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Mora A, Huang X, Jauhari S, Jiang Q, Li X. Chromatin Hubs: A biological and computational outlook. Comput Struct Biotechnol J 2022; 20:3796-3813. [PMID: 35891791 PMCID: PMC9304431 DOI: 10.1016/j.csbj.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/20/2022] Open
Abstract
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
- Corresponding authors.
| | - Xiaowei Huang
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Shaurya Jauhari
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Qin Jiang
- Affiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
- Corresponding authors.
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2
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A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker. Nat Commun 2021; 12:3806. [PMID: 34155213 PMCID: PMC8217497 DOI: 10.1038/s41467-021-23980-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/19/2021] [Indexed: 02/08/2023] Open
Abstract
Many single nucleotide variants (SNVs) associated with human traits and genetic diseases are thought to alter the activity of existing regulatory elements. Some SNVs may also create entirely new regulatory elements which change gene expression, but the mechanism by which they do so is largely unknown. Here we show that a single base change in an otherwise unremarkable region of the human α-globin cluster creates an entirely new promoter and an associated unidirectional transcript. This SNV downregulates α-globin expression causing α-thalassaemia. Of note, the new promoter lying between the α-globin genes and their associated super-enhancer disrupts their interaction in an orientation-dependent manner. Together these observations show how both the order and orientation of the fundamental elements of the genome determine patterns of gene expression and support the concept that active genes may act to disrupt enhancer-promoter interactions in mammals as in Drosophila. Finally, these findings should prompt others to fully evaluate SNVs lying outside of known regulatory elements as causing changes in gene expression by creating new regulatory elements. The role of promoters as potential insulator elements has been largely unexplored in mammals. Here the authors show that a single nucleotide variant in the α-globin locus forms a new promoter and acts as an orientation-dependent enhancer-blocking insulator element.
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3
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Li H, Zeng J, Zhao Y, Xu X. MZF1 regulates α-globin gene transcription via long-range interactions in erythroid differentiation. Blood Cells Mol Dis 2020; 87:102533. [PMID: 33352376 DOI: 10.1016/j.bcmd.2020.102533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
Precise spatiotemporal gene expression regulation is crucial for human erythropoiesis. However, dramatic changes in the chromatin structure and transcriptome involved in α-globin gene expression during erythropoiesis still not fully understand. To identify candidate regulators for α-globin gene regulation, we carried out an integrated approach by integrating publicly available transcriptomic and epigenomic data. We computed active enhancers by overlapping enriched regions marked with H3K4me1 and H3K27ac and correlated their activity with mRNA expression. Next, we cataloged potential transcription factors via de novo motif analysis. We highlighted the discovery of potential novel transcription factor MZF1 of the α-globin gene in erythroid differentiation. To validate the role of MZF1, we quantified the expression level of MZF1 and α-globin gene in HSPCs, early erythroid progenitors and late erythroid precursors cells. Both the mRNA and protein expression patterns of MZF1 were consistent with the α-globin gene. Also, the qPCR result showed that the expression of the α-globin gene was significantly increased by the MZF1 overexpression. To further investigate the role of MZF1 regulating α-globin gene transcriptional activity during erythroid differentiation, we performed ChIP-qPCR at the α-globin locus. Our results showed that MZF1 recruitment both at 4 upstream HS sites and α-globin gene promoter in erythroid precursor cells. To determine the importance of the MZF1 to enhancer-promoter interaction at the α-globin locus, we compared interaction frequency before and after knockdown of MZF1 by chromosome conformation capture (3C) assay. Upon MZF1 depletion, both the expression of the α-globin gene and all 3C signals were significantly decreased. Taken together, MZF1 plays an important role in regulating α-globin gene expression by binding to long-region enhancers and α-globin gene promoter and facilitates the organization of specific 3D chromatin architecture in erythroid differentiation.
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Affiliation(s)
- Haoli Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Jingjing Zeng
- The Central Laboratory, The Second People's Hospital of Shenzhen, Shenzhen 518035, People's Republic of China
| | - Yongzhong Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.
