151
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Vermunt MW, Zhang D, Blobel GA. The interdependence of gene-regulatory elements and the 3D genome. J Cell Biol 2018; 218:12-26. [PMID: 30442643 PMCID: PMC6314554 DOI: 10.1083/jcb.201809040] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 01/12/2023] Open
Abstract
Vermunt et al. discuss the relationship between gene-regulatory elements and nuclear architectural features in transcription. Imaging studies, high-resolution chromatin conformation maps, and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross-talk between gene-regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause–consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer–promoter contacts in gene regulation.
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Affiliation(s)
- Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Di Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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152
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Dozmorov MG. Reforming disease classification system-are we there yet? ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:S30. [PMID: 30613605 DOI: 10.21037/atm.2018.09.36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, USA
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153
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Hug CB, Vaquerizas JM. Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos. J Vis Exp 2018. [PMID: 30346395 PMCID: PMC6235413 DOI: 10.3791/57001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Investigating the three-dimensional architecture of chromatin offers invaluable insight into the mechanisms of gene regulation. Here, we describe a protocol for performing the chromatin conformation capture technique in situ Hi-C on staged Drosophila melanogaster embryo populations. The result is a sequencing library that allows the mapping of all chromatin interactions that occur in the nucleus in a single experiment. Embryo sorting is done manually using a fluorescent stereo microscope and a transgenic fly line containing a nuclear marker. Using this technique, embryo populations from each nuclear division cycle, and with defined cell cycle status, can be obtained with very high purity. The protocol may also be adapted to sort older embryos beyond gastrulation. Sorted embryos are used as inputs for in situ Hi-C. All experiments, including sequencing library preparation, can be completed in five days. The protocol has low input requirements and works reliably using 20 blastoderm stage embryos as input material. The end result is a sequencing library for next generation sequencing. After sequencing, the data can be processed into genome-wide chromatin interaction maps that can be analyzed using a wide range of available tools to gain information about topologically associating domain (TAD) structure, chromatin loops, and chromatin compartments during Drosophila development.
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154
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Espitia Jaimes C, Fish RJ, Neerman-Arbez M. Local chromatin interactions contribute to expression of the fibrinogen gene cluster. J Thromb Haemost 2018; 16:2070-2082. [PMID: 30039577 DOI: 10.1111/jth.14248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Indexed: 02/03/2023]
Abstract
Essentials The fibrinogen gene cluster is flanked by CCCTC-binding factor (CTCF) interaction sites. Chromatin looping of the fibrinogen cluster was demonstrated by chromosome conformation capture. Deleting a CTCF interaction site alters chromatin looping and halves fibrinogen expression. Looping of the human fibrinogen locus is functionally linked to fibrinogen gene expression. SUMMARY Background The coordinately regulated genes encoding human fibrinogen are clustered. This evolutionarily conserved configuration provides a possible mechanism for co-regulation whereby regulatory elements influence gene expression locally. The cluster is flanked by CCCTC-binding factor (CTCF) interaction sites that are candidate insulator regions mediating chromatin looping. Objectives To further our understanding of fibrinogen gene regulation, we aimed to investigate whether interactions exist between parts of the fibrinogen locus and how these contacts contribute to fibrinogen expression. Methods We used chromosome conformation capture in cultured cell lines to detect chromatin interactions at the fibrinogen gene cluster. We generated clonal cell lines where two CTCF interaction sites at one end of the locus were deleted using CRISPR-Cas9-mediated genome editing. Fibrinogen expression and protein production were measured using qRT-PCR and ELISA, respectively. Results We detected proximity between the ends of the fibrinogen locus, regardless of whether cells express fibrinogen. An interaction between the FGA promoter and the edge of the locus was more frequent in fibrinogen-expressing cells. Deletion of a CTCF site at one edge of the cluster altered chromatin interactions, reduced steady-state expression of FGB and FGG mRNA, and led to a halving of secreted fibrinogen. These phenotypes were completely restored by reintroduction of the CTCF interaction motif in previously motif-deleted clones. Conclusions Chromatin interactions are important for the coordinated regulation of the human fibrinogen genes. This finding furthers our comprehension of how fibrinogen is produced and identifies a possible source of variability in plasma fibrinogen levels seen in populations.
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Affiliation(s)
- C Espitia Jaimes
- Department of Genetic Medicine and Development, University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - R J Fish
- Department of Genetic Medicine and Development, University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - M Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva, Faculty of Medicine, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
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155
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Challenges and guidelines toward 4D nucleome data and model standards. Nat Genet 2018; 50:1352-1358. [PMID: 30262815 DOI: 10.1038/s41588-018-0236-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 07/19/2018] [Indexed: 11/09/2022]
Abstract
Due to recent advances in experimental and theoretical approaches, the dynamic three-dimensional organization (3D) of the nucleus has become a very active area of research in life sciences. We now understand that the linear genome is folded in ways that may modulate how genes are expressed during the basic functioning of cells. Importantly, it is now possible to build 3D models of how the genome folds within the nucleus and changes over time (4D). Because genome folding influences its function, this opens exciting new possibilities to broaden our understanding of the mechanisms that determine cell fate. However, the rapid evolution of methods and the increasing complexity of data can result in ambiguity and reproducibility challenges, which may hamper the progress of this field. Here, we describe such challenges ahead and provide guidelines to think about strategies for shared standardized validation of experimental 4D nucleome data sets and models.
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156
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Ladstätter S, Tachibana K. Genomic insights into chromatin reprogramming to totipotency in embryos. J Cell Biol 2018; 218:70-82. [PMID: 30257850 PMCID: PMC6314560 DOI: 10.1083/jcb.201807044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022] Open
Abstract
Ladstätter and Tachibana discuss changes in DNA methylation, chromatin accessibility, and topological architecture occurring during the reprogramming to totipotency in the early embryo. The early embryo is the natural prototype for the acquisition of totipotency, which is the potential of a cell to produce a whole organism. Generation of a totipotent embryo involves chromatin reorganization and epigenetic reprogramming that alter DNA and histone modifications. Understanding embryonic chromatin architecture and how this is related to the epigenome and transcriptome will provide invaluable insights into cell fate decisions. Recently emerging low-input genomic assays allow the exploration of regulatory networks in the sparsely available mammalian embryo. Thus, the field of developmental biology is transitioning from microscopy to genome-wide chromatin descriptions. Ultimately, the prototype becomes a unique model for studying fundamental principles of development, epigenetic reprogramming, and cellular plasticity. In this review, we discuss chromatin reprogramming in the early mouse embryo, focusing on DNA methylation, chromatin accessibility, and higher-order chromatin structure.
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Affiliation(s)
- Sabrina Ladstätter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Kikuë Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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157
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Galupa R, Heard E. X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation. Annu Rev Genet 2018; 52:535-566. [PMID: 30256677 DOI: 10.1146/annurev-genet-120116-024611] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In somatic nuclei of female therian mammals, the two X chromosomes display very different chromatin states: One X is typically euchromatic and transcriptionally active, and the other is mostly silent and forms a cytologically detectable heterochromatic structure termed the Barr body. These differences, which arise during female development as a result of X-chromosome inactivation (XCI), have been the focus of research for many decades. Initial approaches to define the structure of the inactive X chromosome (Xi) and its relationship to gene expression mainly involved microscopy-based approaches. More recently, with the advent of genomic techniques such as chromosome conformation capture, molecular details of the structure and expression of the Xi have been revealed. Here, we review our current knowledge of the 3D organization of the mammalian X-chromosome chromatin and discuss its relationship with gene activity in light of the initiation, spreading, and maintenance of XCI, as well as escape from gene silencing.
