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Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, Bedoya-López AF, Orozco JIJ, Cortés J, Roy A, Forsberg-Nilsson K, DiNome ML, Marzese DM. Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements. Cell Mol Life Sci 2024; 81:274. [PMID: 38902506 DOI: 10.1007/s00018-024-05314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
Abstract
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements involved in gene expression. These gene regulatory elements (GREs) include enhancers, insulators, silencers, and gene promoters. Notably, new evidence shows how mutations within these regions substantially influence gene expression programs, especially in the context of cancer. Advances in high-throughput sequencing technologies have accelerated the identification of somatic and germline single nucleotide mutations in non-coding genomic regions. This review provides an overview of somatic and germline non-coding single nucleotide alterations affecting transcription factor binding sites in GREs, specifically involved in cancer biology. It also summarizes the technologies available for exploring GREs and the challenges associated with studying and characterizing non-coding single nucleotide mutations. Understanding the role of GRE alterations in cancer is essential for improving diagnostic and prognostic capabilities in the precision medicine era, leading to enhanced patient-centered clinical outcomes.
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Affiliation(s)
- Sandra Iñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Andrés F Bedoya-López
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, 08017, Barcelona, Spain
- Medica Scientia Innovation Research SL (MEDSIR), 08018, Barcelona, Spain
- Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, 28670, Madrid, Spain
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Maggie L DiNome
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
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2
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Chowdhury HMAM, Boult T, Oluwadare O. Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness. BMC Bioinformatics 2024; 25:123. [PMID: 38515011 PMCID: PMC10958853 DOI: 10.1186/s12859-024-05713-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Chromosome is one of the most fundamental part of cell biology where DNA holds the hierarchical information. DNA compacts its size by forming loops, and these regions house various protein particles, including CTCF, SMC3, H3 histone. Numerous sequencing methods, such as Hi-C, ChIP-seq, and Micro-C, have been developed to investigate these properties. Utilizing these data, scientists have developed a variety of loop prediction techniques that have greatly improved their methods for characterizing loop prediction and related aspects. RESULTS In this study, we categorized 22 loop calling methods and conducted a comprehensive study of 11 of them. Additionally, we have provided detailed insights into the methodologies underlying these algorithms for loop detection, categorizing them into five distinct groups based on their fundamental approaches. Furthermore, we have included critical information such as resolution, input and output formats, and parameters. For this analysis, we utilized the GM12878 Hi-C datasets at 5 KB, 10 KB, 100 KB and 250 KB resolutions. Our evaluation criteria encompassed various factors, including memory usages, running time, sequencing depth, and recovery of protein-specific sites such as CTCF, H3K27ac, and RNAPII. CONCLUSION This analysis offers insights into the loop detection processes of each method, along with the strengths and weaknesses of each, enabling readers to effectively choose suitable methods for their datasets. We evaluate the capabilities of these tools and introduce a novel Biological, Consistency, and Computational robustness score ( B C C score ) to measure their overall robustness ensuring a comprehensive evaluation of their performance.
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Affiliation(s)
- H M A Mohit Chowdhury
- Department of Computer Science, University of Colorado at Colorado Springs, 1420 Austin Bluffs Pkwy, Colorado Springs, CO, 80918, USA
| | - Terrance Boult
- Department of Computer Science, University of Colorado at Colorado Springs, 1420 Austin Bluffs Pkwy, Colorado Springs, CO, 80918, USA
| | - Oluwatosin Oluwadare
- Department of Computer Science, University of Colorado at Colorado Springs, 1420 Austin Bluffs Pkwy, Colorado Springs, CO, 80918, USA.
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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3
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Tang L, Hill MC, Ellinor PT, Li M. Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies. Genome Biol 2022; 23:30. [PMID: 35063001 PMCID: PMC8780810 DOI: 10.1186/s13059-021-02597-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/30/2021] [Indexed: 01/10/2023] Open
Abstract
Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze these large and complex datasets, computational methods are undergoing rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to identify which commonly used algorithms and processing pipelines need to be improved. Here we present a comprehensive benchmark framework, Bacon, to evaluate the performance of several computational methods. Finally, we provide practical recommendations for users working with HiChIP and/or ChIA-PET analyses.
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Affiliation(s)
- Li Tang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Matthew C Hill
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
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4
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Zha M, Wang N, Zhang C, Wang Z. Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential. Int J Mol Sci 2021; 22:ijms22115914. [PMID: 34072879 PMCID: PMC8199262 DOI: 10.3390/ijms22115914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/23/2021] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis-Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.
