1
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Wang X, Liu Y, Mo Y, Tan N, Huang W, Feng Y, Jiang L. Editorial: Transcriptional and posttranscriptional homeostasis in inflammation and inflammatory diseases. Front Immunol 2024; 15:1391199. [PMID: 38510245 PMCID: PMC10951382 DOI: 10.3389/fimmu.2024.1391199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Affiliation(s)
- Xinyi Wang
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Guangzhou, China
| | - Yaoxin Liu
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Guangzhou, China
| | - Yuanxi Mo
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Guangzhou, China
| | - Ning Tan
- Department of Cardiology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Wei Huang
- Heart, Lung and Vascular Institute, Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH, United States
| | - Yuliang Feng
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Guangdong, China
| | - Lei Jiang
- Department of Cardiology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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2
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Šimková H, Câmara AS, Mascher M. Hi-C techniques: from genome assemblies to transcription regulation. Journal of Experimental Botany 2024:erae085. [PMID: 38430521 DOI: 10.1093/jxb/erae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Indexed: 03/04/2024]
Abstract
The invention of chromosome-conformation capture (3C) techniques, in particular the key method Hi-C providing genome-wide information about chromatin contacts, revolutionized the way we study the three-dimensional (3D) organization of the nuclear genome and how it impacts transcription, replication and DNA repair. Since the frequency of chromatin contacts between pairs of genomic segments predictably relates to the distance in the linear genome, the Hi-C information has also proved useful for scaffolding genomic sequences. Here, we review recent enhancements in experimental procedures of Hi-C and its various derivatives such as Micro-C, HiChIP, and Capture Hi-C. We assess advantages and limitations of the techniques, and present examples of their use in recent plant studies. We also report on progress in computational tools used in assembling genome sequences.
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Affiliation(s)
- Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Slechtitelu 31, CZ-779 00 Olomouc, Czech Republic
| | - Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, D-06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, D-06466 Seeland, Germany
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3
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Della Chiara G, Jiménez C, Virdi M, Crosetto N, Bienko M. Enhancers dysfunction in the 3D genome of cancer cells. Front Cell Dev Biol 2023; 11:1303862. [PMID: 38020908 PMCID: PMC10657884 DOI: 10.3389/fcell.2023.1303862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Eukaryotic genomes are spatially organized inside the cell nucleus, forming a threedimensional (3D) architecture that allows for spatial separation of nuclear processes and for controlled expression of genes required for cell identity specification and tissue homeostasis. Hence, it is of no surprise that mis-regulation of genome architecture through rearrangements of the linear genome sequence or epigenetic perturbations are often linked to aberrant gene expression programs in tumor cells. Increasing research efforts have shed light into the causes and consequences of alterations of 3D genome organization. In this review, we summarize the current knowledge on how 3D genome architecture is dysregulated in cancer, with a focus on enhancer highjacking events and their contribution to tumorigenesis. Studying the functional effects of genome architecture perturbations on gene expression in cancer offers a unique opportunity for a deeper understanding of tumor biology and sets the basis for the discovery of novel therapeutic targets.
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Affiliation(s)
| | | | | | - Nicola Crosetto
- Human Technopole, Milan, Italy
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Magda Bienko
- Human Technopole, Milan, Italy
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- Science for Life Laboratory, Solna, Sweden
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4
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Tortora MMC, Brennan LD, Karpen G, Jost D. HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation. Proc Natl Acad Sci U S A 2023; 120:e2211855120. [PMID: 37549295 PMCID: PMC10438847 DOI: 10.1073/pnas.2211855120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 06/28/2023] [Indexed: 08/09/2023] Open
Abstract
The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid-liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1-chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.
