaction was decreased by depletion of GATA-1 or KLF1. It accompanied reductions of CTCF and Rad21 occupancies and loss of active chromatin structure at the CTCF sites. Furthermore Rad21 occupancy was reduced in the β-globin locus control region (LCR) hypersensitive sites (HSs) by the depletion of GATA-1 or KLF1. The role of GATA-1 in interaction between CTCF sites was revealed by its ectopic expression in 293 cells and by deletion of a GATA-1 site in the LCR HS2. These findings indicate that erythroid specific activator GATA-1 acts at CTCF sites around the β-globin locus to establish tissue-specific chromatin organization.
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Affiliation(s)
- Yujin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Jin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Won Ju Yun
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea.
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28
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Buffry AD, Mendes CC, McGregor AP. The Functionality and Evolution of Eukaryotic Transcriptional Enhancers. ADVANCES IN GENETICS 2016; 96:143-206. [PMID: 27968730 DOI: 10.1016/bs.adgen.2016.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enhancers regulate precise spatial and temporal patterns of gene expression in eukaryotes and, moreover, evolutionary changes in these modular cis-regulatory elements may represent the predominant genetic basis for phenotypic evolution. Here, we review approaches to identify and functionally analyze enhancers and their transcription factor binding sites, including assay for transposable-accessible chromatin-sequencing (ATAC-Seq) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, respectively. We also explore enhancer functionality, including how transcription factor binding sites combine to regulate transcription, as well as research on shadow and super enhancers, and how enhancers can act over great distances and even in trans. Finally, we discuss recent theoretical and empirical data on how transcription factor binding sites and enhancers evolve. This includes how the function of enhancers is maintained despite the turnover of transcription factor binding sites as well as reviewing studies where mutations in enhancers have been shown to underlie morphological change.
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Affiliation(s)
- A D Buffry
- Oxford Brookes University, Oxford, United Kingdom
| | - C C Mendes
- Oxford Brookes University, Oxford, United Kingdom
| | - A P McGregor
- Oxford Brookes University, Oxford, United Kingdom
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29
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Martyn GE, Quinlan KGR, Crossley M. The regulation of human globin promoters by CCAAT box elements and the recruitment of NF-Y. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:525-536. [PMID: 27718361 DOI: 10.1016/j.bbagrm.2016.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/01/2023]
Abstract
CCAAT boxes are motifs found within the proximal promoter of many genes, including the human globin genes. The highly conserved nature of CCAAT box motifs within the promoter region of both α-like and β-like globin genes emphasises the functional importance of the CCAAT sequence in globin gene regulation. Mutations within the β-globin CCAAT box result in β-thalassaemia, while mutations within the distal γ-globin CCAAT box cause the Hereditary Persistence of Foetal Haemoglobin, a benign condition which results in continued γ-globin expression during adult life. Understanding the transcriptional regulation of the globin genes is of particular interest, as reactivating the foetal γ-globin gene alleviates the symptoms of β-thalassaemia and sickle cell anaemia. NF-Y is considered to be the primary activating transcription factor which binds to globin CCAAT box motifs. Here we review recruitment of NF-Y to globin CCAAT boxes and the role NF-Y plays in regulating globin gene expression. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Gabriella E Martyn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia.
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30
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Tasan I, Jain S, Zhao H. Use of genome-editing tools to treat sickle cell disease. Hum Genet 2016; 135:1011-28. [PMID: 27250347 PMCID: PMC5002234 DOI: 10.1007/s00439-016-1688-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 05/11/2016] [Indexed: 12/26/2022]
Abstract
Recent advances in genome-editing techniques have made it possible to modify any desired DNA sequence by employing programmable nucleases. These next-generation genome-modifying tools are the ideal candidates for therapeutic applications, especially for the treatment of genetic disorders like sickle cell disease (SCD). SCD is an inheritable monogenic disorder which is caused by a point mutation in the β-globin gene. Substantial success has been achieved in the development of supportive therapeutic strategies for SCD, but unfortunately there is still a lack of long-term universal cure. The only existing curative treatment is based on allogeneic stem cell transplantation from healthy donors; however, this treatment is applicable to a limited number of patients only. Hence, a universally applicable therapy is highly desirable. In this review, we will discuss the three programmable nucleases that are commonly used for genome-editing purposes: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9). We will continue by exemplifying uses of these methods to correct the sickle cell mutation. Additionally, we will present induction of fetal globin expression as an alternative approach to cure sickle cell disease. We will conclude by comparing the three methods and explaining the concerns about their use in therapy.