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Affiliation(s)
- Mengsheng Zha
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, 118 College Dr, Hattiesburg, MS 39406, USA; (M.Z.); (C.Z.)
| | - Nan Wang
- Department of Computer Science, New Jersey City University, 2039 Kennedy Blvd, Jersey City, NJ 07305, USA;
| | - Chaoyang Zhang
- School of Computing Sciences and Computer Engineering, University of Southern Mississippi, 118 College Dr, Hattiesburg, MS 39406, USA; (M.Z.); (C.Z.)
| | - Zheng Wang
- Department of Computer Science, University of Miami, 1364 Memorial Drive, Coral Gables, FL 33124, USA
- Correspondence:
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5
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Belaghzal H, Borrman T, Stephens AD, Lafontaine DL, Venev SV, Weng Z, Marko JF, Dekker J. Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nat Genet 2021; 53:367-378. [PMID: 33574602 PMCID: PMC7946813 DOI: 10.1038/s41588-021-00784-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/11/2021] [Indexed: 01/30/2023]
Abstract
Nuclear compartmentalization of active and inactive chromatin is thought to occur through microphase separation mediated by interactions between loci of similar type. The nature and dynamics of these interactions are not known. We developed liquid chromatin Hi-C to map the stability of associations between loci. Before fixation and Hi-C, chromosomes are fragmented, which removes strong polymeric constraint, enabling detection of intrinsic locus-locus interaction stabilities. Compartmentalization is stable when fragments are larger than 10-25 kb. Fragmentation of chromatin into pieces smaller than 6 kb leads to gradual loss of genome organization. Lamin-associated domains are most stable, whereas interactions for speckle- and polycomb-associated loci are more dynamic. Cohesin-mediated loops dissolve after fragmentation. Liquid chromatin Hi-C provides a genome-wide view of chromosome interaction dynamics.
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Affiliation(s)
- Houda Belaghzal
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrew D Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | - Denis L Lafontaine
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sergey V Venev
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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6
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Davis SZ, Hollin T, Lenz T, Le Roch KG. Three-dimensional chromatin in infectious disease-A role for gene regulation and pathogenicity? PLoS Pathog 2021; 17:e1009207. [PMID: 33539484 PMCID: PMC7861443 DOI: 10.1371/journal.ppat.1009207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The recent Coronavirus Disease 2019 pandemic has once again reminded us the importance of understanding infectious diseases. One important but understudied area in infectious disease research is the role of nuclear architecture or the physical arrangement of the genome in the nucleus in controlling gene regulation and pathogenicity. Recent advances in research methods, such as Genome-wide chromosome conformation capture using high-throughput sequencing (Hi-C), have allowed for easier analysis of nuclear architecture and chromosomal reorganization in both the infectious disease agents themselves as well as in their host cells. This review will discuss broadly on what is known about nuclear architecture in infectious disease, with an emphasis on chromosomal reorganization, and briefly discuss what steps are required next in the field.
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Affiliation(s)
- Sage Z. Davis
- Department of Molecular, Cell and Systems Biology (MCSB), University of California Riverside, California, United States of America
| | - Thomas Hollin
- Department of Molecular, Cell and Systems Biology (MCSB), University of California Riverside, California, United States of America
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology (MCSB), University of California Riverside, California, United States of America
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology (MCSB), University of California Riverside, California, United States of America
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7
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Hollin T, Le Roch KG. From Genes to Transcripts, a Tightly Regulated Journey in Plasmodium. Front Cell Infect Microbiol 2020; 10:618454. [PMID: 33425787 PMCID: PMC7793691 DOI: 10.3389/fcimb.2020.618454] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past decade, we have witnessed significant progresses in understanding gene regulation in Apicomplexa including the human malaria parasite, Plasmodium falciparum. This parasite possesses the ability to convert in multiple stages in various hosts, cell types, and environments. Recent findings indicate that P. falciparum is talented at using efficient and complementary molecular mechanisms to ensure a tight control of gene expression at each stage of its life cycle. Here, we review the current understanding on the contribution of the epigenome, atypical transcription factors, and chromatin organization to regulate stage conversion in P. falciparum. The adjustment of these regulatory mechanisms occurring during the progression of the life cycle will be extensively discussed.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
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8
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Straub J, Venigalla S, Newman JJ. Mediator's Kinase Module: A Modular Regulator of Cell Fate. Stem Cells Dev 2020; 29:1535-1551. [PMID: 33161841 DOI: 10.1089/scd.2020.0164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Selective gene expression is crucial in maintaining the self-renewing and multipotent properties of stem cells. Mediator is a large, evolutionarily conserved, multi-subunit protein complex that modulates gene expression by relaying signals from cell type-specific transcription factors to RNA polymerase II. In humans, this complex consists of 30 subunits arranged in four modules. One critical module of the Mediator complex is the kinase module consisting of four subunits: MED12, MED13, CDK8, and CCNC. The kinase module exists in variable association with the 26-subunit Mediator core and affects transcription through phosphorylation of transcription factors and by controlling Mediator structure and function. Many studies have shown the kinase module to be a key player in the maintenance of stem cells that is distinct from a general role in transcription. Genetic studies have revealed that dysregulation of this kinase subunit contributes to the development of many human diseases. In this review, we discuss the importance of the Mediator kinase module by examining how this module functions with the more recently identified transcriptional super-enhancers, how changes in the kinase module and its activity can lead to the development of human disease, and the role of this unique module in directing and maintaining cell state. As we look to use stem cells to understand human development and treat human disease through both cell-based therapies and tissue engineering, we need to remain aware of the on-going research and address critical gaps in knowledge related to the molecular mechanisms that control cell fate.