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Affiliation(s)
- Maxime M. C. Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
| | - Lucy D. Brennan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Gary Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of BioEngineering and BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
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5
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Guo Y, Luo L, Zhu J, Li C. Multi-Omics Research Strategies for Psoriasis and Atopic Dermatitis. Int J Mol Sci 2023; 24:ijms24098018. [PMID: 37175722 PMCID: PMC10178671 DOI: 10.3390/ijms24098018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/08/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Psoriasis and atopic dermatitis (AD) are multifactorial and heterogeneous inflammatory skin diseases, while years of research have yielded no cure, and the costs associated with caring for people suffering from psoriasis and AD are a huge burden on society. Integrating several omics datasets will enable coordinate-based simultaneous analysis of hundreds of genes, RNAs, chromatins, proteins, and metabolites in particular cells, revealing networks of links between various molecular levels. In this review, we discuss the latest developments in the fields of genomes, transcriptomics, proteomics, and metabolomics and discuss how they were used to identify biomarkers and understand the main pathogenic mechanisms underlying these diseases. Finally, we outline strategies for achieving multi-omics integration and how integrative omics and systems biology can advance our knowledge of, and ability to treat, psoriasis and AD.
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Affiliation(s)
- Youming Guo
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Lingling Luo
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Jing Zhu
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
| | - Chengrang Li
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China
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6
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Wang SZ, Jiang F, Zhu DL, Yang TL, Guo Y. Application of Hi-C technology in three-dimensional genomics research and disease pathogenesis analysis. Yi Chuan 2023; 45:279-294. [PMID: 37077163 DOI: 10.16288/j.yczz.22-390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
3D genomics aims to investigate the spatial structure of chromatin in the nucleus on the basis of genomic sequences, gene structures and relevant regulatory elements. The spatial organization of chromosomes is fundamental for gene expression regulation. Recent advances of high-throughput chromosome conformation capture (Hi-C) technology and its derivatives, has enabled capture of chromatin architecture with high resolution. In this review, we summarize the development and applications of various technologies of 3D genomes in disease research, particularly in the elucidation of pathogenic mechanisms in cancers and other systemic disorders.
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Affiliation(s)
- Shun-Ze Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
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7
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Chen M, Liu X, Liu Q, Shi D, Li H. 3D genomics and its applications in precision medicine. Cell Mol Biol Lett 2023; 28:19. [PMID: 36879202 PMCID: PMC9987123 DOI: 10.1186/s11658-023-00428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
Three-dimensional (3D) genomics is an emerging discipline that studies the three-dimensional structure of chromatin and the three-dimensional and functions of genomes. It mainly studies the three-dimensional conformation and functional regulation of intranuclear genomes, such as DNA replication, DNA recombination, genome folding, gene expression regulation, transcription factor regulation mechanism, and the maintenance of three-dimensional conformation of genomes. Self-chromosomal conformation capture (3C) technology has been developed, and 3D genomics and related fields have developed rapidly. In addition, chromatin interaction analysis techniques developed by 3C technologies, such as paired-end tag sequencing (ChIA-PET) and whole-genome chromosome conformation capture (Hi-C), enable scientists to further study the relationship between chromatin conformation and gene regulation in different species. Thus, the spatial conformation of plant, animal, and microbial genomes, transcriptional regulation mechanisms, interaction patterns of chromosomes, and the formation mechanism of spatiotemporal specificity of genomes are revealed. With the help of new experimental technologies, the identification of key genes and signal pathways related to life activities and diseases is sustaining the rapid development of life science, agriculture, and medicine. In this paper, the concept and development of 3D genomics and its application in agricultural science, life science, and medicine are introduced, which provides a theoretical basis for the study of biological life processes.
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Affiliation(s)
- Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China
| | - Xingyu Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.,Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.