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Affiliation(s)
- Ipek Tasan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Surbhi Jain
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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31
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Zhang Y, Huang L, Fu H, Smith OK, Lin CM, Utani K, Rao M, Reinhold WC, Redon CE, Ryan M, Kim R, You Y, Hanna H, Boisclair Y, Long Q, Aladjem MI. A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells. Nat Commun 2016; 7:11748. [PMID: 27272143 PMCID: PMC4899857 DOI: 10.1038/ncomms11748] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/26/2016] [Indexed: 12/28/2022] Open
Abstract
Mammalian chromosome replication starts from distinct sites; however, the principles governing initiation site selection are unclear because proteins essential for DNA replication do not exhibit sequence-specific DNA binding. Here we identify a replication-initiation determinant (RepID) protein that binds a subset of replication-initiation sites. A large fraction of RepID-binding sites share a common G-rich motif and exhibit elevated replication initiation. RepID is required for initiation of DNA replication from RepID-bound replication origins, including the origin at the human beta-globin (HBB) locus. At HBB, RepID is involved in an interaction between the replication origin (Rep-P) and the locus control region. RepID-depleted murine embryonic fibroblasts exhibit abnormal replication fork progression and fewer replication-initiation events. These observations are consistent with a model, suggesting that RepID facilitates replication initiation at a distinct group of human replication origins. Origins of mammalian DNA replication are poorly characterised because they lack an Identifiable consensus sequence. Here the authors identify RepID, a protein that binds to a subset of G-rich replication origins and facilitates initiation from those origins.
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Affiliation(s)
- Ya Zhang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Liang Huang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Owen K Smith
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chii Mei Lin
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Koichi Utani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mishal Rao
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael Ryan
- In Silico Solutions, Fairfax, Virginia 22033, USA
| | - RyangGuk Kim
- In Silico Solutions, Fairfax, Virginia 22033, USA
| | - Yang You
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Harlington Hanna
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yves Boisclair
- Department of Animal Science, Cornell University, Ithaca, New York 14853-4801, USA
| | - Qiaoming Long
- Department of Animal Science, Cornell University, Ithaca, New York 14853-4801, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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32
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Bronkhorst AJ, Aucamp J, Wentzel JF, Pretorius PJ. Reference gene selection for in vitro cell-free DNA analysis and gene expression profiling. Clin Biochem 2016; 49:606-8. [PMID: 26851157 DOI: 10.1016/j.clinbiochem.2016.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/13/2016] [Accepted: 01/28/2016] [Indexed: 12/17/2022]
Abstract
OBJECTIVES (i) To optimize cell-free DNA (cfDNA) and mRNA quantification using eight housekeeping genes (HKGs), (ii) to determine if there is a difference in the occurrence of HKGs in the cfDNA and mRNA of normal cells and cancer cells, and (iii) to investigate whether there is some selectivity involved in the release of cfDNA. DESIGN AND METHODS cfDNA was isolated directly from the growth medium of 3 cultured cancer cell lines and one non-malignant, primary cell line. At the same time interval, mRNA was isolated from these cells and cDNA was synthesized. CfDNA and cDNA were then amplified with real-time PCR utilizing eight different HKGs. RESULTS For all cell lines tested, Beta-actin (ACTB) is the most appropriate HKG to use as a control for cfDNA and mRNA quantification. There was no clear difference in the occurrence of HKGs between cancer cells and healthy cells. Lastly, there is a consistent and distinct difference between the mRNA expression and cfDNA of all cell lines. CONCLUSIONS This study reveals a new candidate HKG for a robust control in cfDNA analysis and gene expression profiling, and should be considered for optimal analysis. Furthermore, results indicate that cfDNA is selectively released from cells into culture medium.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa.