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Affiliation(s)
- Rafael Galupa
- Genetics and Developmental Biology Unit and Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris, France; .,Current affiliation: Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Edith Heard
- Genetics and Developmental Biology Unit and Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris, France; .,Collège de France, 75231 Paris, France
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158
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Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells. Immunity 2018; 48:227-242.e8. [PMID: 29466755 DOI: 10.1016/j.immuni.2018.01.013] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/19/2017] [Accepted: 01/26/2018] [Indexed: 12/23/2022]
Abstract
How chromatin reorganization coordinates differentiation and lineage commitment from hematopoietic stem and progenitor cells (HSPCs) to mature immune cells has not been well understood. Here, we carried out an integrative analysis of chromatin accessibility, topologically associating domains, AB compartments, and gene expression from HSPCs to CD4+CD8+ T cells. We found that abrupt genome-wide changes at all three levels of chromatin organization occur during the transition from double-negative stage 2 (DN2) to DN3, accompanying the T lineage commitment. The transcription factor BCL11B, a critical regulator of T cell commitment, is associated with increased chromatin interaction, and Bcl11b deletion compromised chromatin interaction at its target genes. We propose that these large-scale and concerted changes in chromatin organization present an energy barrier to prevent the cell from reversing its fate to earlier stages or redirecting to alternatives and thus lock the cell fate into the T lineages.
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159
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Diament A, Tuller T. Modeling three-dimensional genomic organization in evolution and pathogenesis. Semin Cell Dev Biol 2018; 90:78-93. [PMID: 30030143 DOI: 10.1016/j.semcdb.2018.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/08/2018] [Indexed: 12/17/2022]
Abstract
The regulation of gene expression is mediated via the complex three-dimensional (3D) conformation of the genetic material and its interactions with various intracellular factors. Various experimental and computational approaches have been developed in recent years for understating the relation between the 3D conformation of the genome and the phenotypes of cells in normal condition and diseases. In this review, we will discuss novel approaches for analyzing and modeling the 3D genomic conformation, focusing on deciphering disease-causing mutations that affect gene expression. We conclude that as this is a very challenging mission, an important direction should involve the comparative analysis of various 3D models from various organisms or cells.
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Affiliation(s)
- Alon Diament
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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160
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Majumder K, Wang J, Boftsi M, Fuller MS, Rede JE, Joshi T, Pintel DJ. Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection. eLife 2018; 7:37750. [PMID: 30028293 PMCID: PMC6095691 DOI: 10.7554/elife.37750] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 07/19/2018] [Indexed: 01/15/2023] Open
Abstract
We have developed a generally adaptable, novel high-throughput Viral Chromosome Conformation Capture assay (V3C-seq) for use in trans that allows genome-wide identification of the direct interactions of a lytic virus genome with distinct regions of the cellular chromosome. Upon infection, we found that the parvovirus Minute Virus of Mice (MVM) genome initially associated with sites of cellular DNA damage that in mock-infected cells also exhibited DNA damage as cells progressed through S-phase. As infection proceeded, new DNA damage sites were induced, and virus subsequently also associated with these. Sites of association identified biochemically were confirmed microscopically and MVM could be targeted specifically to artificially induced sites of DNA damage. Thus, MVM established replication at cellular DNA damage sites, which provide replication and expression machinery, and as cellular DNA damage accrued, virus spread additionally to newly damaged sites to amplify infection. MVM-associated sites overlap significantly with previously identified topologically-associated domains (TADs). Viruses are small infectious particles that can only reproduce with the help of a host. Once they are inside their victim, they hijack the cells’ genetic material and reprogram it to become a virus factory that produces more virus particles. Parvoviruses, for example, are among the simplest of viruses and need all resources a cell has to offer to successfully replicate. This process often takes place at so-called replication centers that contain these necessary factors. It was previously thought that parvoviruses set up such centers randomly, and gather the required molecules such as proteins to these sites. However, it was not well understood how they do this. Now, Majumder et al. have developed a new method that enabled them to study in detail how parvoviruses gain access to the resources of the cell they need to initiate and amplify replication. The results show that parvoviruses set up their replication centers at sites on the host DNA that are already rich in proteins needed to repair and then replicate damaged DNA. Some of these sites already exist in the cell’s genetic material as a consequence of naturally occurring processes, but others are created during infection by the virus. These findings may have important implications for how other viruses may establish their replication. Viruses, including parvoviruses, are important pathogens. Like many microbes, viruses can be beneficial for our health and environment. Others, however, can be harmful. A clearer understanding of how viruses establish and amplify an infection may provide new treatment opportunities.
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Affiliation(s)
- Kinjal Majumder
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, Columbia, United States
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, Columbia, United States.,Christopher S. Bond Life Sciences Center, Columbia, United States
| | - Maria Boftsi
- Pathobiology Area Graduate Program, Christopher S. Bond Life Sciences Center, Columbia, United States
| | - Matthew S Fuller
- Ultragenyx Pharmaceutical, Christopher S. Bond Life Sciences Center, Columbia, United States
| | - Jordan E Rede
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, Columbia, United States
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, Columbia, United States.,Christopher S. Bond Life Sciences Center, Columbia, United States.,Department of Health Management and Informatics, School of Medicine, University of Missouri-Columbia, Columbia, United States.,MU Informatics Institute, University of Missouri-Columbia, Columbia, United States
| | - David J Pintel
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, Columbia, United States
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161
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Enhancer hubs and loop collisions identified from single-allele topologies. Nat Genet 2018; 50:1151-1160. [PMID: 29988121 DOI: 10.1038/s41588-018-0161-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/11/2018] [Indexed: 11/08/2022]
Abstract
Chromatin folding contributes to the regulation of genomic processes such as gene activity. Existing conformation capture methods characterize genome topology through analysis of pairwise chromatin contacts in populations of cells but cannot discern whether individual interactions occur simultaneously or competitively. Here we present multi-contact 4C (MC-4C), which applies Nanopore sequencing to study multi-way DNA conformations of individual alleles. MC-4C distinguishes cooperative from random and competing interactions and identifies previously missed structures in subpopulations of cells. We show that individual elements of the β-globin superenhancer can aggregate into an enhancer hub that can simultaneously accommodate two genes. Neighboring chromatin domain loops can form rosette-like structures through collision of their CTCF-bound anchors, as seen most prominently in cells lacking the cohesin-unloading factor WAPL. Here, massive collision of CTCF-anchored chromatin loops is believed to reflect 'cohesin traffic jams'. Single-allele topology studies thus help us understand the mechanisms underlying genome folding and functioning.
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162
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Sotelo-Silveira M, Chávez Montes RA, Sotelo-Silveira JR, Marsch-Martínez N, de Folter S. Entering the Next Dimension: Plant Genomes in 3D. TRENDS IN PLANT SCIENCE 2018; 23:598-612. [PMID: 29703667 DOI: 10.1016/j.tplants.2018.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/19/2018] [Accepted: 03/26/2018] [Indexed: 05/07/2023]
Abstract
After linear sequences of genomes and epigenomic landscape data, the 3D organization of chromatin in the nucleus is the next level to be explored. Different organisms present a general hierarchical organization, with chromosome territories at the top. Chromatin interaction maps, obtained by chromosome conformation capture (3C)-based methodologies, for eight plant species reveal commonalities, but also differences, among them and with animals. The smallest structures, found in high-resolution maps of the Arabidopsis genome, are single genes. Epigenetic marks (histone modification and DNA methylation), transcriptional activity, and chromatin interaction appear to be correlated, and whether structure is the cause or consequence of the function of interacting regions is being actively investigated.