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Affiliation(s)
- Joseph Straub
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Sree Venigalla
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Jamie J Newman
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
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9
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Tjalsma SJ, de Laat W. Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture. Curr Opin Genet Dev 2020; 67:10-17. [PMID: 33220512 DOI: 10.1016/j.gde.2020.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 12/22/2022]
Abstract
Recent years have seen a vast expansion of knowledge on three-dimensional (3D) genome organization. The majority of studies on chromosome topology consists of pairwise interaction data of bulk populations of cells and therefore conceals heterogenic and more complex folding patterns. Here, we discuss novel methodologies to study the variation in genome topologies between different cells and techniques that allow analysis of complex, multi-way interactions. These technologies will aid the interpretation of genome-wide chromosome conformation data and provide strategies to further dissect the interplay between genome architecture and transcription regulation.
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Affiliation(s)
- Sjoerd Jd Tjalsma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
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10
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Meluzzi D, Arya G. Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. Methods 2020; 181-182:24-34. [PMID: 31470090 PMCID: PMC7044057 DOI: 10.1016/j.ymeth.2019.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/24/2019] [Accepted: 08/23/2019] [Indexed: 02/08/2023] Open
Abstract
Chromosome conformation capture (3C) and its variants are powerful experimental techniques for probing intra- and inter-chromosomal interactions within cell nuclei at high resolution and in a high-throughput, quantitative manner. The contact maps derived from such experiments provide an avenue for inferring the 3D spatial organization of the genome. This review provides an overview of the various computational methods developed in the past decade for addressing the very important but challenging problem of deducing the detailed 3D structure or structure population of chromosomal domains, chromosomes, and even entire genomes from 3C contact maps.
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Affiliation(s)
- Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, United States.
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11
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Dynamic Chromatin Structure and Epigenetics Control the Fate of Malaria Parasites. Trends Genet 2020; 37:73-85. [PMID: 32988634 DOI: 10.1016/j.tig.2020.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022]
Abstract
Multiple hosts and various life cycle stages prompt the human malaria parasite, Plasmodium falciparum, to acquire sophisticated molecular mechanisms to ensure its survival, spread, and transmission to its next host. To face these environmental challenges, increasing evidence suggests that the parasite has developed complex and complementary layers of regulatory mechanisms controlling gene expression. Here, we discuss the recent developments in the discovery of molecular components that contribute to cell replication and differentiation and highlight the major contributions of epigenetics, transcription factors, and nuclear architecture in controlling gene regulation and life cycle progression in Plasmodium spp.
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12
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Sandoval-Velasco M, Rodríguez JA, Perez Estrada C, Zhang G, Lieberman Aiden E, Marti-Renom MA, Gilbert MTP, Smith O. Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform. Gigascience 2020; 9:giaa087. [PMID: 32845983 PMCID: PMC7448675 DOI: 10.1093/gigascience/giaa087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/15/2020] [Accepted: 07/23/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the industry-standard Illumina sequencing. With new next-generation sequencing platforms such as BGISEQ-500 becoming more widely available, protocol adaptations to fit platform-specific requirements are useful to give increased choice to researchers who routinely generate sequencing data. RESULTS We describe an in situ Hi-C protocol adapted to be compatible with the BGISEQ-500 high-throughput sequencing platform. Using zebra finch (Taeniopygia guttata) as a biological sample, we demonstrate how Hi-C libraries can be constructed to generate informative data using the BGISEQ-500 platform, following circularization and DNA nanoball generation. Our protocol is a modification of an Illumina-compatible method, based around blunt-end ligations in library construction, using un-barcoded, distally overhanging double-stranded adapters, followed by amplification using indexed primers. The resulting libraries are ready for circularization and subsequent sequencing on the BGISEQ series of platforms and yield data similar to what can be expected using Illumina-compatible approaches. CONCLUSIONS Our straightforward modification to an Illumina-compatible in situHi-C protocol enables data generation on the BGISEQ series of platforms, thus expanding the options available for researchers who wish to utilize the powerful Hi-C techniques in their research.