| | - Janine Aucamp
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
| | - Johannes F Wentzel
- Centre of Excellence for Pharmaceutical Sciences (PHARMACEN), North-West University, Potchefstroom 2520, South Africa
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom 2520, South Africa
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33
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Djekidel MN, Liang Z, Wang Q, Hu Z, Li G, Chen Y, Zhang MQ. 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Genome Biol 2015; 16:288. [PMID: 26694485 PMCID: PMC4716632 DOI: 10.1186/s13059-015-0851-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/02/2015] [Indexed: 12/11/2022] Open
Abstract
Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they may control, making it a valuable downstream analysis tool in chromatin conformation studies. 3CPET does so by combining data from ChIA-PET, transcription factor binding sites, and protein interactions. 3CPET results show biologically significant and accurate predictions when validated against experimental and simulation data.
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Affiliation(s)
- Mohamed Nadhir Djekidel
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Zhengyu Liang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Qi Wang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Zhirui Hu
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Guipeng Li
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing, 100084, China. .,Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas, Dallas, 800 West Campbell Road, RL11, Richardson, TX, 75080-3021, USA.
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34
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Editing the genome to introduce a beneficial naturally occurring mutation associated with increased fetal globin. Nat Commun 2015; 6:7085. [PMID: 25971621 DOI: 10.1038/ncomms8085] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/31/2015] [Indexed: 12/15/2022] Open
Abstract
Genetic disorders resulting from defects in the adult globin genes are among the most common inherited diseases. Symptoms worsen from birth as fetal γ-globin expression is silenced. Genome editing could permit the introduction of beneficial single-nucleotide variants to ameliorate symptoms. Here, as proof of concept, we introduce the naturally occurring Hereditary Persistance of Fetal Haemoglobin (HPFH) -175T>C point mutation associated with elevated fetal γ-globin into erythroid cell lines. We show that this mutation increases fetal globin expression through de novo recruitment of the activator TAL1 to promote chromatin looping of distal enhancers to the modified γ-globin promoter.
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35
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Gorkin DU, Leung D, Ren B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 2015; 14:762-75. [PMID: 24905166 DOI: 10.1016/j.stem.2014.05.017] [Citation(s) in RCA: 282] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It can be convenient to think of the genome as simply a string of nucleotides, the linear order of which encodes an organism's genetic blueprint. However, the genome does not exist as a linear entity within cells where this blueprint is actually utilized. Inside the nucleus, the genome is organized in three-dimensional (3D) space, and lineage-specific transcriptional programs that direct stem cell fate are implemented in this native 3D context. Here, we review principles of 3D genome organization in mammalian cells. We focus on the emerging relationship between genome organization and lineage-specific transcriptional regulation, which we argue are inextricably linked.
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Affiliation(s)
- David U Gorkin
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Danny Leung
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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36
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Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A. Constraint and divergence of global gene expression in the mammalian embryo. eLife 2015; 4:e05538. [PMID: 25871848 PMCID: PMC4417935 DOI: 10.7554/elife.05538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 04/13/2015] [Indexed: 11/18/2022] Open
Abstract
The effects of genetic variation on gene regulation in the developing mammalian embryo remain largely unexplored. To globally quantify these effects, we crossed two divergent mouse strains and asked how genotype of the mother or of the embryo drives gene expression phenotype genomewide. Embryonic expression of 331 genes depends on the genotype of the mother. Embryonic genotype controls allele-specific expression of 1594 genes and a highly overlapping set of cis-expression quantitative trait loci (eQTL). A marked paucity of trans-eQTL suggests that the widespread expression differences do not propagate through the embryonic gene regulatory network. The cis-eQTL genes exhibit lower-than-average evolutionary conservation and are depleted for developmental regulators, consistent with purifying selection acting on expression phenotype of pattern formation genes. The widespread effect of maternal and embryonic genotype in conjunction with the purifying selection we uncovered suggests that embryogenesis is an important and understudied reservoir of phenotypic variation.