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4
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Portnoi MF, Dumargne MC, Rojo S, Witchel SF, Duncan AJ, Eozenou C, Bignon-Topalovic J, Yatsenko SA, Rajkovic A, Reyes-Mugica M, Almstrup K, Fusee L, Srivastava Y, Chantot-Bastaraud S, Hyon C, Louis-Sylvestre C, Validire P, de Malleray Pichard C, Ravel C, Christin-Maitre S, Brauner R, Rossetti R, Persani L, Charreau EH, Dain L, Chiauzzi VA, Mazen I, Rouba H, Schluth-Bolard C, MacGowan S, McLean WHI, Patin E, Rajpert-De Meyts E, Jauch R, Achermann JC, Siffroi JP, McElreavey K, Bashamboo A. Mutations involving the SRY-related gene SOX8 are associated with a spectrum of human reproductive anomalies. Hum Mol Genet 2018; 27:1228-1240. [PMID: 29373757 PMCID: PMC6159538 DOI: 10.1093/hmg/ddy037] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/14/2017] [Accepted: 01/18/2018] [Indexed: 11/13/2022] Open
Abstract
SOX8 is an HMG-box transcription factor closely related to SRY and SOX9. Deletion of the gene encoding Sox8 in mice causes reproductive dysfunction but the role of SOX8 in humans is unknown. Here, we show that SOX8 is expressed in the somatic cells of the early developing gonad in the human and influences human sex determination. We identified two individuals with 46, XY disorders/differences in sex development (DSD) and chromosomal rearrangements encompassing the SOX8 locus and a third individual with 46, XY DSD and a missense mutation in the HMG-box of SOX8. In vitro functional assays indicate that this mutation alters the biological activity of the protein. As an emerging body of evidence suggests that DSDs and infertility can have common etiologies, we also analysed SOX8 in a cohort of infertile men (n = 274) and two independent cohorts of women with primary ovarian insufficiency (POI; n = 153 and n = 104). SOX8 mutations were found at increased frequency in oligozoospermic men (3.5%; P < 0.05) and POI (5.06%; P = 4.5 × 10-5) as compared with fertile/normospermic control populations (0.74%). The mutant proteins identified altered SOX8 biological activity as compared with the wild-type protein. These data demonstrate that SOX8 plays an important role in human reproduction and SOX8 mutations contribute to a spectrum of phenotypes including 46, XY DSD, male infertility and 46, XX POI.
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Affiliation(s)
- Marie-France Portnoi
- APHP Département de Génétique Médicale, Hôpital Armand Trousseau, Paris
75012, France
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
| | | | - Sandra Rojo
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
| | - Selma F Witchel
- Division of Pediatric Endocrinology, Children’s Hospital of Pittsburgh
of UPMC, Pittsburgh, PA 15224, USA
| | - Andrew J Duncan
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of
Child Health, London WC1N 1EH, UK
| | - Caroline Eozenou
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
| | | | - Svetlana A Yatsenko
- Department of Obstetrics, Gynecology and Reproductive Sciences,
Magee-Women’s Research Institute
- Department of Human Genetics, University of Pittsburgh School of
Medicine, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine,
Pittsburgh, PA 15213, USA
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology and Reproductive Sciences,
Magee-Women’s Research Institute
- Department of Human Genetics, University of Pittsburgh School of
Medicine, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine,
Pittsburgh, PA 15213, USA
| | - Miguel Reyes-Mugica
- Department of Obstetrics, Gynecology and Reproductive Sciences,
Magee-Women’s Research Institute
- Department of Human Genetics, University of Pittsburgh School of
Medicine, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine,
Pittsburgh, PA 15213, USA
| | - Kristian Almstrup
- University Department of Growth and Reproduction, Rigshospitalet,
DK-2100 Copenhagen, Denmark
| | - Leila Fusee
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
| | - Yogesh Srivastava
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China
Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of
Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Key Laboratory of Regenerative Biology, South China Institute for Stem
Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health,
Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative
Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou
Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530,
China
| | - Sandra Chantot-Bastaraud
- APHP Département de Génétique Médicale, Hôpital Armand Trousseau, Paris
75012, France
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
| | - Capucine Hyon
- APHP Département de Génétique Médicale, Hôpital Armand Trousseau, Paris
75012, France
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
| | | | - Pierre Validire
- Département d’Anatomie Pathologique, Institut Mutualiste Montsouris,
Paris 75014, France
| | | | - Celia Ravel
- Biology of Reproduction, CHU Rennes, Rennes 35033, France
| | - Sophie Christin-Maitre
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
- Service d'Endocrinologie, Diabétologie et Endocrinologie de la
Reproduction, Hôpital Saint-Antoine, Paris 75012, France
| | - Raja Brauner
- Université Paris Descartes and Pediatric Endocrinology Unit, Fondation
Ophtalmologique Adolphe de Rothschild, Paris 75019, France
| | - Raffaella Rossetti
- Department of Clinical Sciences & Community Health, University of
Milan, Milan 20122, Italy
- Laboratory of Endocrine & Metabolic Research and Division of
Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan 20149,
Italy
| | - Luca Persani
- Department of Clinical Sciences & Community Health, University of