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Affiliation(s)
- Mariana Sotelo-Silveira
- Departamento de Biología Vegetal, Laboratorio de Bioquímica, Facultad de Agronomía, Garzón 809, 12900 Montevideo, Uruguay
| | - Ricardo A Chávez Montes
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36824 Irapuato, Guanajuato, Mexico
| | - Jose R Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600 Montevideo, Uruguay; Sección Biología Celular, Dept. Cell and Molecular Biology, Facultad de Ciencias, Universidad de la Republica, Igua 4225, Montevideo, Uruguay
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36824 Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36824 Irapuato, Guanajuato, Mexico.
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163
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Jain S, Ba Z, Zhang Y, Dai HQ, Alt FW. CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning. Cell 2018; 174:102-116.e14. [PMID: 29804837 PMCID: PMC6026039 DOI: 10.1016/j.cell.2018.04.035] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/07/2018] [Accepted: 04/25/2018] [Indexed: 01/06/2023]
Abstract
RAG endonuclease initiates antibody heavy chain variable region exon assembly from V, D, and J segments within a chromosomal V(D)J recombination center (RC) by cleaving between paired gene segments and flanking recombination signal sequences (RSSs). The IGCR1 control region promotes DJH intermediate formation by isolating Ds, JHs, and RCs from upstream VHs in a chromatin loop anchored by CTCF-binding elements (CBEs). How VHs access the DJHRC for VH to DJH rearrangement was unknown. We report that CBEs immediately downstream of frequently rearranged VH-RSSs increase recombination potential of their associated VH far beyond that provided by RSSs alone. This CBE activity becomes particularly striking upon IGCR1 inactivation, which allows RAG, likely via loop extrusion, to linearly scan chromatin far upstream. VH-associated CBEs stabilize interactions of D-proximal VHs first encountered by the DJHRC during linear RAG scanning and thereby promote dominant rearrangement of these VHs by an unanticipated chromatin accessibility-enhancing CBE function.
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MESH Headings
- Animals
- CCCTC-Binding Factor/metabolism
- Cell Line
- Chromatin/metabolism
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- DNA-Binding Proteins/deficiency
- DNA-Binding Proteins/genetics
- Homeodomain Proteins/metabolism
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/metabolism
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/metabolism
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Mutagenesis
- Protein Sorting Signals
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- V(D)J Recombination
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Suvi Jain
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhaoqing Ba
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yu Zhang
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hai-Qiang Dai
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute; Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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164
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Weidemann BJ, Ramsey KM, Bass J. A day in the life of chromatin: how enhancer-promoter loops shape daily behavior. Genes Dev 2018; 32:321-323. [PMID: 29593064 PMCID: PMC5900705 DOI: 10.1101/gad.314187.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This Outlook by Weidemann et al. highlights two recent studies, one of which, by Mermet et al., is in this issue of Genes & Development. They examine how “time of day”-dependent changes in chromatin drive core clock oscillations and show that waking up involves highly dynamic changes in the three dimensional positioning of genes within the cell. Each spring, we get out of bed 1 h ahead of our biological wake-up time due to the misalignment of internal clocks with the light–dark cycle. Genetic discoveries revealed that clock genes encode transcription factors that are expressed throughout many tissues, yet a gap has remained in understanding the temporal dynamics of transcription. Two groups now apply circular chromosome conformation capture and high-throughput sequencing to dissect how “time of day”-dependent changes in chromatin drive core clock oscillations. A surprise is the finding that disruption of enhancer–promoter contacts within chromatin leads to an advance in the “wake-up” time of mice. Furthermore, the assembly of transcriptionally active domains of chromatin requires the ordered recruitment of core clock transcription factors each day. These studies show that waking up involves highly dynamic changes in the three-dimensional positioning of genes within the cell.
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Affiliation(s)
- Benjamin J Weidemann
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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165
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Melamed A, Yaguchi H, Miura M, Witkover A, Fitzgerald TW, Birney E, Bangham CR. The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis. eLife 2018; 7:36245. [PMID: 29941091 PMCID: PMC6019074 DOI: 10.7554/elife.36245] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022] Open
Abstract
Chromatin looping controls gene expression by regulating promoter-enhancer contacts, the spread of epigenetic modifications, and the segregation of the genome into transcriptionally active and inactive compartments. We studied the impact on the structure and expression of host chromatin by the human retrovirus HTLV-1. We show that HTLV-1 disrupts host chromatin structure by forming loops between the provirus and the host genome; certain loops depend on the critical chromatin architectural protein CTCF, which we recently discovered binds to the HTLV-1 provirus. We show that the provirus causes two distinct patterns of abnormal transcription of the host genome in cis: bidirectional transcription in the host genome immediately flanking the provirus, and clone-specific transcription in cis at non-contiguous loci up to >300 kb from the integration site. We conclude that HTLV-1 causes insertional mutagenesis up to the megabase range in the host genome in >104 persistently-maintained HTLV-1+ T-cell clones in vivo.
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Affiliation(s)
- Anat Melamed
- Division of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Hiroko Yaguchi
- Division of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Michi Miura
- Division of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Aviva Witkover
- Division of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Tomas W Fitzgerald
- The European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Ewan Birney
- The European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Charles Rm Bangham
- Division of Infectious Diseases, Imperial College London, London, United Kingdom
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166
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Fishman VS, Salnikov PA, Battulin NR. Interpreting Chromosomal Rearrangements in the Context of 3-Dimentional Genome Organization: A Practical Guide for Medical Genetics. BIOCHEMISTRY (MOSCOW) 2018; 83:393-401. [PMID: 29626926 DOI: 10.1134/s0006297918040107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this exciting era of "next-gen cytogenetics", the use of novel molecular methods such as comparative genome hybridization and whole genome and whole exome sequencing becomes more and more common in clinics. This results in generation of large amounts of high-resolution patient-specific data and challenges the development of new approaches for interpretation of obtained information. Usually, interpretation of chromosomal rearrangements is focused on alterations of linear genome sequence, underestimating the role of spatial chromatin organization. In this article, we describe the main features of 3-dimentional genome organization, emphasizing their role in normal and pathological development. We highlight some tips to help physicians estimating the impact of chromosomal rearrangements on the patient phenotype. A separate section describes available tools that can be used to visualize and analyze human genome architecture.
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Affiliation(s)
- V S Fishman
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 63009, Russia.
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167
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Rada-Iglesias A, Grosveld FG, Papantonis A. Forces driving the three-dimensional folding of eukaryotic genomes. Mol Syst Biol 2018; 14:e8214. [PMID: 29858282 PMCID: PMC6024091 DOI: 10.15252/msb.20188214] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The last decade has radically renewed our understanding of higher order chromatin folding in the eukaryotic nucleus. As a result, most current models are in support of a mostly hierarchical and relatively stable folding of chromosomes dividing chromosomal territories into A‐ (active) and B‐ (inactive) compartments, which are then further partitioned into topologically associating domains (TADs), each of which is made up from multiple loops stabilized mainly by the CTCF and cohesin chromatin‐binding complexes. Nonetheless, the structure‐to‐function relationship of eukaryotic genomes is still not well understood. Here, we focus on recent work highlighting the biophysical and regulatory forces that contribute to the spatial organization of genomes, and we propose that the various conformations that chromatin assumes are not so much the result of a linear hierarchy, but rather of both converging and conflicting dynamic forces that act on it.