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Affiliation(s)
- Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Juan Antonio Rodríguez
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Baldiri i Reixach, 4-8, 08028 Barcelona, Spain
| | - Cynthia Perez Estrada
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Computer Science and Computational Applied Mathematics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Baldiri i Reixach, 4-8, 08028 Barcelona, Spain
- Centre for Genomic Regulation, Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
- Pompeu Fabra University, Doctor Aiguader 88, Barcelona 08003, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
- Micropathology Ltd, University of Warwick Science Park, Coventry CV4 7EZ, UK
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13
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Azagra A, Marina-Zárate E, Ramiro AR, Javierre BM, Parra M. From Loops to Looks: Transcription Factors and Chromatin Organization Shaping Terminal B Cell Differentiation. Trends Immunol 2019; 41:46-60. [PMID: 31822368 DOI: 10.1016/j.it.2019.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 12/18/2022]
Abstract
B lymphopoiesis is tightly regulated at the level of gene transcription. In recent years, investigators have shed light on the transcription factor networks and the epigenetic machinery involved at all differentiation steps of mammalian B cell development. During terminal differentiation, B cells undergo dramatic changes in gene transcriptional programs to generate germinal center B cells, plasma cells and memory B cells. Recent evidence indicates that mature B cell formation involves an essential contribution from 3D chromatin conformations through its interplay with transcription factors and epigenetic machinery. Here, we provide an up-to-date overview of the coordination between transcription factors, epigenetic changes, and chromatin architecture during terminal B cell differentiation, focusing on recent discoveries and technical advances for studying 3D chromatin structures.
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Affiliation(s)
- Alba Azagra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Badalona, Spain
| | - Ester Marina-Zárate
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Almudena R Ramiro
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Biola M Javierre
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Badalona, Spain.
| | - Maribel Parra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Badalona, Spain.
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14
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Wang XQD, Cameron CJF, Paquette D, Segal D, Warsaba R, Blanchette M, Dostie J. 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing. BMC Genomics 2019; 20:162. [PMID: 30819105 PMCID: PMC6394006 DOI: 10.1186/s12864-019-5532-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/15/2019] [Indexed: 11/12/2022] Open
Abstract
Background Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expression studies, and while genome-wide methods are available, high-throughput approaches to analyze defined regions are lacking. Results Here, we present carbon copy-ChIP (2C-ChIP), a versatile, inexpensive, and high-throughput technique to quantitatively measure the abundance of DNA sequences in ChIP samples. This method combines ChIP with ligation-mediated amplification (LMA) and deep sequencing to probe large genomic regions of interest. 2C-ChIP recapitulates results from benchmark ChIP approaches. We applied 2C-ChIP to the HOXA cluster to find that a region where H3K27me3 and SUZ12 linger encodes HOXA-AS2, a long non-coding RNA that enhances gene expression during cellular differentiation. Conclusions 2C-ChIP fills the need for a robust molecular biology tool designed to probe dedicated genomic regions in a high-throughput setting. The flexible nature of the 2C-ChIP approach allows rapid changes in experimental design at relatively low cost, making it a highly efficient method for chromatin analysis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5532-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue Qing David Wang
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Christopher J F Cameron
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada.,School of Computer Science and McGill Center for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Denis Paquette
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Dana Segal
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Reid Warsaba
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Mathieu Blanchette
- School of Computer Science and McGill Center for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Josée Dostie
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada.
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15
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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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16
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Pulikkan JA, Hegde M, Ahmad HM, Belaghzal H, Illendula A, Yu J, O'Hagan K, Ou J, Muller-Tidow C, Wolfe SA, Zhu LJ, Dekker J, Bushweller JH, Castilla LH. CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell 2018; 174:172-186.e21. [PMID: 29958106 PMCID: PMC6211564 DOI: 10.1016/j.cell.2018.05.048] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 02/12/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022]
Abstract
The fusion oncoprotein CBFβ-SMMHC, expressed in leukemia cases with chromosome 16 inversion, drives leukemia development and maintenance by altering the activity of the transcription factor RUNX1. Here, we demonstrate that CBFβ-SMMHC maintains cell viability by neutralizing RUNX1-mediated repression of MYC expression. Upon pharmacologic inhibition of the CBFβ-SMMHC/RUNX1 interaction, RUNX1 shows increased binding at three MYC distal enhancers, where it represses MYC expression by mediating the replacement of the SWI/SNF complex component BRG1 with the polycomb-repressive complex component RING1B, leading to apoptosis. Combining the CBFβ-SMMHC inhibitor with the BET inhibitor JQ1 eliminates inv(16) leukemia in human cells and a mouse model. Enhancer-interaction analysis indicated that the three enhancers are physically connected with the MYC promoter, and genome-editing analysis demonstrated that they are functionally implicated in deregulation of MYC expression. This study reveals a mechanism whereby CBFβ-SMMHC drives leukemia maintenance and suggests that inhibitors targeting chromatin activity may prove effective in inv(16) leukemia therapy.