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8
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Ouyang W, Li X. Mapping Active Gene-Associated Chromatin Loops by ChIA-PET in Rice. Methods Mol Biol 2023; 2698:183-194. [PMID: 37682476 DOI: 10.1007/978-1-0716-3354-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Hierarchical chromatin structures are critical for transcriptional regulation and many biological processes. It has been widely known that the linear genome of many plants and animals is partitioned into various chromatin interacting domains or gene regulatory modules with specific chromatin features, such as H3K4me3-related active interacting domains, H3K27me3 or Polycomb-related repressive domains, and H3K9me2-related heterochromatin domains. ChIA-PET, which combines chromatin immunoprecipitation (ChIP) assay with proximity ligation, can detect gene contact networks that are connected by co-regulated genes by pulling down specific chromatin complexes using an antibody of interest. Here, we describe a detailed, long-read ChIA-PET protocol for mapping promoter-centered active gene modules in plants.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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9
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Sengupta K, Denkiewicz M, Chiliński M, Szczepińska T, Mollah AF, Korsak S, D'Souza R, Ruan Y, Plewczynski D. Multi-scale phase separation by explosive percolation with single-chromatin loop resolution. Comput Struct Biotechnol J 2022; 20:3591-3603. [PMID: 35860407 PMCID: PMC9283880 DOI: 10.1016/j.csbj.2022.06.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 12/03/2022] Open
Abstract
The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical human genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis of chromatin features. We also include dynamics of loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds in 3D space into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that at least 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our in-silico model integrates the high-throughput 3D genome interaction experimental data with the novel theoretical concept of phase separation, which allows us to model event-based time dynamics of chromatin loop formation and folding trajectories.
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Affiliation(s)
- Kaustav Sengupta
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Michał Denkiewicz
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Mateusz Chiliński
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Teresa Szczepińska
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Centre for Advanced Materials and Technologies, Warsaw University of Technology, Warsaw, Poland
| | - Ayatullah Faruk Mollah
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Department of Computer Science and Engineering, Aliah University, Kolkata, West Bengal, India
| | - Sevastianos Korsak
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Raissa D'Souza
- Department of Computer Science, University of California, Davis, USA
- The Santa Fe Institute, Santa Fe, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, USA
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Department of Computer Science, University of California, Davis, USA
- The Jackson Laboratory for Genomic Medicine, USA
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10
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Bouwman BAM, Crosetto N, Bienko M. The era of 3D and spatial genomics. Trends Genet 2022:S0168-9525(22)00118-4. [PMID: 35680466 DOI: 10.1016/j.tig.2022.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/28/2022]
Abstract
Over a decade ago the advent of high-throughput chromosome conformation capture (Hi-C) sparked a new era of 3D genomics. Since then the number of methods for mapping the 3D genome has flourished, enabling an ever-increasing understanding of how DNA is packaged in the nucleus and how the spatiotemporal organization of the genome orchestrates its vital functions. More recently, the next generation of spatial genomics technologies has begun to reveal how genome sequence and 3D genome organization vary between cells in their tissue context. We summarize how the toolkit for charting genome topology has evolved over the past decade and discuss how new technological developments are advancing the field of 3D and spatial genomics.
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11
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Orozco G, Schoenfelder S, Walker N, Eyre S, Fraser P. 3D genome organization links non-coding disease-associated variants to genes. Front Cell Dev Biol 2022; 10:995388. [PMID: 36340032 PMCID: PMC9631826 DOI: 10.3389/fcell.2022.995388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing has revealed over 300 million genetic variations in human populations. Over 90% of variants are single nucleotide polymorphisms (SNPs), the remainder include short deletions or insertions, and small numbers of structural variants. Hundreds of thousands of these variants have been associated with specific phenotypic traits and diseases through genome wide association studies which link significant differences in variant frequencies with specific phenotypes among large groups of individuals. Only 5% of disease-associated SNPs are located in gene coding sequences, with the potential to disrupt gene expression or alter of the function of encoded proteins. The remaining 95% of disease-associated SNPs are located in non-coding DNA sequences which make up 98% of the genome. The role of non-coding, disease-associated SNPs, many of which are located at considerable distances from any gene, was at first a mystery until the discovery that gene promoters regularly interact with distal regulatory elements to control gene expression. Disease-associated SNPs are enriched at the millions of gene regulatory elements that are dispersed throughout the non-coding sequences of the genome, suggesting they function as gene regulation variants. Assigning specific regulatory elements to the genes they control is not straightforward since they can be millions of base pairs apart. In this review we describe how understanding 3D genome organization can identify specific interactions between gene promoters and distal regulatory elements and how 3D genomics can link disease-associated SNPs to their target genes. Understanding which gene or genes contribute to a specific disease is the first step in designing rational therapeutic interventions.