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Affiliation(s)
- Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany .,CECAD, University of Cologne, Cologne, Germany
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus Medical Center, GE Rotterdam, Netherlands
| | - Argyris Papantonis
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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168
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Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z. Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Methods 2018; 142:59-73. [PMID: 29382556 PMCID: PMC5993575 DOI: 10.1016/j.ymeth.2018.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/14/2017] [Accepted: 01/25/2018] [Indexed: 01/09/2023] Open
Abstract
The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods.
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Affiliation(s)
- Wenxiu Ma
- Department of Genome Sciences, University of Washington, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, USA
| | - Gunhan Gulsoy
- Department of Genome Sciences, University of Washington, USA
| | - Xinxian Deng
- Department of Pathology, University of Washington, USA
| | - Savannah Cook
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Department of Comparative Medicine, University of Washington, USA
| | - Jennifer Hesson
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Department of Comparative Medicine, University of Washington, USA
| | - Christopher Cavanaugh
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Department of Comparative Medicine, University of Washington, USA
| | - Carol B Ware
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Department of Comparative Medicine, University of Washington, USA
| | - Anton Krumm
- Department of Radiation Oncology, University of Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, USA; Howard Hughes Medical Institute, Seattle, WA 98195-8056, USA
| | - C Anthony Blau
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA
| | | | - William S Noble
- Department of Genome Sciences, University of Washington, USA.
| | - ZhiJun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA.
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169
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Waldispühl J, Zhang E, Butyaev A, Nazarova E, Cyr Y. Storage, visualization, and navigation of 3D genomics data. Methods 2018; 142:74-80. [PMID: 29792917 DOI: 10.1016/j.ymeth.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 01/27/2023] Open
Abstract
The field of 3D genomics grew at increasing rates in the last decade. The volume and complexity of 2D and 3D data produced is progressively outpacing the capacities of the technology previously used for distributing genome sequences. The emergence of new technologies provides also novel opportunities for the development of innovative approaches. In this paper, we review the state-of-the-art computing technology, as well as the solutions adopted by the platforms currently available.
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Affiliation(s)
| | - Eric Zhang
- School of Computer Science, McGill University, Montréal, Canada
| | | | - Elena Nazarova
- School of Computer Science, McGill University, Montréal, Canada
| | - Yan Cyr
- Beam Me Up Labs, Montréal, Canada
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170
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Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R. The Energetics and Physiological Impact of Cohesin Extrusion. Cell 2018; 173:1165-1178.e20. [PMID: 29706548 PMCID: PMC6065110 DOI: 10.1016/j.cell.2018.03.072] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 12/29/2017] [Accepted: 03/27/2018] [Indexed: 12/25/2022]
Abstract
Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural "stripes," where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.
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Affiliation(s)
- Laura Vian
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | | | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Laura Baranello
- Gene Regulation, Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA
| | - Su-Chen Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Marei Dose
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | | | - Adrian L Sanborn
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Andres Canela
- Laboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA
| | - Yaakov Maman
- Laboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA
| | - Anna Oksanen
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Wolfgang Resch
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Xingwang Li
- The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA
| | | | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA
| | | | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Ido Machol
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elena K Stamenova
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA
| | | | - David Levens
- Gene Regulation, Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
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171
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Gallagher MD, Chen-Plotkin AS. The Post-GWAS Era: From Association to Function. Am J Hum Genet 2018; 102:717-730. [PMID: 29727686 DOI: 10.1016/j.ajhg.2018.04.002] [Citation(s) in RCA: 474] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
During the past 12 years, genome-wide association studies (GWASs) have uncovered thousands of genetic variants that influence risk for complex human traits and diseases. Yet functional studies aimed at delineating the causal genetic variants and biological mechanisms underlying the observed statistical associations with disease risk have lagged. In this review, we highlight key advances in the field of functional genomics that may facilitate the derivation of biological meaning post-GWAS. We highlight the evidence suggesting that causal variants underlying disease risk often function through regulatory effects on the expression of target genes and that these expression effects might be modest and cell-type specific. We moreover discuss specific studies as proof-of-principle examples for current statistical, bioinformatic, and empirical bench-based approaches to downstream elucidation of GWAS-identified disease risk loci.
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172
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Affiliation(s)
- Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.
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173
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Lin D, Hong P, Zhang S, Xu W, Jamal M, Yan K, Lei Y, Li L, Ruan Y, Fu ZF, Li G, Cao G. Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nat Genet 2018; 50:754-763. [DOI: 10.1038/s41588-018-0111-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/08/2018] [Indexed: 01/06/2023]
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174
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Oddes S, Zelig A, Kaplan N. Three invariant Hi-C interaction patterns: Applications to genome assembly. Methods 2018; 142:89-99. [PMID: 29684640 DOI: 10.1016/j.ymeth.2018.04.013] [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: 11/03/2017] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 01/08/2023] Open
Abstract
Assembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the central principles underlying Hi-C-based assembly approaches, by quantitatively defining and characterizing three invariant Hi-C interaction patterns on which these approaches can build: Intrachromosomal interaction enrichment, distance-dependent interaction decay and local interaction smoothness. Specifically, we evaluate to what degree each invariant pattern holds on a single locus level in different species, cell types and Hi-C map resolutions. We find that these patterns are generally consistent across species and cell types but are affected by sequencing depth, and that matrix balancing improves consistency of loci with all three invariant patterns. Finally, we overview current Hi-C-based assembly approaches in light of these invariant patterns and demonstrate how local interaction smoothness can be used to easily detect scaffolding errors in extremely sparse Hi-C maps. We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods.
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Affiliation(s)
- Sivan Oddes
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aviv Zelig
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Noam Kaplan
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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175
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Nucleosome-level 3D organization of the genome. Biochem Soc Trans 2018; 46:491-501. [PMID: 29626147 DOI: 10.1042/bst20170388] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/26/2018] [Accepted: 03/01/2018] [Indexed: 01/19/2023]
Abstract
Nucleosomes are the unitary structures of chromosome folding, and their arrangements are intimately coupled to the regulation of genome activities. Conventionally, structural analyses using electron microscopy and X-ray crystallography have been used to study such spatial nucleosome arrangements. In contrast, recent improvements in the resolution of sequencing-based methods allowed investigation of nucleosome arrangements separately at each genomic locus, enabling exploration of gene-dependent regulation mechanisms. Here, we review recent studies on nucleosome folding in chromosomes from these two methodological perspectives: conventional structural analyses and DNA sequencing, and discuss their implications for future research.
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176
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Morgan GT. Imaging the dynamics of transcription loops in living chromosomes. Chromosoma 2018; 127:361-374. [PMID: 29610944 PMCID: PMC6096578 DOI: 10.1007/s00412-018-0667-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/21/2022]
Abstract
When in the lampbrush configuration, chromosomes display thousands of visible DNA loops that are transcribed at exceptionally high rates by RNA polymerase II (pol II). These transcription loops provide unique opportunities to investigate not only the detailed architecture of pol II transcription sites but also the structural dynamics of chromosome looping, which is receiving fresh attention as the organizational principle underpinning the higher-order structure of all chromosome states. The approach described here allows for extended imaging of individual transcription loops and transcription units under conditions in which loop RNA synthesis continues. In intact nuclei from lampbrush-stage Xenopus oocytes isolated under mineral oil, highly specific targeting of fluorescent fusions of the RNA-binding protein CELF1 to nascent transcripts allowed functional transcription loops to be observed and their longevity assessed over time. Some individual loops remained extended and essentially static structures over time courses of up to an hour. However, others were less stable and shrank markedly over periods of 30-60 min in a manner that suggested that loop extension requires continued dense coverage with nascent transcripts. In stable loops and loop-derived structures, the molecular dynamics of the visible nascent RNP component were addressed using photokinetic approaches. The results suggested that CELF1 exchanges freely between the accumulated nascent RNP and the surrounding nucleoplasm, and that it exits RNP with similar kinetics to its entrance. Overall, it appears that on transcription loops, nascent transcripts contribute to a dynamic self-organizing structure that exemplifies a phase-separated nuclear compartment.