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MESH Headings
- Animals
- Apoptosis/drug effects
- Azepines/pharmacology
- Azepines/therapeutic use
- Benzimidazoles/pharmacology
- Benzimidazoles/therapeutic use
- Cell Line, Tumor
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Inversion/drug effects
- Core Binding Factor Alpha 2 Subunit/chemistry
- Core Binding Factor Alpha 2 Subunit/metabolism
- DNA/chemistry
- DNA/metabolism
- DNA Helicases/metabolism
- Disease Models, Animal
- Humans
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Nuclear Proteins/metabolism
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Oncogene Proteins, Fusion/metabolism
- Polycomb Repressive Complex 1/metabolism
- Promoter Regions, Genetic
- Protein Binding
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Transcription Factors/chemistry
- Transcription Factors/metabolism
- Triazoles/pharmacology
- Triazoles/therapeutic use
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Affiliation(s)
- John Anto Pulikkan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mahesh Hegde
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hafiz Mohd Ahmad
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Houda Belaghzal
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anuradha Illendula
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kelsey O'Hagan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jianhong Ou
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Carsten Muller-Tidow
- Department of Medicine, Hematology, Oncology, and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Hackett Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Lucio Hernán Castilla
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
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17
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Kim JH, Titus KR, Gong W, Beagan JA, Cao Z, Phillips-Cremins JE. 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. Methods 2018; 142:39-46. [PMID: 29772275 PMCID: PMC5993643 DOI: 10.1016/j.ymeth.2018.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 03/01/2018] [Accepted: 05/08/2018] [Indexed: 01/13/2023] Open
Abstract
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher-resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C.
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Affiliation(s)
- Ji Hun Kim
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katelyn R Titus
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanfeng Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A Beagan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhendong Cao
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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18
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Jia R, Chai P, Zhang H, Fan X. Novel insights into chromosomal conformations in cancer. Mol Cancer 2017; 16:173. [PMID: 29149895 PMCID: PMC5693495 DOI: 10.1186/s12943-017-0741-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/06/2017] [Indexed: 12/20/2022] Open
Abstract
Exploring gene function is critical for understanding the complexity of life. DNA sequences and the three-dimensional organization of chromatin (chromosomal interactions) are considered enigmatic factors underlying gene function, and interactions between two distant fragments can regulate transactivation activity via mediator proteins. Thus, a series of chromosome conformation capture techniques have been developed, including chromosome conformation capture (3C), circular chromosome conformation capture (4C), chromosome conformation capture carbon copy (5C), and high-resolution chromosome conformation capture (Hi-C). The application of these techniques has expanded to various fields, but cancer remains one of the major topics. Interactions mediated by proteins or long noncoding RNAs (lncRNAs) are typically found using 4C-sequencing and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). Currently, Hi-C is used to identify chromatin loops between cancer risk-associated single-nucleotide polymorphisms (SNPs) found by genome-wide association studies (GWAS) and their target genes. Chromosomal conformations are responsible for altered gene regulation through several typical mechanisms and contribute to the biological behavior and malignancy of different tumors, particularly prostate cancer, breast cancer and hematologic neoplasms. Moreover, different subtypes may exhibit different 3D-chromosomal conformations. Thus, C-tech can be used to help diagnose cancer subtypes and alleviate cancer progression by destroying specific chromosomal conformations. Here, we review the fundamentals and improvements in chromosome conformation capture techniques and their clinical applications in cancer to provide insight for future research.
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Affiliation(s)
- Ruobing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China
| | - He Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, People's Republic of China.
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19
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Wang XQD, Dostie J. Reciprocal regulation of chromatin state and architecture by HOTAIRM1 contributes to temporal collinear HOXA gene activation. Nucleic Acids Res 2017; 45:1091-1104. [PMID: 28180285 PMCID: PMC5388432 DOI: 10.1093/nar/gkw966] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/05/2016] [Accepted: 10/22/2016] [Indexed: 12/19/2022] Open
Abstract
Thousands of long non-coding RNAs (lncRNAs) have been identified in mammals, many of which represent important regulators of gene expression. However, the mechanisms used by lncRNAs to control transcription remain largely uncharacterized. Here, we report on HOTAIRM1, a promising lncRNA biomarker in leukemia and solid tumors. We find that HOTAIRM1 contributes to three-dimensional chromatin organization changes required for the temporal collinear activation of HOXA genes. We show that distinct HOTAIRM1 variants preferentially associate with either UTX/MLL or PRC2 complexes to modulate the levels of activating and silencing marks at the bivalent domain. HOTAIRM1 contributes to physical dissociation of chromatin loops at the cluster proximal end, which delays recruitment of the histone demethylase UTX and transcription of central HOXA genes. Interestingly, we find overall proximal HOXA gene activation without chromatin conformation changes by HOTAIRM1 in a different cell type. Our results reveal a previously unappreciated relationship between chromatin structure, architecture and lncRNA function.