Milan, Milan 20122, Italy
- Laboratory of Endocrine & Metabolic Research and Division of
Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan 20149,
Italy
| | - Eduardo H Charreau
- Centro Nacional de Genética Médica, Administración Nacional de
Laboratorios e Institutos de Salud (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires C1428ADN,
Argentina
- Department of Physiology, Instituto de Biología y Medicina
Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (IBYME-CONICET),
Buenos Aires C1428ADN, Argentina
| | - Liliana Dain
- Centro Nacional de Genética Médica, Administración Nacional de
Laboratorios e Institutos de Salud (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires C1428ADN,
Argentina
- Department of Physiology, Instituto de Biología y Medicina
Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (IBYME-CONICET),
Buenos Aires C1428ADN, Argentina
| | - Violeta A Chiauzzi
- Centro Nacional de Genética Médica, Administración Nacional de
Laboratorios e Institutos de Salud (ANLIS) Dr. Carlos G. Malbrán, Buenos Aires C1428ADN,
Argentina
- Department of Physiology, Instituto de Biología y Medicina
Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (IBYME-CONICET),
Buenos Aires C1428ADN, Argentina
| | - Inas Mazen
- Department of Clinical Genetics, National Research Centre, Cairo 12622,
Egypt
| | - Hassan Rouba
- Human Genetics Unit, Institut Pasteur of Morocco, Casablanca 20250,
Morocco
| | | | - Stuart MacGowan
- Centre for Dermatology and Genetic Medicine, School of Life Sciences,
University of Dundee, Dundee DD1 5EH, UK
| | - W H Irwin McLean
- Centre for Dermatology and Genetic Medicine, School of Life Sciences,
University of Dundee, Dundee DD1 5EH, UK
| | - Etienne Patin
- Human Evolutionary Genetics, Institut Pasteur, Paris 75724,
France
| | - Ewa Rajpert-De Meyts
- University Department of Growth and Reproduction, Rigshospitalet,
DK-2100 Copenhagen, Denmark
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China
Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of
Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Key Laboratory of Regenerative Biology, South China Institute for Stem
Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health,
Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative
Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou
Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530,
China
| | - John C Achermann
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of
Child Health, London WC1N 1EH, UK
| | - Jean-Pierre Siffroi
- APHP Département de Génétique Médicale, Hôpital Armand Trousseau, Paris
75012, France
- UPMC, University Paris 06, INSERM UMR_S933, Hôpital Armand Trousseau,
Paris 75012, France
| | - Ken McElreavey
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
| | - Anu Bashamboo
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris
75724, France
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5
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Ulirsch JC, Nandakumar SK, Wang L, Giani FC, Zhang X, Rogov P, Melnikov A, McDonel P, Do R, Mikkelsen TS, Sankaran VG. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits. Cell 2016; 165:1530-1545. [PMID: 27259154 PMCID: PMC4893171 DOI: 10.1016/j.cell.2016.04.048] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/12/2015] [Accepted: 04/12/2016] [Indexed: 11/24/2022]
Abstract
Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay (MPRA) to simultaneously screen 2,756 variants in strong linkage disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with endogenous erythroid regulatory activity. Across 23 sentinel variants, we conservatively identified 32 MPRA functional variants (MFVs). We used targeted genome editing to demonstrate endogenous enhancer activity across 3 MFVs that predominantly affect the transcription of SMIM1, RBM38, and CD164. Functional follow-up of RBM38 delineates a key role for this gene in the alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type-specific transcriptional regulatory pathways.
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Affiliation(s)
- Jacob C Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Felix C Giani
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Xiaolan Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter Rogov
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Patrick McDonel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ron Do
- Department of Genetics and Genomic Sciences and The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tarjei S Mikkelsen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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6
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Yang R, Kerschner JL, Gosalia N, Neems D, Gorsic LK, Safi A, Crawford GE, Kosak ST, Leir SH, Harris A. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res 2016; 44:3082-94. [PMID: 26673704 PMCID: PMC4838340 DOI: 10.1093/nar/gkv1358] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/21/2015] [Accepted: 11/24/2015] [Indexed: 12/18/2022] Open
Abstract
Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms.CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and siRNA-mediated depletion of architectural proteins to determine the relative contribution of structural elements and enhancers to the higher order structure and expression of the CFTR locus. We found the boundaries of the CFTRTAD are conserved among diverse cell types and are dependent on CTCF and cohesin complex. Removal of an upstream CTCF-binding insulator alters the interaction profile, but has little effect on CFTR expression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreases CFTR expression, but has minor effect on its 3D structure.