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Affiliation(s)
- Garry T Morgan
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK.
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177
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.Tiana G, Giorgetti L. Integrating experiment, theory and simulation to determine the structure and dynamics of mammalian chromosomes. Curr Opin Struct Biol 2018; 49:11-17. [DOI: 10.1016/j.sbi.2017.10.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 01/09/2023]
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178
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Abstract
Enhancers are short noncoding segments of DNA (100-1000 bp) that control the temporal and spatial activity of genes in an orientation-independent manner. They can be separated from their target genes by large distances and are thus known as distal regulatory elements. One consequence of the variability in the distance separating enhancers and their target promoters is that it is difficult to determine which elements are involved in the regulation of a particular gene. Moreover, enhancers can be found in clusters in which multiple regulatory elements control expression of the same target gene. However, little is known about how the individual elements contribute to gene expression. Here, we describe how chromatin conformation promotes and constraints enhancer activity. Further, we discuss enhancer clusters and what is known about the contribution of individual elements to the regulation of target genes. Finally, we examine the reliability of different methods used to identify enhancers.
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Affiliation(s)
- Valentina Snetkova
- Department of Pathology, New York University School of Medicine, 550 First Avenue, MSB 599, New York, NY 10016, USA.,MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, 550 First Avenue, MSB 599, New York, NY 10016, USA
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179
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Computational methods for analyzing genome-wide chromosome conformation capture data. Curr Opin Biotechnol 2018; 54:98-105. [PMID: 29550705 DOI: 10.1016/j.copbio.2018.01.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/31/2017] [Accepted: 01/22/2018] [Indexed: 11/23/2022]
Abstract
In all organisms, chromatin is packed to fulfil structural constraints and functional requirements. The hierarchical model of chromatin organization in the 3D nuclear space encompasses different topologies at diverse scale lengths, with chromosomes occupying distinct volumes, further organized in compartments, inside which the chromatin fibers fold into large domains and short-range loops. In the recent years, the combination of chromosome conformation capture (3C) techniques and high-throughput sequencing allowed probing chromatin spatial organization at the whole genome-scale. 3C-based methods produce enormous amounts of genomic data that are analyzed using ad-hoc computational procedures. Here, we review the common pipelines and methods for the analysis of genome-wide chromosome conformation capture data, highlighting recent developments in key steps for the identification of chromatin structures.
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180
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Kocanova S, Goiffon I, Bystricky K. 3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines. Methods 2018; 142:3-15. [PMID: 29501423 DOI: 10.1016/j.ymeth.2018.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/19/2017] [Accepted: 02/14/2018] [Indexed: 11/28/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a common technique used to label DNA and/or RNA for detection of a genomic region of interest. However, the technique can be challenging, in particular when applied to single genes in human cancer cells. Here, we provide a step-by-step protocol for analysis of short (35 kb-300 kb) genomic regions in three dimensions (3D). We discuss the experimental design and provide practical considerations for 3D imaging and data analysis to determine chromatin folding. We demonstrate that 3D FISH using BACs (Bacterial Artificial Chromosomes) or fosmids can provide detailed information of the architecture of gene domains. More specifically, we show that mapping of specific chromatin landscapes informs on changes associated with estrogen stimulated gene activity in human breast cancer cell lines.
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Affiliation(s)
- Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA, France.
| | - Isabelle Goiffon
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France.
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA, France.
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181
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Comoglio F, Park HJ, Schoenfelder S, Barozzi I, Bode D, Fraser P, Green AR. Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures. Genome Res 2018; 28:295-309. [PMID: 29429976 PMCID: PMC5848609 DOI: 10.1101/gr.227272.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/26/2018] [Indexed: 12/13/2022]
Abstract
Thrombopoietin (TPO) is a critical cytokine regulating hematopoietic stem cell maintenance and differentiation into the megakaryocytic lineage. However, the transcriptional and chromatin dynamics elicited by TPO signaling are poorly understood. Here, we study the immediate early transcriptional and cis-regulatory responses to TPO in hematopoietic stem/progenitor cells (HSPCs) and use this paradigm of cytokine signaling to chromatin to dissect the relationship between cis-regulatory activity and chromatin architecture. We show that TPO profoundly alters the transcriptome of HSPCs, with key hematopoietic regulators being transcriptionally repressed within 30 min of TPO. By examining cis-regulatory dynamics and chromatin architectures, we demonstrate that these changes are accompanied by rapid and extensive epigenome remodeling of cis-regulatory landscapes that is spatially coordinated within topologically associating domains (TADs). Moreover, TPO-responsive enhancers are spatially clustered and engage in preferential homotypic intra- and inter-TAD interactions that are largely refractory to TPO signaling. By further examining the link between cis-regulatory dynamics and chromatin looping, we show that rapid modulation of cis-regulatory activity is largely independent of chromatin looping dynamics. Finally, we show that, although activated and repressed cis-regulatory elements share remarkably similar DNA sequence compositions, transcription factor binding patterns accurately predict rapid cis-regulatory responses to TPO.
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Affiliation(s)
- Federico Comoglio
- Cambridge Institute for Medical Research, Medical Research Council/Wellcome Trust Stem Cell Institute, and Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Hyun Jung Park
- Cambridge Institute for Medical Research, Medical Research Council/Wellcome Trust Stem Cell Institute, and Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Iros Barozzi
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Daniel Bode
- Cambridge Institute for Medical Research, Medical Research Council/Wellcome Trust Stem Cell Institute, and Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Department of Biological Science, Florida State University, Tallahassee, Florida 32301, USA
| | - Anthony R Green
- Cambridge Institute for Medical Research, Medical Research Council/Wellcome Trust Stem Cell Institute, and Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
- Department of Haematology, Addenbrooke's Hospital, Cambridge CB2 0XY, United Kingdom
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182
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Howard BH, Hirai TH, Russanova VR. Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology. PLoS One 2018; 13:e0191033. [PMID: 29466355 PMCID: PMC5821309 DOI: 10.1371/journal.pone.0191033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/27/2017] [Indexed: 11/19/2022] Open
Abstract
Substantial evidence has accumulated linking epigenome change to alterations in stem cell function during postnatal development and aging. Yet much remains to be learned about causal relationships, and large gaps remain in our understanding of epigenome-transcriptome interactions. Here we investigate structural features of large histone H3K27me3-enriched regions in human stem cell-like monocytes and their dendritic cell derivatives, where the H3K27me3 modification is considered to demarcate Polycomb (PcG) domains. Both differentiation- and postnatal development-related change are explored, initially by confirming expected reciprocal relationships between transcript abundance and span of PcG domains overlapping transcribed regions. PcG-associated postnatal transcriptome change specific to the stem cell-like monocytes is found to be incompletely explained by conventional measures of PcG region structure. To address this, we introduce algorithms that quantify local nucleosome-scale conservation of PcG-region topology. It is shown that topology-based comparisons can reveal broad statistical linkage between postnatal gene down-regulation and epigenome remodeling; further, such comparisons provide access to a previously unexplored dimension of epigenome architecture.