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Affiliation(s)
- Xue Q D Wang
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
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20
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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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21
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Denker A, de Laat W. The second decade of 3C technologies: detailed insights into nuclear organization. Genes Dev 2017; 30:1357-82. [PMID: 27340173 PMCID: PMC4926860 DOI: 10.1101/gad.281964.116] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The relevance of three-dimensional (3D) genome organization for transcriptional regulation and thereby for cellular fate at large is now widely accepted. Our understanding of the fascinating architecture underlying this function is based on microscopy studies as well as the chromosome conformation capture (3C) methods, which entered the stage at the beginning of the millennium. The first decade of 3C methods rendered unprecedented insights into genome topology. Here, we provide an update of developments and discoveries made over the more recent years. As we discuss, established and newly developed experimental and computational methods enabled identification of novel, functionally important chromosome structures. Regulatory and architectural chromatin loops throughout the genome are being cataloged and compared between cell types, revealing tissue invariant and developmentally dynamic loops. Architectural proteins shaping the genome were disclosed, and their mode of action is being uncovered. We explain how more detailed insights into the 3D genome increase our understanding of transcriptional regulation in development and misregulation in disease. Finally, to help researchers in choosing the approach best tailored for their specific research question, we explain the differences and commonalities between the various 3C-derived methods.
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Affiliation(s)
- Annette Denker
- Hubrecht Institute-Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) and University Medical Center Utrecht, 3584CT Utrecht, the Netherlands
| | - Wouter de Laat
- Hubrecht Institute-Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) and University Medical Center Utrecht, 3584CT Utrecht, the Netherlands
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22
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Belaghzal H, Dekker J, Gibcus JH. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods 2017; 123:56-65. [PMID: 28435001 DOI: 10.1016/j.ymeth.2017.04.004] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/13/2017] [Accepted: 04/10/2017] [Indexed: 10/19/2022] Open
Abstract
Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops.
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Affiliation(s)
- Houda Belaghzal
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA.
| | - Johan H Gibcus
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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23
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Frank-Bertoncelj M, Klein K, Gay S. Interplay between genetic and epigenetic mechanisms in rheumatoid arthritis. Epigenomics 2017; 9:493-504. [PMID: 28322583 DOI: 10.2217/epi-2016-0142] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genetic and environmental factors contribute to the risk for rheumatoid arthritis (RA), with epigenetics serving as a possible interface through which risk factors contribute to RA. High-throughput technologies for interrogating genome and epigenome, and the availability of genetic and epigenetic datasets across a diversity of cell types, enable the identification of candidate causal genetic variants for RA to study their function in core RA processes. To date, RA risk variants were studied in the immune cells but not joint resident cells, for example, synovial fibroblasts. Synovial fibroblasts from different joints are distinct, anatomically specialized cells, defined by joint-specific transcriptomes, epigenomes and phenotypes. Cell type-specific analysis of epigenetic changes, together with genetic fine mapping and interrogation of chromatin 3D interactions may identify new disease relevant pathways, potential therapeutic targets and biomarkers for RA progression or therapy response.
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Affiliation(s)
| | - Kerstin Klein
- Center of Experimental Rheumatology, University Hospital Zurich, Switzerland
| | - Steffen Gay
- Center of Experimental Rheumatology, University Hospital Zurich, Switzerland
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24
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Tu WJ, Hardy K, Sutton CR, McCuaig R, Li J, Dunn J, Tan A, Brezar V, Morris M, Denyer G, Lee SK, Turner SJ, Seddiki N, Smith C, Khanna R, Rao S. Priming of transcriptional memory responses via the chromatin accessibility landscape in T cells. Sci Rep 2017; 7:44825. [PMID: 28317936 PMCID: PMC5357947 DOI: 10.1038/srep44825] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
Memory T cells exhibit transcriptional memory and “remember” their previous pathogenic encounter to increase transcription on re-infection. However, how this transcriptional priming response is regulated is unknown. Here we performed global FAIRE-seq profiling of chromatin accessibility in a human T cell transcriptional memory model. Primary activation induced persistent accessibility changes, and secondary activation induced secondary-specific opening of previously less accessible regions associated with enhanced expression of memory-responsive genes. Increased accessibility occurred largely in distal regulatory regions and was associated with increased histone acetylation and relative H3.3 deposition. The enhanced re-stimulation response was linked to the strength of initial PKC-induced signalling, and PKC-sensitive increases in accessibility upon initial stimulation showed higher accessibility on re-stimulation. While accessibility maintenance was associated with ETS-1, accessibility at re-stimulation-specific regions was linked to NFAT, especially in combination with ETS-1, EGR, GATA, NFκB, and NR4A. Furthermore, NFATC1 was directly regulated by ETS-1 at an enhancer region. In contrast to the factors that increased accessibility, signalling from bHLH and ZEB family members enhanced decreased accessibility upon re-stimulation. Interplay between distal regulatory elements, accessibility, and the combined action of sequence-specific transcription factors allows transcriptional memory-responsive genes to “remember” their initial environmental encounter.