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Affiliation(s)
- Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom.,NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, United Kingdom
| | - Stefan Schoenfelder
- Enhanc3D Genomics Ltd., Cambridge, United Kingdom.,Epigenetics Programme, The Babraham Institute, Babraham Research Campus, CB22 3AT Cambridge, Cambridge, United Kingdom
| | | | - Stephan Eyre
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom.,NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, United Kingdom
| | - Peter Fraser
- Enhanc3D Genomics Ltd., Cambridge, United Kingdom.,Department of Biological Science, Florida State University, Tallahassee, FL, United States
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12
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Cheng Y, Liu M, Hu M, Wang S. TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations. Genome Biol 2021; 22:309. [PMID: 34749781 PMCID: PMC8574027 DOI: 10.1186/s13059-021-02523-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing lead to the discovery of cohesin-independent TAD-like structures, also known as single-cell domains, which are highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains. RESULTS Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components and transcription mostly do not affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains. CONCLUSIONS In sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.
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Affiliation(s)
- Yubao Cheng
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
| | - Miao Liu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
| | - Mengwei Hu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06510 USA
- Molecular Cell Biology, Genetics and Development Program, Yale University, New Haven, CT 06510 USA
- Biochemistry, Quantitative Biology, Biophysics and Structural Biology Program, Yale University, New Haven, CT 06510 USA
- M.D.-Ph.D. Program, Yale University, New Haven, CT 06510 USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06510 USA
- Yale Liver Center, Yale University School of Medicine, New Haven, CT 06510 USA
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13
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Li Z, Yang H, Wang Y, Chou SH, He J. The spatial position effect: synthetic biology enters the era of 3D genomics. Trends Biotechnol 2021:S0167-7799(21)00196-7. [PMID: 34607694 DOI: 10.1016/j.tibtech.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022]
Abstract
Microbial cell factories are critical to achieving green biomanufacturing. A position effect occurs when a synthetic gene circuit is expressed from different positions in the chassis strain genome. Here, we propose the concept of the 'spatial position effect,' which uses technologies in 3D genomics to reveal the spatial structure characteristics of the 3D genome of the chassis. On this basis, we propose to rationally design the integration sites of synthetic gene circuits, use reporter genes for preliminary screening, and integrate synthetic gene circuits into promising sites for further experiments. This approach can produce stable and efficient chassis strains for green biomanufacturing. The proposed spatial position effect brings synthetic biology into the era of 3D genomics.
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14
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Himadewi P, Wang XQD, Feng F, Gore H, Liu Y, Yu L, Kurita R, Nakamura Y, Pfeifer GP, Liu J, Zhang X. 3'HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression. eLife 2021; 10:e70557. [PMID: 34585664 PMCID: PMC8500713 DOI: 10.7554/elife.70557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in the adult β-globin gene can lead to a variety of hemoglobinopathies, including sickle cell disease and β-thalassemia. An increase in fetal hemoglobin expression throughout adulthood, a condition named hereditary persistence of fetal hemoglobin (HPFH), has been found to ameliorate hemoglobinopathies. Deletional HPFH occurs through the excision of a significant portion of the 3' end of the β-globin locus, including a CTCF binding site termed 3'HS1. Here, we show that the deletion of this CTCF site alone induces fetal hemoglobin expression in both adult CD34+ hematopoietic stem and progenitor cells and HUDEP-2 erythroid progenitor cells. This induction is driven by the ectopic access of a previously postulated distal enhancer located in the OR52A1 gene downstream of the locus, which can also be insulated by the inversion of the 3'HS1 CTCF site. This suggests that genetic editing of this binding site can have therapeutic implications to treat hemoglobinopathies.