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Affiliation(s)
- Rui Yang
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jenny L Kerschner
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nehal Gosalia
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Daniel Neems
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lidija K Gorsic
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alexias Safi
- Division of Medical Genetics, Department of Pediatrics and Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA
| | - Gregory E Crawford
- Division of Medical Genetics, Department of Pediatrics and Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27708, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shih-Hsing Leir
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ann Harris
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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7
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Davies JO, Telenius JM, McGowan S, Roberts NA, Taylor S, Higgs DR, Hughes JR. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat Methods 2016; 13:74-80. [PMID: 26595209 PMCID: PMC4724891 DOI: 10.1038/nmeth.3664] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022]
Abstract
Methods for analyzing chromosome conformation in mammalian cells are either low resolution or low throughput and are technically challenging. In next-generation (NG) Capture-C, we have redesigned the Capture-C method to achieve unprecedented levels of sensitivity and reproducibility. NG Capture-C can be used to analyze many genetic loci and samples simultaneously. High-resolution data can be produced with as few as 100,000 cells, and single-nucleotide polymorphisms can be used to generate allele-specific tracks. The method is straightforward to perform and should greatly facilitate the investigation of many questions related to gene regulation as well as the functional dissection of traits examined in genome-wide association studies.
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Affiliation(s)
- James O.J. Davies
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Jelena M. Telenius
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Simon McGowan
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Nigel A. Roberts
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Stephen Taylor
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Douglas R. Higgs
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Jim R. Hughes
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
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8
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Proudhon C, Hao B, Raviram R, Chaumeil J, Skok JA. Long-Range Regulation of V(D)J Recombination. Adv Immunol 2015; 128:123-82. [PMID: 26477367 DOI: 10.1016/bs.ai.2015.07.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Given their essential role in adaptive immunity, antigen receptor loci have been the focus of analysis for many years and are among a handful of the most well-studied genes in the genome. Their investigation led initially to a detailed knowledge of linear structure and characterization of regulatory elements that confer control of their rearrangement and expression. However, advances in DNA FISH and imaging combined with new molecular approaches that interrogate chromosome conformation have led to a growing appreciation that linear structure is only one aspect of gene regulation and in more recent years, the focus has switched to analyzing the impact of locus conformation and nuclear organization on control of recombination. Despite decades of work and intense effort from numerous labs, we are still left with an incomplete picture of how the assembly of antigen receptor loci is regulated. This chapter summarizes our advances to date and points to areas that need further investigation.
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Affiliation(s)
- Charlotte Proudhon
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Bingtao Hao
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, USA
| | - Julie Chaumeil
- Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, USA.
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9
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Abstract
Abstract
An intimate relationship exists between nuclear architecture and gene activity. Unraveling the fine-scale three-dimensional structure of the genome and its impact on gene regulation is a major goal of current epigenetic research, one with direct implications for understanding the molecular mechanisms underlying human phenotypic variation and disease susceptibility. In this context, the novel revolutionary genome editing technologies and emerging new ways to manipulate genome folding offer new promises for the treatment of human disorders.
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 2014; 46:205-12. [PMID: 24413732 DOI: 10.1038/ng.2871] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 12/12/2013] [Indexed: 12/19/2022]
Abstract
Gene expression during development and differentiation is regulated in a cell- and stage-specific manner by complex networks of intergenic and intragenic cis-regulatory elements whose numbers and representation in the genome far exceed those of structural genes. Using chromosome conformation capture, it is now possible to analyze in detail the interaction between enhancers, silencers, boundary elements and promoters at individual loci, but these techniques are not readily scalable. Here we present a high-throughput approach (Capture-C) to analyze cis interactions, interrogating hundreds of specific interactions at high resolution in a single experiment. We show how this approach will facilitate detailed, genome-wide analysis to elucidate the general principles by which cis-acting sequences control gene expression. In addition, we show how Capture-C will expedite identification of the target genes and functional effects of SNPs that are associated with complex diseases, which most frequently lie in intergenic cis-acting regulatory elements.
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van Heyningen V, Bickmore W. Regulation from a distance: long-range control of gene expression in development and disease. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120372. [PMID: 23650642 DOI: 10.1098/rstb.2012.0372] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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