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Affiliation(s)
- Noah Spies
- Department of Pathology, Stanford University School of Medicine, Stanford, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Cheryl L Smith
- Department of Pathology, Stanford University School of Medicine, Stanford, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Jesse M Rodriguez
- Department of Computer Science, Stanford University, Stanford, United States
- Biomedical Informatics Program, Stanford University School of Medicine, Stanford, United States
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Serafim Batzoglou
- Department of Computer Science, Stanford University, Stanford, United States
| | - Arend Sidow
- Department of Pathology, Stanford University School of Medicine, Stanford, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
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37
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O'Sullivan JM, Doynova MD, Antony J, Pichlmuller F, Horsfield JA. Insights from space: potential role of diet in the spatial organization of chromosomes. Nutrients 2014; 6:5724-39. [PMID: 25514390 PMCID: PMC4276994 DOI: 10.3390/nu6125724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 02/07/2023] Open
Abstract
We can now sequence and identify genome wide epigenetic patterns and perform a variety of "genomic experiments" within relatively short periods of time-ranging from days to weeks. Yet, despite these technological advances, we have a poor understanding of the inter-relationships between epigenetics, genome structure-function, and nutrition. Perhaps this limitation lies, in part, in our propensity to study epigenetics in terms of the linear arrangement of elements and genes. Here we propose that a more complete understanding of how nutrition impacts on epigenetics and cellular development resides within the inter-relationships between DNA and histone modification patterns and genome function, in the context of spatial organization of chromatin and the epigenome.
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Affiliation(s)
- Justin M O'Sullivan
- The Liggins Institute, The University of Auckland, Private Bag 92019 AMC, Auckland 1142, New Zealand.
| | - Malina D Doynova
- The Liggins Institute, The University of Auckland, Private Bag 92019 AMC, Auckland 1142, New Zealand.
| | - Jisha Antony
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin 9054, New Zealand.
| | - Florian Pichlmuller
- The Liggins Institute, The University of Auckland, Private Bag 92019 AMC, Auckland 1142, New Zealand.
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin 9054, New Zealand.
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38
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Expansion of stochastic expression repertoire by tandem duplication in mouse Protocadherin-α cluster. Sci Rep 2014; 4:6263. [PMID: 25179445 PMCID: PMC4151104 DOI: 10.1038/srep06263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/13/2014] [Indexed: 11/08/2022] Open
Abstract
Tandem duplications are concentrated within the Pcdh cluster throughout vertebrate evolution and as copy number variations (CNVs) in human populations, but the effects of tandem duplication in the Pcdh cluster remain elusive. To investigate the effects of tandem duplication in the Pcdh cluster, here we generated and analyzed a new line of the Pcdh cluster mutant mice. In the mutant allele, a 218-kb region containing the Pcdh-α2 to Pcdh-αc2 variable exons with their promoters was duplicated and the individual duplicated Pcdh isoforms can be disctinguished. The individual duplicated Pcdh-α isoforms showed diverse expression level with stochastic expression manner, even though those have an identical promoter sequence. Interestingly, the 5'-located duplicated Pcdh-αc2, which is constitutively expressed in the wild-type brain, shifted to stochastic expression accompanied by increased DNA methylation. These results demonstrate that tandem duplication in the Pcdh cluster expands the stochastic expression repertoire irrespective of sequence divergence.
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Gushchanskaya ES, Artemov AV, Ulyanov SV, Logacheva MD, Penin AA, Kotova ES, Akopov SB, Nikolaev LG, Iarovaia OV, Sverdlov ED, Gavrilov AA, Razin SV. The clustering of CpG islands may constitute an important determinant of the 3D organization of interphase chromosomes. Epigenetics 2014; 9:951-63. [PMID: 24736527 DOI: 10.4161/epi.28794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We used the 4C-Seq technique to characterize the genome-wide patterns of spatial contacts of several CpG islands located on chromosome 14 in cultured chicken lymphoid and erythroid cells. We observed a clear tendency for the spatial clustering of CpG islands present on the same and different chromosomes, regardless of the presence or absence of promoters within these CpG islands. Accordingly, we observed preferential spatial contacts between Sp1 binding motifs and other GC-rich genomic elements, including the DNA sequence motifs capable of forming G-quadruplexes. However, an anchor placed in a gene/CpG island-poor area formed spatial contacts with other gene/CpG island-poor areas on chromosome 14 and other chromosomes. These results corroborate the two-compartment model of the spatial organization of interphase chromosomes and suggest that the clustering of CpG islands constitutes an important determinant of the 3D organization of the eukaryotic genome in the cell nucleus. Using the ChIP-Seq technique, we mapped the genome-wide CTCF deposition sites in the chicken lymphoid and erythroid cells that were used for the 4C analysis. We observed a good correlation between the density of CTCF deposition sites and the level of 4C signals for the anchors located in CpG islands but not for an anchor located in a gene desert. It is thus possible that CTCF contributes to the clustering of CpG islands observed in our experiments.