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Affiliation(s)
- Pamela Himadewi
- Center for Epigenetics, Van Andel Research InstituteGrand RapidsUnited States
| | - Xue Qing David Wang
- Center for Epigenetics, Van Andel Research InstituteGrand RapidsUnited States
| | - Fan Feng
- Department of Computational Medicine and Bioinformatics, University of MichiganAnn ArborUnited States
| | - Haley Gore
- Center for Epigenetics, Van Andel Research InstituteGrand RapidsUnited States
| | - Yushuai Liu
- Center for Epigenetics, Van Andel Research InstituteGrand RapidsUnited States
| | - Lei Yu
- Cell and Development Biology, University of MichiganAnn ArborUnited States
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross SocietyTokyoJapan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research CenterTsukubaJapan
- Faculty of Medicine, University of TsukubaTsukubaJapan
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research InstituteGrand RapidsUnited States
| | - Jie Liu
- Department of Computational Medicine and Bioinformatics, University of MichiganAnn ArborUnited States
| | - Xiaotian Zhang
- Center for Epigenetics, Van Andel Research InstituteGrand RapidsUnited States
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15
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MacPhillamy C, Pitchford WS, Alinejad-Rokny H, Low WY. Opportunity to improve livestock traits using 3D genomics. Anim Genet 2021; 52:785-798. [PMID: 34494283 DOI: 10.1111/age.13135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 11/30/2022]
Abstract
The advent of high-throughput chromosome conformation capture and sequencing (Hi-C) has enabled researchers to probe the 3D architecture of the mammalian genome in a genome-wide manner. Simultaneously, advances in epigenomic assays, such as chromatin immunoprecipitation and sequencing (ChIP-seq) and DNase-seq, have enabled researchers to study cis-regulatory interactions and chromatin accessibility across the same genome-wide scale. The use of these data has revealed many unique insights into gene regulation and disease pathomechanisms in several model organisms. With the advent of these high-throughput sequencing technologies, there has been an ever-increasing number of datasets available for study; however, this is often limited to model organisms. Livestock species play critical roles in the economies of developing and developed nations alike. Despite this, they are greatly underrepresented in the 3D genomics space; Hi-C and related technologies have the potential to revolutionise livestock breeding by enabling a more comprehensive understanding of how production traits are controlled. The growth in human and model organism Hi-C data has seen a surge in the availability of computational tools for use in 3D genomics, with some tools using machine learning techniques to predict features and improve dataset quality. In this review, we provide an overview of the 3D genome and discuss the status of 3D genomics in livestock before delving into advancing the field by drawing inspiration from research in human and mouse. We end by offering future directions for livestock research in the field of 3D genomics.
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Affiliation(s)
- C MacPhillamy
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
| | - W S Pitchford
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
| | - H Alinejad-Rokny
- Biological & Medical Machine Learning Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Computer Science and Engineering, The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia
| | - W Y Low
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
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16
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Abstract
Hematopoiesis is a convenient model to study how chromatin dynamics plays a decisive role in regulation of cell fate. During erythropoiesis a population of stem and progenitor cells becomes increasingly lineage restricted, giving rise to terminally differentiated progeny. The concerted action of transcription factors and epigenetic modifiers leads to a silencing of the multipotent transcriptome and activation of the transcriptional program that controls terminal differentiation. This article reviews some aspects of the biology of red blood cells production with the focus on the extensive chromatin reorganization during differentiation.
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Affiliation(s)
- Anastasia Ryzhkova
- Institute of Cytology and Genetics SB RAS, Laboratory of Developmental Genetics, 630090 Novosibirsk, Russia;
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, Laboratory of Developmental Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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17
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Pei L, Li G, Lindsey K, Zhang X, Wang M. Plant 3D genomics: the exploration and application of chromatin organization. New Phytol 2021; 230:1772-1786. [PMID: 33560539 PMCID: PMC8252774 DOI: 10.1111/nph.17262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/01/2021] [Indexed: 05/29/2023]
Abstract
Eukaryotic genomes are highly folded for packing into higher-order chromatin structures in the nucleus. With the emergence of state-of-the-art chromosome conformation capture methods and microscopic imaging techniques, the spatial organization of chromatin and its functional implications have been interrogated. Our knowledge of 3D chromatin organization in plants has improved dramatically in the past few years, building on the early advances in animal systems. Here, we review recent advances in 3D genome mapping approaches, our understanding of the sophisticated organization of spatial structures, and the application of 3D genomic principles in plants. We also discuss directions for future developments in 3D genomics in plants.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Guoliang Li
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanHubei430070China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
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18
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Baroux C. Three-dimensional genome organization in epigenetic regulations: cause or consequence? Curr Opin Plant Biol 2021; 61:102031. [PMID: 33819713 DOI: 10.1016/j.pbi.2021.102031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
The evolution of the nucleus is an evolutionary milestone. By enabling genome compartmentalization, it contributes to the fine-tuning of genome functions. The genome is partitioned into functional domains differing in spatial positioning and topological folding at different scales. The rise of '3D Genomics' embracing experimental, theoretical, and modeling approaches allowed the proposal of a multiscale model of the eukaryotic genome, capturing its organizing principles and functionalities. In these efforts, resolving causality remains an important objective. Are positioning and folding the cause or consequence of functional states? This minireview presents emerging answers to this question, borrowing examples from recent studies of the three-dimensional genome in both plants and animals.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Switzerland.