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Affiliation(s)
- Wen Juan Tu
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Kristine Hardy
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Christopher R Sutton
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Robert McCuaig
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Jasmine Li
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology &Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Jenny Dunn
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Abel Tan
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Vedran Brezar
- INSERM U955 Eq16 Faculte de medicine Henri Mondor and Universite Paris-Est, Creteil/Vaccine Research Institute, Creteil 94010, France
| | - Melanie Morris
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Gareth Denyer
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia
| | - Sau Kuen Lee
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology &Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Nabila Seddiki
- INSERM U955 Eq16 Faculte de medicine Henri Mondor and Universite Paris-Est, Creteil/Vaccine Research Institute, Creteil 94010, France
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rajiv Khanna
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sudha Rao
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
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25
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Abstract
Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects DNA replication, transcription and the repair of DNA damage. Thus, a thorough understanding of nuclear architecture is fundamental to the study of nuclear processes in eukaryotic cells. Recent years have seen rapid proliferation of technologies to investigate genome organization and function. Here, we review experimental and computational methodologies for 3D genome analysis, with special focus on recent advances in high-throughput chromatin conformation capture (3C) techniques and data analysis.
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Affiliation(s)
- Anthony D Schmitt
- Ludwig Institute for Cancer Research and the University of California, San Diego (UCSD) Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Ming Hu
- Department of Population Health, Division of Biostatistics, New York University School of Medicine, 650 First Avenue, Room 540, New York, New York 10016, USA
- Present address: Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genomic Medicine, University of California, San Diego (UCSD) School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
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26
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Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma 2016; 126:33-44. [DOI: 10.1007/s00412-016-0593-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 04/10/2016] [Accepted: 04/12/2016] [Indexed: 12/17/2022]
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27
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Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science 2016; 351:1454-1458. [PMID: 26940867 PMCID: PMC4884612 DOI: 10.1126/science.aad9024] [Citation(s) in RCA: 682] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/18/2016] [Indexed: 12/17/2022]
Abstract
Oncogenes are activated through well-known chromosomal alterations such as gene fusion, translocation, and focal amplification. In light of recent evidence that the control of key genes depends on chromosome structures called insulated neighborhoods, we investigated whether proto-oncogenes occur within these structures and whether oncogene activation can occur via disruption of insulated neighborhood boundaries in cancer cells. We mapped insulated neighborhoods in T cell acute lymphoblastic leukemia (T-ALL) and found that tumor cell genomes contain recurrent microdeletions that eliminate the boundary sites of insulated neighborhoods containing prominent T-ALL proto-oncogenes. Perturbation of such boundaries in nonmalignant cells was sufficient to activate proto-oncogenes. Mutations affecting chromosome neighborhood boundaries were found in many types of cancer. Thus, oncogene activation can occur via genetic alterations that disrupt insulated neighborhoods in malignant cells.
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Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Abraham S. Weintraub
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Daniel S. Day
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Anne-Laure Valton
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Rasmus O. Bak
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Charles H. Li
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Johanna Goldmann
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Bryan R. Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alla A. Sigova
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Jessica Reddy
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Diego Borges-Rivera
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew H. Porteus
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
- Howard Hughes Medical Institute
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Abstract
The role of genome architecture in transcription regulation has become the focus of an increasing number of studies over the past decade. Chromatin organization can have a significant impact on gene expression by promoting or restricting the physical proximity between regulatory DNA elements. Given that any change in chromatin state has the potential to alter DNA folding and the proximity between control elements, the spatial organization of chromatin is inherently linked to its molecular composition. In this review, we explore how modulators of chromatin state and organization might keep gene expression in check. We discuss recent findings and present some of the less well-studied aspects of spatial genome organization such as chromatin dynamics and regulation by non-coding RNAs.
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Smith EM, Lajoie BR, Jain G, Dekker J. Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus. Am J Hum Genet 2016; 98:185-201. [PMID: 26748519 PMCID: PMC4716690 DOI: 10.1016/j.ajhg.2015.12.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/03/2015] [Indexed: 11/29/2022] Open
Abstract
Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation.
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Affiliation(s)
- Emily M Smith
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA
| | - Gaurav Jain
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA; Howard Hughes Medical Institute.
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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33
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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34
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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35
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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Barutcu AR, Fritz AJ, Zaidi SK, vanWijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016; 231:31-5. [PMID: 26059817 PMCID: PMC4586368 DOI: 10.1002/jcp.25062] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022]
Abstract
Three-dimensional organization of the chromatin has important roles in transcription, replication, DNA repair, and pathologic events such as translocations. There are two fundamental ways to study higher-order chromatin organization: microscopic and molecular approaches. In this review, we briefly introduce the molecular approaches, focusing on chromosome conformation capture or "3C" technology and its derivatives, which can be used to probe chromatin folding at resolutions beyond that provided by microscopy techniques. We further discuss the different types of data generated by the 3C-based methods and how they can be used to answer distinct biological questions.