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Affiliation(s)
- Ekaterina S Gushchanskaya
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Molecular Biology; Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Artem V Artemov
- Faculty of Bioengineering and Bioinformatics; Lomonosov Moscow State University; Moscow, Russia; Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow, Russia
| | - Sergey V Ulyanov
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Maria D Logacheva
- Laboratory of Evolutionary Genomics; Lomonosov Moscow State University; Moscow, Russia
| | - Aleksey A Penin
- Laboratory of Evolutionary Genomics; Lomonosov Moscow State University; Moscow, Russia
| | - Elena S Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Sergey B Akopov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Lev G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Olga V Iarovaia
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Eugene D Sverdlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia; Department of Molecular Biology; Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Villejuif, France and Moscow, Russia
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Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science 2013; 342:253-7. [PMID: 24115442 PMCID: PMC4018826 DOI: 10.1126/science.1242088] [Citation(s) in RCA: 460] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWASs) have ascertained numerous trait-associated common genetic variants, frequently localized to regulatory DNA. We found that common genetic variation at BCL11A associated with fetal hemoglobin (HbF) level lies in noncoding sequences decorated by an erythroid enhancer chromatin signature. Fine-mapping uncovers a motif-disrupting common variant associated with reduced transcription factor (TF) binding, modestly diminished BCL11A expression, and elevated HbF. The surrounding sequences function in vivo as a developmental stage-specific, lineage-restricted enhancer. Genome engineering reveals the enhancer is required in erythroid but not B-lymphoid cells for BCL11A expression. These findings illustrate how GWASs may expose functional variants of modest impact within causal elements essential for appropriate gene expression. We propose the GWAS-marked BCL11A enhancer represents an attractive target for therapeutic genome engineering for the β-hemoglobinopathies.
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Affiliation(s)
- Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
- Harvard Medical School, Boston, MA, 02115
| | - Sophia C. Kamran
- Harvard Medical School, Boston, MA, 02115
- Howard Hughes Medical Institute, Boston, MA, 02115
| | - Samuel Lessard
- Montreal Heart Institute and Université Montréal, Montreal, Quebec, H1T 1C8, Canada
| | - Jian Xu
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
- Harvard Medical School, Boston, MA, 02115
| | - Yuko Fujiwara
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | - Carrie Lin
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | - Zhen Shao
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | | | - Elenoe C. Smith
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | - Luca Pinello
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Peter J. Sabo
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, 98195
| | - Jeff Vierstra
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, 98195
| | - Richard A. Voit
- Department of Pediatrics, Stanford University, Palo Alto, CA, 94304
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115
- Harvard School of Public Health, Boston, MA, 02115
| | | | | | - Guillaume Lettre
- Montreal Heart Institute and Université Montréal, Montreal, Quebec, H1T 1C8, Canada
| | - Stuart H. Orkin
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
- Harvard Medical School, Boston, MA, 02115
- Howard Hughes Medical Institute, Boston, MA, 02115
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41
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DNA double-strand breaks: linking gene expression to chromosome morphology and mobility. Chromosoma 2013; 123:103-15. [DOI: 10.1007/s00412-013-0432-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 08/06/2013] [Accepted: 08/08/2013] [Indexed: 11/27/2022]
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Razin SV, Gavrilov AA, Ioudinkova ES, Iarovaia OV. Communication of genome regulatory elements in a folded chromosome. FEBS Lett 2013; 587:1840-7. [PMID: 23651551 DOI: 10.1016/j.febslet.2013.04.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
The most popular model of gene activation by remote enhancers postulates that the enhancers interact directly with target promoters via the looping of intervening DNA fragments. This interaction is thought to be necessary for the stabilization of the Pol II pre-initiation complex and/or for the transfer of transcription factors and Pol II, which are initially accumulated at the enhancer, to the promoter. The direct interaction of enhancer(s) and promoter(s) is only possible when these elements are located in close proximity within the nuclear space. Here, we discuss the molecular mechanisms for maintaining the close proximity of the remote regulatory elements of the eukaryotic genome. The models of an active chromatin hub (ACH) and an active nuclear compartment are considered, focusing on the role of chromatin folding in juxtaposing remote DNA sequences. The interconnection between the functionally dependent architecture of the interphase chromosome and nuclear compartmentalization is also discussed.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia.