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19
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Lu J, Wang X, Sun K, Lan X. Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data. Brief Bioinform 2021; 22:6278150. [PMID: 34013331 PMCID: PMC8574949 DOI: 10.1093/bib/bbab181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/13/2021] [Indexed: 01/02/2023] Open
Abstract
Hi-C is a genome-wide assay based on Chromosome Conformation Capture and high-throughput sequencing to decipher 3D chromatin organization in the nucleus. However, computational methods to detect functional interactions utilizing Hi-C data face challenges including the correction for various sources of biases and the identification of functional interactions with low counts of interacting fragments. We present Chrom-Lasso, a lasso linear regression model that removes complex biases assumption-free and identifies functional interacting loci with increased power by combining information of local reads distribution surrounding the area of interest. We showed that interacting regions identified by Chrom-Lasso are more enriched for 5C validated interactions and functional GWAS hits than that of GOTHiC and Fit-Hi-C. To further demonstrate the ability of Chrom-Lasso to detect interactions of functional importance, we performed time-series Hi-C and RNA-seq during T cell activation and exhaustion. We showed that the dynamic changes in gene expression and chromatin interactions identified by Chrom-Lasso were largely concordant with each other. Finally, we experimentally confirmed Chrom-Lasso’s finding that Erbb3 was co-regulated with distinct neighboring genes at different states during T cell activation. Our results highlight Chrom-Lasso’s utility in detecting weak functional interaction between cis-regulatory elements, such as promoters and enhancers.
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Affiliation(s)
- Jingzhe Lu
- School of Medicine, Tsinghua University, Beijing, China
| | - Xu Wang
- School of Medicine and the Tsinghua-Peking Center for Life science, Tsinghua University, Beijing, China
| | - Keyong Sun
- School of Medicine and the Tsinghua-Peking Center for Life science, Tsinghua University, Beijing, China
| | - Xun Lan
- School of Medicine and the Tsinghua-Peking Center for Life science, Tsinghua University, Beijing, China
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20
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Zhang X, Jeong M, Huang X, Wang XQ, Wang X, Zhou W, Shamim MS, Gore H, Himadewi P, Liu Y, Bochkov ID, Reyes J, Doty M, Huang YH, Jung H, Heikamp E, Aiden AP, Li W, Su J, Aiden EL, Goodell MA. Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity. Mol Cell 2020; 78:506-521.e6. [PMID: 32386543 DOI: 10.1016/j.molcel.2020.04.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/06/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022]
Abstract
Higher-order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we find that large (>7.3 kb) DNA methylation nadirs (termed "grand canyons") can form long loops connecting anchor loci that may be dozens of megabases (Mb) apart, as well as inter-chromosomal links. The interacting loci cover a total of ∼3.5 Mb of the human genome. The strongest interactions are associated with repressive marks made by the Polycomb complex and are diminished upon EZH2 inhibitor treatment. The data are suggestive of the formation of these loops by interactions between repressive elements in the loci, forming a genomic subcompartment, rather than by cohesion/CTCF-mediated extrusion. Interestingly, unlike previously characterized subcompartments, these interactions are present only in particular cell types, such as stem and progenitor cells. Our work reveals that H3K27me3-marked large DNA methylation grand canyons represent a set of very-long-range loops associated with cellular identity.