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Affiliation(s)
- Bruce H. Howard
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Tazuko H. Hirai
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Valya R. Russanova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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183
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Laarman MD, Vermunt MW, Kleinloog R, de Boer-Bergsma JJ, Brain Bank N, Rinkel GJ, Creyghton MP, Mokry M, Bakkers J, Ruigrok YM. Intracranial Aneurysm–Associated Single-Nucleotide Polymorphisms Alter Regulatory DNA in the Human Circle of Willis. Stroke 2018; 49:447-453. [DOI: 10.1161/strokeaha.117.018557] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 10/17/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022]
Abstract
Background and Purpose—
Genome-wide association studies significantly link intracranial aneurysm (IA) to single-nucleotide polymorphisms (SNPs) in 6 genomic loci. To gain insight into the relevance of these IA-associated SNPs, we aimed to identify regulatory regions and analyze overall gene expression in the human circle of Willis (CoW), on which these aneurysms develop.
Methods—
We performed chromatin immunoprecipitation and sequencing for histone modifications H3K4me1 and H3K27ac to identify regulatory regions, including distal enhancers and active promoters, in postmortem specimens of the human CoW. These experiments were complemented with RNA sequencing on the same specimens. We determined whether these regulatory regions overlap with IA-associated SNPs, using computational methods. By combining our results with publicly available data, we investigated the effect of IA-associated SNPs on the newly identified regulatory regions and linked them to potential target genes.
Results—
We find that IA-associated SNPs are significantly enriched in CoW regulatory regions. Some of the IA-associated SNPs that overlap with a regulatory region are likely to alter transcription factor binding, and in proximity to these regulatory regions are 102 genes that are expressed in the CoW. In addition, gene expression in the CoW is enriched for genes related to cell adhesion and the extracellular matrix.
Conclusions—
CoW regulatory regions link IA-associated SNPs to genes with a potential role in the development of IAs. Our data refine previous predictions on SNPs associated with IA and provide a substantial resource from which candidates for follow-up studies can be prioritized.
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Affiliation(s)
- Melanie D. Laarman
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Marit W. Vermunt
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Rachel Kleinloog
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Jelkje J. de Boer-Bergsma
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Netherlands Brain Bank
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Gabriël J.E. Rinkel
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Menno P. Creyghton
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Michal Mokry
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Jeroen Bakkers
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
| | - Ynte M. Ruigrok
- From the Department of Neurology and Neurosurgery (M.D.L., R.K., G.J.E., Y.M.R.), Hubrecht Institute-KNAW, and Division of Heart and Lungs, Department of Medical Physiology (J.B.), University Medical Center Utrecht, the Netherlands (M.D.L., M.W.V., M.P.C., J.B.); Department of Genetics, University Medical Center Groningen, University of Groningen, the Netherlands (J.J.d.B.-B.); Netherlands Institute for Neuroscience, Amsterdam (N.B.B.); and Division of Pediatrics, Wilhelmina Children’s Hospital,
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184
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Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat Genet 2018; 50:238-249. [PMID: 29335546 PMCID: PMC5810905 DOI: 10.1038/s41588-017-0030-7] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 12/01/2017] [Indexed: 01/28/2023]
Abstract
Chromosomal architecture is known to influence gene expression, yet its role in controlling cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem cells (PSCs) by the transcription factors (TFs) OCT4, SOX2, KLF4 and MYC offers an opportunity to address this question but is severely limited by the low proportion of responding cells. We have recently developed a highly efficient reprogramming protocol that synchronously converts somatic into pluripotent stem cells. Here, we used this system to integrate time-resolved changes in genome topology with gene expression, TF binding and chromatin-state dynamics. The results showed that TFs drive topological genome reorganization at multiple architectural levels, often before changes in gene expression. Removal of locus-specific topological barriers can explain why pluripotency genes are activated sequentially, instead of simultaneously, during reprogramming. Together, our results implicate genome topology as an instructive force for implementing transcriptional programs and cell fate in mammals.
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Affiliation(s)
- Ralph Stadhouders
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.
| | - Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François Serra
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Bruno Di Stefano
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University and Harvard Medical School, Cambridge, MA, USA
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Antonio Gomez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Samuel Collombet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, Paris, France
| | - Clara Berenguer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Jochen Hecht
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genomics Unit, CRG, BIST, Barcelona, Spain
| | - Guillaume J Filion
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc A Marti-Renom
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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185
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Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature 2018; 549:219-226. [PMID: 28905911 DOI: 10.1038/nature23884] [Citation(s) in RCA: 437] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/27/2017] [Indexed: 12/19/2022]
Abstract
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.
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Affiliation(s)
- Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Howard Hughes Medical Institute, Worcester, Massachusetts 01605, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Victor O Leshyk
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York 10027, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Clodagh C O'Shea
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, University of California San Diego, La Jolla California 92093, USA
| | - Joan C Ritland Politz
- Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Howard Hughes Medical Institute, Seattle, Washington 98109, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
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186
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Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF. Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Mol Biol Cell 2018; 29:220-233. [PMID: 29142071 PMCID: PMC5909933 DOI: 10.1091/mbc.e17-06-0410] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/17/2017] [Accepted: 11/08/2017] [Indexed: 01/29/2023] Open
Abstract
Nuclear shape and architecture influence gene localization, mechanotransduction, transcription, and cell function. Abnormal nuclear morphology and protrusions termed "blebs" are diagnostic markers for many human afflictions including heart disease, aging, progeria, and cancer. Nuclear blebs are associated with both lamin and chromatin alterations. A number of prior studies suggest that lamins dictate nuclear morphology, but the contributions of altered chromatin compaction remain unclear. We show that chromatin histone modification state dictates nuclear rigidity, and modulating it is sufficient to both induce and suppress nuclear blebs. Treatment of mammalian cells with histone deacetylase inhibitors to increase euchromatin or histone methyltransferase inhibitors to decrease heterochromatin results in a softer nucleus and nuclear blebbing, without perturbing lamins. Conversely, treatment with histone demethylase inhibitors increases heterochromatin and chromatin nuclear rigidity, which results in reduced nuclear blebbing in lamin B1 null nuclei. Notably, increased heterochromatin also rescues nuclear morphology in a model cell line for the accelerated aging disease Hutchinson-Gilford progeria syndrome caused by mutant lamin A, as well as cells from patients with the disease. Thus, chromatin histone modification state is a major determinant of nuclear blebbing and morphology via its contribution to nuclear rigidity.