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Noordermeer D, Duboule D. Chromatin looping and organization at developmentally regulated gene loci. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2013; 2:615-30. [PMID: 24014450 DOI: 10.1002/wdev.103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Developmentally regulated genes are often controlled by distant enhancers, silencers and insulators, to implement their correct transcriptional programs. In recent years, the development of 3C and derived techniques (4C, 5C, HiC, ChIA-PET, etc.) has confirmed that chromatin looping is an important mechanism for the transfer of regulatory information in mammalian cells. At many developmentally regulated gene loci, transcriptional activation is indeed accompanied by the formation of chromatin loops between genes and distant enhancers. Similarly, dynamic looping between insulator elements and changes in local 3D organization may be observed upon variation in transcriptional activity. Chromatin looping also occurs at silent gene loci, where its function remains less understood. In lineage-committed cells, partial 3D configurations are detected at loci that are activated at later stages. However, these partial configurations usually lack promoter-enhancer loops that accompany transcriptional activation, suggesting they have structural functions. Definitive evidence for a repressive role of chromatin looping is still lacking. Chromatin loops have been reported at repressed loci but, alternatively, they may act as a distraction for active loops. Together, these mechanisms allow fine-tuning of regulatory programs, thus providing further diversity in the transcriptional control of developmentally regulated gene loci.
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Affiliation(s)
- Daan Noordermeer
- National Research Centre Frontiers in Genetics, School of Life Sciences, Ecole Polytechnique Frale (EPFL), Lausanne, Switzerland
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Abstract
The globin gene disorders including the thalassemias are among the most common human genetic diseases with more than 300,000 severely affected individuals born throughout the world every year. Because of the easy accessibility of purified, highly specialized, mature erythroid cells from peripheral blood, the hemoglobinopathies were among the first tractable human molecular diseases. From the 1970s onward, the analysis of the large repertoire of mutations underlying these conditions has elucidated many of the principles by which mutations occur and cause human genetic diseases. This work will summarize our current knowledge of the α-thalassemias, illustrating how detailed analysis of this group of diseases has contributed to our understanding of the general molecular mechanisms underlying many orphan and common diseases.
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Affiliation(s)
- Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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Moleirinho A, Seixas S, Lopes AM, Bento C, Prata MJ, Amorim A. Evolutionary constraints in the β-globin cluster: the signature of purifying selection at the δ-globin (HBD) locus and its role in developmental gene regulation. Genome Biol Evol 2013; 5:559-71. [PMID: 23431002 PMCID: PMC3622298 DOI: 10.1093/gbe/evt029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2013] [Indexed: 12/15/2022] Open
Abstract
Human hemoglobins, the oxygen carriers in the blood, are composed by two α-like and two β-like globin monomers. The β-globin gene cluster located at 11p15.5 comprises one pseudogene and five genes whose expression undergoes two critical switches: the embryonic-to-fetal and fetal-to-adult transition. HBD encodes the δ-globin chain of the minor adult hemoglobin (HbA2), which is assumed to be physiologically irrelevant. Paradoxically, reduced diversity levels have been reported for this gene. In this study, we sought a detailed portrait of the genetic variation within the β-globin cluster in a large human population panel from different geographic backgrounds. We resequenced the coding and noncoding regions of the two adult β-globin genes (HBD and HBB) in European and African populations, and analyzed the data from the β-globin cluster (HBE, HBG2, HBG1, HBBP1, HBD, and HBB) in 1,092 individuals representing 14 populations sequenced as part of the 1000 Genomes Project. Additionally, we assessed the diversity levels in nonhuman primates using chimpanzee sequence data provided by the PanMap Project. Comprehensive analyses, based on classic neutrality tests, empirical and haplotype-based studies, revealed that HBD and its neighbor pseudogene HBBP1 have mainly evolved under purifying selection, suggesting that their roles are essential and nonredundant. Moreover, in the light of recent studies on the chromatin conformation of the β-globin cluster, we present evidence sustaining that the strong functional constraints underlying the decreased contemporary diversity at these two regions were not driven by protein function but instead are likely due to a regulatory role in ontogenic switches of gene expression.