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Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Andrew J. Fritz
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Sayyed K. Zaidi
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - André J. vanWijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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Fraser J, Williamson I, Bickmore WA, Dostie J. An Overview of Genome Organization and How We Got There: from FISH to Hi-C. Microbiol Mol Biol Rev 2015; 79:347-72. [PMID: 26223848 PMCID: PMC4517094 DOI: 10.1128/mmbr.00006-15] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In humans, nearly two meters of genomic material must be folded to fit inside each micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA replication, and DNA repair. This fact highlights the need for mechanisms governing genome organization during any activity and to maintain the physical organization of chromosomes at all times. Insight into the functions and three-dimensional structures of genomes comes mostly from the application of visual techniques such as fluorescence in situ hybridization (FISH) and molecular approaches including chromosome conformation capture (3C) technologies. Recent developments in both types of approaches now offer the possibility of exploring the folded state of an entire genome and maybe even the identification of how complex molecular machines govern its shape. In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals.
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Affiliation(s)
- James Fraser
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Iain Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Josée Dostie
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
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Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, Dostie J. Classifying leukemia types with chromatin conformation data. Genome Biol 2014; 15:R60. [PMID: 24995990 PMCID: PMC4038739 DOI: 10.1186/gb-2014-15-4-r60] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/30/2014] [Indexed: 11/10/2022] Open
Abstract
Background Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. Results Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. Conclusions Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.
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Rousseau M, Crutchley JL, Miura H, Suderman M, Blanchette M, Dostie J. Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res 2014; 42:1524-40. [PMID: 24174538 PMCID: PMC3919592 DOI: 10.1093/nar/gkt998] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 08/28/2013] [Accepted: 10/02/2013] [Indexed: 12/26/2022] Open
Abstract
Three-dimensional genome organization is an important higher order transcription regulation mechanism that can be studied with the chromosome conformation capture techniques. Here, we combined chromatin organization analysis by chromosome conformation capture-carbon copy, computational modeling and epigenomics to achieve the first integrated view, through time, of a connection between chromatin state and its architecture. We used this approach to examine the chromatin dynamics of the HoxA cluster in a human myeloid leukemia cell line at various stages of differentiation. We found that cellular differentiation involves a transient activation of the 5'-end HoxA genes coinciding with a loss of contacts throughout the cluster, and by specific silencing at the 3'-end with H3K27 methylation. The 3D modeling of the data revealed an extensive reorganization of the cluster between the two previously reported topologically associated domains in differentiated cells. Our results support a model whereby silencing by polycomb group proteins and reconfiguration of CTCF interactions at a topologically associated domain boundary participate in changing the HoxA cluster topology, which compartmentalizes the genes following differentiation.
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Affiliation(s)
- Mathieu Rousseau
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Jennifer L. Crutchley
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Hisashi Miura
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Matthew Suderman
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Mathieu Blanchette
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
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Abstract
The GTC Cancer Summit: Novel Approaches to Drug Discovery was divided into two parallel tracks: the 2nd Cancer Epigenetics Conference, and the Protein Kinases and Drug Design Conference. The 2nd Cancer Epigenetics Conference focused on exciting changes in drug discovery that include an unprecedented private and public collaboration on drug discovery in epigenetics through the Structural Genomics Consortium (SGC), which has led to several major breakthroughs including: the development of small-molecule inhibitors that interfere with protein interactions, especially bromodomain-containing protein acetylation readers; the indirect but successful targeting of the elusive MYC oncogene; and the identification of epigenetic drugs that are disease-specific. Also reported were the development of clinically useful DNA methylation assays; cell, peptide and protein arrays for testing antibody- and protein-binding specificity; and tools for chromatin capture and DNA modification analysis. Several groups reported on the lack of specificity of some commercial, but unnamed, antibodies used for epigenetic studies.
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43
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Gavrilov AA, Golov AK, Razin SV. Actual ligation frequencies in the chromosome conformation capture procedure. PLoS One 2013; 8:e60403. [PMID: 23555968 PMCID: PMC3608588 DOI: 10.1371/journal.pone.0060403] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/25/2013] [Indexed: 11/19/2022] Open
Abstract
Chromosome conformation capture (3C) and derivative experimental procedures are used to estimate the spatial proximity between different genomic elements, thus providing information about the 3D organization of genomic domains and whole genomes within the nucleus. All C-methods are based on the proximity ligation-the preferential ligation of joined DNA fragments obtained upon restriction enzyme digestion of in vivo cross-linked chromatin. Here, using the mouse beta-globin genes in erythroid cells as a model, we estimated the actual frequencies of ligation between the fragments bearing the promoter of the major beta-globin gene and its distant enhancers and showed that the number of ligation products produced does not exceed 1% of all fragments subjected to the ligation. Although this low yield of 3C ligation products may be explained entirely by technical issues, it may as well reflect a low frequency of interaction between DNA regulatory elements in vivo.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia.
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