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Affiliation(s)
- Andrew D Stephens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Patrick Z Liu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Edward J Banigan
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
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187
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Zepeda-Mendoza CJ, Bardon A, Kammin T, Harris DJ, Cox H, Redin C, Ordulu Z, Talkowski ME, Morton CC. Phenotypic interpretation of complex chromosomal rearrangements informed by nucleotide-level resolution and structural organization of chromatin. Eur J Hum Genet 2018; 26:374-381. [PMID: 29321672 DOI: 10.1038/s41431-017-0068-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/20/2017] [Accepted: 10/31/2017] [Indexed: 01/06/2023] Open
Abstract
Molecular characterization of balanced chromosomal abnormalities constitutes a powerful tool in understanding the pathogenic mechanisms of complex genetic disorders. Here we report a male with severe global developmental delay in the presence of a complex karyotype and normal microarray and exome studies. The subject, referred to as DGAP294, has two de novo apparently balanced translocations involving chromosomes 1 and 14, and chromosomes 4 and 10, disrupting several different transcripts of adhesion G protein-coupled receptor L2 (ADGRL2) and protocadherin 15 (PCDH15). In addition, a maternally inherited inversion disrupts peptidyl arginine deiminase types 3 and 4 (PADI3 and PADI4) on chromosome 1. None of these gene disruptions explain the patient's phenotype. Using genome regulatory annotations and chromosome conformation data, we predict a position effect ~370 kb upstream of a translocation breakpoint located at 14q12. The position effect involves forkhead box G1 (FOXG1), mutations in which are associated with the congenital form of Rett syndrome and FOXG1 syndrome. We believe the FOXG1 position effect largely accounts for the clinical phenotype in DGAP294, which can be classified as FOXG1 syndrome like. Our findings emphasize the significance of not only analyzing disrupted genes by chromosomal rearrangements, but also evaluating potential long-range position effects in clinical diagnoses.
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Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Tammy Kammin
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - David J Harris
- Harvard Medical School, Boston, MA, USA.,Boston Children's Hospital, Boston, MA, USA
| | - Helen Cox
- West Midlands Regional Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Claire Redin
- Harvard Medical School, Boston, MA, USA.,Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Zehra Ordulu
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Harvard Medical School, Boston, MA, USA.,Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA. .,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA. .,Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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188
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Schilit SLP, Morton CC. 3C-PCR: a novel proximity ligation-based approach to phase chromosomal rearrangement breakpoints with distal allelic variants. Hum Genet 2018; 137:55-62. [PMID: 29196799 PMCID: PMC5790632 DOI: 10.1007/s00439-017-1853-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/11/2017] [Indexed: 01/07/2023]
Abstract
Recent advances in molecular cytogenetics highlight the importance of noncoding structural variation in human disease. Genomic rearrangements can disrupt chromatin architecture, leading to long-range alterations in gene expression. With increasing ability to assess distal gene dysregulation comes new challenges in clinical interpretation of rearrangements. While haplotyping methods to determine compound heterozygosity in a single gene with two pathogenic variants are established, such methods are insufficient for phasing larger distances between a pathogenic variant and a genomic rearrangement breakpoint. Herein, we present an inexpensive and efficient proximity ligation-based method called 3C-PCR for phasing chromosomal rearrangement breakpoints with distal allelic variants. 3C-PCR uses canonical chromosome conformation capture (3C) libraries for targeted distal phasing by implementing a novel nested PCR strategy with primers anchored across the rearrangement breakpoints and subsequent Sanger sequencing. As a proof of concept, 3C-PCR was used to phase a highly variable region 1.3 Mb upstream of a chromosomal rearrangement breakpoint in a balanced translocation. We found that the nested PCR approach amplified the derivative chromosome substrate exclusively and identified the same haplotype by Sanger sequencing reliably. Given its efficacy and versatility, 3C-PCR is ideal for use in phasing chromosomal rearrangement breakpoints with allelic variants located at a genomic distance over a megabase.
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Affiliation(s)
- Samantha L P Schilit
- Biological and Biomedical Sciences Program, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
- Program in Genetics and Genomics, Department of Genetics, Harvard Medical School, Boston, MA, USA
- Leder Human Biology and Translational Medicine Program, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Cynthia C Morton
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
- Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Centre, Manchester, UK.
- Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital and Harvard Medical School, New Research Building, Room 160D, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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189
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190
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Abstract
Recent advances in next-generation sequencing (NGS) and chromosome conformation capture (3C) analysis have led to the development of Hi-C, a genome-wide version of the 3C method. Hi-C has identified new levels of chromosome organization such as A/B compartments, topologically associating domains (TADs) as well as large megadomains on the inactive X chromosome, while allowing the identification of chromatin loops at the genome scale. Despite its powerfulness, Hi-C data analysis is much more involved compared to conventional NGS applications such as RNA-seq or ChIP-seq and requires many more steps. This presents a significant hurdle for those who wish to implement Hi-C technology into their laboratory. On the other hand, genomics data repository sites sometimes contain processed Hi-C data sets, allowing researchers to perform further analysis without the need for high-spec workstations and servers. In this chapter, we provide a detailed description on how to calculate A/B compartment profiles from processed Hi-C data on the autosomes and the active/inactive X chromosomes.
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191
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Abstract
The spatial organization of genomes is based on their hierarchical compartmentalization in topological domains. There is growing evidence that bacterial genomes are organized into insulated domains similar to the Topologically Associating Domains (TADs) detected in eukaryotic cells. Chromosome conformation capture (3C) technologies are used to analyze in vivo DNA proximity based on ligation of distal DNA segments crossed-linked by bridging proteins. By combining 3C and high-throughput sequencing, the Hi-C method reveals genome-wide interactions within topological domains and global genome structure as a whole. This chapter provides detailed guidelines for the preparation of Hi-C sequencing libraries for bacteria.
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192
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Lando D, Stevens TJ, Basu S, Laue ED. Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols. Nucleus 2018; 9:190-201. [PMID: 29431585 PMCID: PMC5883084 DOI: 10.1080/19491034.2018.1438799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/02/2018] [Accepted: 02/02/2018] [Indexed: 11/17/2022] Open
Abstract
Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforward computation of realistic chromosome conformations that may be compared and combined with other, independent, techniques to study 3D structure. Here we discuss how single-cell Hi-C and subsequent 3D genome structure determination allows comparison with data from microscopy. We then carry out a systematic evaluation of recently published single-cell Hi-C datasets to establish a computational approach for the evaluation of single-cell Hi-C protocols. We show that the calculation of genome structures provides a useful tool for assessing the quality of single-cell Hi-C data because it requires a self-consistent network of interactions, relating to the underlying 3D conformation, with few errors, as well as sufficient longer-range cis- and trans-chromosomal contacts.
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Affiliation(s)
- David Lando
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tim J. Stevens
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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193
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Goldstein I, Hager GL. Dynamic enhancer function in the chromatin context. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10:10.1002/wsbm.1390. [PMID: 28544514 PMCID: PMC6638546 DOI: 10.1002/wsbm.1390] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 12/28/2022]
Abstract
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding. More recently, fluorescent microscopy techniques, including fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, and single molecule tracking (SMT), reveal a highly dynamic binding behavior for these factors in live cells. Furthermore, a refined analysis of genomic footprinting suggests that many transcription factors leave minimal or no footprints in chromatin, even when present and active in a given cell type. In this study, we review the implications of these new approaches for an accurate understanding of enhancer function in real time. In vivo SMT, in particular, has recently evolved as a promising methodology to probe enhancer function in live cells. Integration of findings from the many approaches now employed in the study of enhancer function suggest a highly dynamic view for the action of enhancer activating factors, viewed on a time scale of milliseconds to seconds, rather than minutes to hours. WIREs Syst Biol Med 2018, 10:e1390. doi: 10.1002/wsbm.1390 This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > Imaging.