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Affiliation(s)
- Ana Moleirinho
- Institute of Molecular Pathology and Immunology of University of Porto (IPATIMUP), Porto, Portugal.
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Arnone JT, Robbins-Pianka A, Arace JR, Kass-Gergi S, McAlear MA. The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes. BMC Genomics 2012; 13:546. [PMID: 23051624 PMCID: PMC3500266 DOI: 10.1186/1471-2164-13-546] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 10/03/2012] [Indexed: 11/16/2022] Open
Abstract
Background Coordinated cell growth and development requires that cells regulate the expression of large sets of genes in an appropriate manner, and one of the most complex and metabolically demanding pathways that cells must manage is that of ribosome biogenesis. Ribosome biosynthesis depends upon the activity of hundreds of gene products, and it is subject to extensive regulation in response to changing cellular conditions. We previously described an unusual property of the genes that are involved in ribosome biogenesis in yeast; a significant fraction of the genes exist on the chromosomes as immediately adjacent gene pairs. The incidence of gene pairing can be as high as 24% in some species, and the gene pairs are found in all of the possible tandem, divergent, and convergent orientations. Results We investigated co-regulated gene sets in S. cerevisiae beyond those related to ribosome biogenesis, and found that a number of these regulons, including those involved in DNA metabolism, heat shock, and the response to cellular stressors were also significantly enriched for adjacent gene pairs. We found that as a whole, adjacent gene pairs were more tightly co-regulated than unpaired genes, and that the specific gene pairing relationships that were most widely conserved across divergent fungal lineages were correlated with those genes that exhibited the highest levels of transcription. Finally, we investigated the gene positions of ribosome related genes across a widely divergent set of eukaryotes, and found a significant level of adjacent gene pairing well beyond yeast species. Conclusion While it has long been understood that there are connections between genomic organization and transcriptional regulation, this study reveals that the strategy of organizing genes from related, co-regulated pathways into pairs of immediately adjacent genes is widespread, evolutionarily conserved, and functionally significant.
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Affiliation(s)
- James T Arnone
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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Peterson KR, Fedosyuk H, Harju-Baker S. LCR 5' hypersensitive site specificity for globin gene activation within the active chromatin hub. Nucleic Acids Res 2012; 40:11256-69. [PMID: 23042246 PMCID: PMC3526258 DOI: 10.1093/nar/gks900] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The DNaseI hypersensitive sites (HSs) of the human β-globin locus control region (LCR) may function as part of an LCR holocomplex within a larger active chromatin hub (ACH). Differential activation of the globin genes during development may be controlled in part by preferential interaction of each gene with specific individual HSs during globin gene switching, a change in conformation of the LCR holocomplex, or both. To distinguish between these possibilities, human β-globin locus yeast artificial chromosome (β-YAC) lines were produced in which the ε-globin gene was replaced with a second marked β-globin gene (βm), coupled to an intact LCR, a 5′HS3 complete deletion (5′ΔHS3) or a 5′HS3 core deletion (5′ΔHS3c). The 5′ΔHS3c mice expressed βm-globin throughout development; γ-globin was co-expressed in the embryonic yolk sac, but not in the fetal liver; and wild-type β-globin was co-expressed in adult mice. Although the 5′HS3 core was not required for βm-globin expression, previous work showed that the 5′HS3 core is necessary for ε-globin expression during embryonic erythropoiesis. A similar phenotype was observed in 5′HS complete deletion mice, except βm-globin expression was higher during primitive erythropoiesis and γ-globin expression continued into fetal definitive erythropoiesis. These data support a site specificity model of LCR HS-globin gene interaction.