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Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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194
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The 10-nm chromatin fiber and its relationship to interphase chromosome organization. Biochem Soc Trans 2017; 46:67-76. [PMID: 29263138 PMCID: PMC5818668 DOI: 10.1042/bst20170101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/09/2023]
Abstract
A chromosome is a single long DNA molecule assembled along its length with nucleosomes and proteins. During interphase, a mammalian chromosome exists as a highly organized supramolecular globule in the nucleus. Here, we discuss new insights into how genomic DNA is packaged and organized within interphase chromosomes. Our emphasis is on the structural principles that underlie chromosome organization, with a particular focus on the intrinsic contributions of the 10-nm chromatin fiber, but not the regular 30-nm fiber. We hypothesize that the hierarchical globular organization of an interphase chromosome is fundamentally established by the self-interacting properties of a 10-nm zig-zag array of nucleosomes, while histone post-translational modifications, histone variants, and chromatin-associated proteins serve to mold generic chromatin domains into specific structural and functional entities.
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195
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CTCF driven TERRA transcription facilitates completion of telomere DNA replication. Nat Commun 2017; 8:2114. [PMID: 29235471 PMCID: PMC5727389 DOI: 10.1038/s41467-017-02212-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022] Open
Abstract
Telomere repeat DNA forms a nucleo-protein structure that can obstruct chromosomal DNA replication, especially under conditions of replication stress. Transcription of telomere repeats can initiate at subtelomeric CTCF-binding sites to generate telomere repeat-encoding RNA (TERRA), but the role of transcription, CTCF, and TERRA in telomere replication is not known. Here, we have used CRISPR/Cas9 gene editing to mutate CTCF-binding sites at the putative start site of TERRA transcripts for a class of subtelomeres. Under replication stress, telomeres lacking CTCF-driven TERRA exhibit sister-telomere loss and upon entry into mitosis, exhibit the formation of ultra-fine anaphase bridges and micronuclei. Importantly, these phenotypes could be rescued by the forced transcription of TERRA independent of CTCF binding. Our findings indicate that subtelomeric CTCF facilitates telomeric DNA replication by promoting TERRA transcription. Our findings also demonstrate that CTCF-driven TERRA transcription acts in cis to facilitate telomere repeat replication and chromosome stability. TERRA RNA is involved in maintaining stability during telomere repeat replication. Here the authors, by using CRISPR/Cas9, mutate CTCF-binding sites at start site of TERRA transcripts and find that subtelomeric CTCF facilitates telomeric DNA replication by promoting TERRA transcription.
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196
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Abstract
The central role of hormonal 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] is to regulate calcium and phosphorus homeostasis via actions in intestine, kidney, and bone. These and other actions in many cell types not involved in mineral metabolism are mediated by the vitamin D receptor. Recent studies using genome-wide scale techniques have extended fundamental ideas regarding vitamin D-mediated control of gene expression while simultaneously revealing a series of new concepts. This article summarizes the current view of the biological actions of the vitamin D hormone and focuses on new concepts that drive the understanding of the mechanisms through which vitamin D operates.
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Affiliation(s)
- J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Biochem Addition, Room 543D, 433 Babcock Drive, Madison, WI 53706, USA.
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
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197
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Hao N, Shearwin KE, Dodd IB. Programmable DNA looping using engineered bivalent dCas9 complexes. Nat Commun 2017; 8:1628. [PMID: 29158476 PMCID: PMC5696343 DOI: 10.1038/s41467-017-01873-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 10/23/2017] [Indexed: 12/31/2022] Open
Abstract
DNA looping is a ubiquitous and critical feature of gene regulation. Although DNA looping can be efficiently detected, tools to readily manipulate DNA looping are limited. Here we develop CRISPR-based DNA looping reagents for creation of programmable DNA loops. Cleavage-defective Cas9 proteins of different specificity are linked by heterodimerization or translational fusion to create bivalent complexes able to link two separate DNA regions. After model-directed optimization, the reagents are validated using a quantitative DNA looping assay in E. coli. Looping efficiency is ~15% for a 4.7 kb loop, but is significantly improved by loop multiplexing with additional guides. Bivalent dCas9 complexes are also used to activate endogenous norVW genes by rewiring chromosomal DNA to bring distal enhancer elements to the gene promoters. Such reagents should allow manipulation of DNA looping in a variety of cell types, aiding understanding of endogenous loops and enabling creation of new regulatory connections. DNA loops are a ubiquitious feature of gene regulation across the kingdoms of life. Here the authors design a Cas9-based dimerization system for inducing DNA loops in E. coli, allowing activation and rewiring of gene expression.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Keith E Shearwin
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
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198
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Jamge S, Stam M, Angenent GC, Immink RGH. A cautionary note on the use of chromosome conformation capture in plants. PLANT METHODS 2017; 13:101. [PMID: 29177001 PMCID: PMC5691870 DOI: 10.1186/s13007-017-0251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The chromosome conformation capture (3C) technique is a method to study chromatin interactions at specific genomic loci. Initially established for yeast the 3C technique has been adapted to plants in recent years in order to study chromatin interactions and their role in transcriptional gene regulation. As the plant scientific community continues to implement this technology, a discussion on critical controls, validations steps and interpretation of 3C data is essential to fully benefit from 3C in plants. RESULTS Here we assess the reliability and robustness of the 3C technique for the detection of chromatin interactions in Arabidopsis. As a case study, we applied this methodology to the genomic locus of a floral integrator gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), and demonstrate the need of several controls and standard validation steps to allow a meaningful interpretation of 3C data. The intricacies of this promising but challenging technique are discussed in depth. CONCLUSIONS The 3C technique offers an interesting opportunity to study chromatin interactions at a resolution infeasible by microscopy. However, for interpretation of 3C interaction data and identification of true interactions, 3C technology demands a stringent experimental setup and extreme caution.
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Affiliation(s)
- Suraj Jamge
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. H. Immink
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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199
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Joyce EF. Toward High-Throughput and Multiplexed Imaging of Genome Organization. Assay Drug Dev Technol 2017; 15:11-14. [PMID: 28092459 DOI: 10.1089/adt.2016.770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dr. Eric Joyce from the Department of Genetics at the University of Pennsylvania was awarded The President's Innovation award at the annual Society of Biomolecular Imaging and Informatics meeting held in Boston, September 2016. Chromosome interactions are a fundamental aspect of nuclear organization that can activate and silence genes or even direct chromosome rearrangements. However, the molecular mechanisms underlying how chromosomal segments find each other and form stable interactions within cells remain unknown. To address this gap, we have recently developed two technologies that use fluorescent in situ hybridization (FISH) to interrogate chromosome positioning at single-cell resolution. The first is a technology for high-throughput FISH, and the other, called Oligopaints, is a new type of probe that reduces the cost and increases the resolution of FISH. Here, I review our use of these two technologies to uncover and characterize the molecular mechanisms that govern chromosome pairing in Drosophila. I further describe how these methods should benefit a broad spectrum of research fields, including those focusing on chromatin looping, compaction, replication, homologous recombination, and DNA repair.
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Affiliation(s)
- Eric F Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
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200
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Nizovtseva EV, Todolli S, Olson WK, Studitsky VM. Towards quantitative analysis of gene regulation by enhancers. Epigenomics 2017; 9:1219-1231. [PMID: 28799793 DOI: 10.2217/epi-2017-0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enhancers are regulatory DNA sequences that can activate transcription over large distances. Recent studies have revealed the widespread role of distant activation in eukaryotic gene regulation and in the development of various human diseases, including cancer. Here we review recent progress in the field, focusing on new experimental and computational approaches that quantify the role of chromatin structure and dynamics during enhancer-promoter interactions in vitro and in vivo.
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Affiliation(s)
- Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Stefjord Todolli
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Moscow State University, Moscow 119991, Russia.,Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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