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Affiliation(s)
- Kenneth R Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Abstract
The level of fetal hemoglobin (HbF) modifies the severity of the common β-globin disorders. Knowledge of the normal mechanisms that repress HbF in the adult stage has remained limited until recently despite nearly 3 decades of molecular investigation, in part because of imperfect model systems. Recent studies have provided new insights into the developmental regulation of globin genes and identified specific transcription factors and epigenetic regulators responsible for physiologic silencing of HbF. Most prominent among these regulators is BCL11A, a transcriptional repressor that inhibits adult-stage HbF expression. KLF1 and c-Myb are additional critical HbF-regulating erythroid transcription factors more broadly involved in erythroid gene expression programs. Chromatin modifiers, including histone deacetylases and DNA methyltransferases, also play key roles in orchestrating appropriate globin gene expression. Taken together, these discoveries present novel therapeutic targets for further consideration. Although substantial hurdles remain, opportunities are now rich for the rational design of HbF inducers.
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Ganis JJ, Hsia N, Trompouki E, de Jong JLO, DiBiase A, Lambert JS, Jia Z, Sabo PJ, Weaver M, Sandstrom R, Stamatoyannopoulos JA, Zhou Y, Zon LI. Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR. Dev Biol 2012; 366:185-94. [PMID: 22537494 DOI: 10.1016/j.ydbio.2012.03.021] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 02/20/2012] [Accepted: 03/19/2012] [Indexed: 02/02/2023]
Abstract
Globin gene switching is a complex, highly regulated process allowing expression of distinct globin genes at specific developmental stages. Here, for the first time, we have characterized all of the zebrafish globins based on the completed genomic sequence. Two distinct chromosomal loci, termed major (chromosome 3) and minor (chromosome 12), harbor the globin genes containing α/β pairs in a 5'-3' to 3'-5' orientation. Both these loci share synteny with the mammalian α-globin locus. Zebrafish globin expression was assayed during development and demonstrated two globin switches, similar to human development. A conserved regulatory element, the locus control region (LCR), was revealed by analyzing DNase I hypersensitive sites, H3K4 trimethylation marks and GATA1 binding sites. Surprisingly, the position of these sites with relation to the globin genes is evolutionarily conserved, despite a lack of overall sequence conservation. Motifs within the zebrafish LCR include CACCC, GATA, and NFE2 sites, suggesting functional interactions with known transcription factors but not the same LCR architecture. Functional homology to the mammalian α-LCR MCS-R2 region was confirmed by robust and specific reporter expression in erythrocytes of transgenic zebrafish. Our studies provide a comprehensive characterization of the zebrafish globin loci and clarify the regulation of globin switching.
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Affiliation(s)
- Jared J Ganis
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital and Dana Farber Cancer Institute, and Harvard Stem Cell Institute, Harvard Medical School, 1 Blackfan Cir., Karp 7, Boston, MA 02115, USA.
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Prevention of transcriptional silencing by a replicator-binding complex consisting of SWI/SNF, MeCP1, and hnRNP C1/C2. Mol Cell Biol 2011; 31:3472-84. [PMID: 21690294 DOI: 10.1128/mcb.05587-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional silencing selectively impedes gene expression. Silencing is often accompanied by replication delay and can be prevented by replicator sequences. Here we report a replicator-binding protein complex involved in the prevention of transcriptional silencing. The protein complex interacts with an essential asymmetric region within the human β-globin Rep-P replicator and includes hnRNP C1/C2, SWI/SNF complex, and MeCP1, which are members of the locus control region (LCR)-associated remodeling complex (LARC). Interaction between LARC and Rep-P prevented transcriptional silencing and replication delay. Transgenes that did not contain the asymmetric LARC-binding region of Rep-P replicated late and exhibited stable silencing that could not be affected by a DNA methylation inhibitor. In contrast, transgenes that contain a mutation of the asymmetric region of Rep-P that could not bind LARC exhibited a silent state that could transiently be reactivated by DNA demethylation. The effect of DNA demethylation was transient, and prolonged exposure to a methylation inhibitor induced distinct, stable, methylation-independent silencing. These observations suggest that the interaction of LARC complex with replicators plays a role in preventing gene silencing and provides support for a novel, epigenetic mechanism of resistance to methylation inhibitors.
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