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Affiliation(s)
- Xiaotian Zhang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Mira Jeong
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Xingfan Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics & Department of Computer Science, Rice University, Houston, TX, USA
| | - Xue Qing Wang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Xinyu Wang
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Medical Student Training Program, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics & Department of Computer Science, Rice University, Houston, TX, USA
| | - Haley Gore
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Pamela Himadewi
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Yushuai Liu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Ivan D Bochkov
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jaime Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Madison Doty
- Molecular Genetic Technology Program, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yung-Hsin Huang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Developmental Biology Program, Baylor College of Medicine, Houston, TX, USA
| | - Haiyoung Jung
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea, USA
| | - Emily Heikamp
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Aviva Presser Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Developmental Biology Program, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Wei Li
- Department of Bioinformatics, Biological Chemistry, University of California, Irvine CA, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jianzhong Su
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics & Department of Computer Science, Rice University, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China.
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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21
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Zhang Y, Li G. Advances in technologies for 3D genomics research. Sci China Life Sci 2020; 63:811-24. [PMID: 32394244 DOI: 10.1007/s11427-019-1704-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023]
Abstract
The spatial structure of the orderly organized chromatin in the nucleus has important roles in maintaining normal cell function and in regulation of gene expression, and the high-throughput Hi-C and ChIA-PET methods have been widely used in various biological studies for determining potential spatial genome structures and their functions. However, there are still great difficulties and challenges in three-dimensional (3D) genomics research. More efficient, economical, and unbiased approaches to studying 3D genomics need to be developed for more widespread and easier applications. Here, we review the most recent studies on new 3D genomics research technologies, such as improvements of the traditional Hi-C and ChIA-PET methods, new approaches based on non-proximal-ligation strategies, and imaging-based methods improved in recent years. Especially, we review the CRISPR-based methods for functional validations in 3D genomics, which could be the forthcoming directions. We hope this review can show some insights into the potential improvements for future 3D genomics.
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22
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Hong P, Jiang H, Xu W, Lin D, Xu Q, Cao G, Li G. The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis. Genes (Basel) 2020; 11:E289. [PMID: 32164155 DOI: 10.3390/genes11030289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/25/2020] [Accepted: 03/07/2020] [Indexed: 01/12/2023] Open
Abstract
It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.
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23
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Lyu HQ, Hao LL, Liu EH, Wu ZF, Han JQ, Liu Y. Current status and future perspectives in bioinformatical analysis of Hi-C data. Yi Chuan 2020; 42:87-99. [PMID: 31956099 DOI: 10.16288/j.yczz.19-163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The spatial interaction of chromosomes is regarded as an important issue affecting the regulation of gene expression, and the high-throughput chromosome conformation capture (Hi-C) technology has become the primary tool to explore the temporal and spatial interactions of chromosomes in three-dimensional genomics. With the continuous accumulation of Hi-C samples and the increasing complexity of pipelines, the bioinformatic analysis of Hi-C data has been considered an opportunity and a challenge for understanding the spatial regulation mechanism of gene expression. In this paper, the current status and development outline of bioinformatic methods for Hi-C data are introduced, including data normalization, multi-level structure analysis, data visualization and 3D modeling, especially of multi-level structure at A/B compartments, topological associated domains (TADs) and chromain looping levels. Based on this, we provide the outlook of future hotspots and trends in this area. Hopefully our insight will be beneficial for the exploration of gene expression regulation from the traditional linear model to the 3D mode.
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Affiliation(s)
- Hong Qiang Lyu
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Le le Hao
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Er Hu Liu
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhi Fang Wu
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jiu Qiang Han
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yuan Liu
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
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24
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Kim M, Zheng M, Tian SZ, Lee B, Chuang JH, Ruan Y. MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms. Genome Biol 2019; 20:251. [PMID: 31767038 PMCID: PMC6876102 DOI: 10.1186/s13059-019-1868-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022] Open
Abstract
The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chromatin organization, yet introduce new computational challenges. Thus, we developed MIA-Sig, an algorithmic solution based on signal processing and information theory. We demonstrate its ability to de-noise the multiplex data, assess the statistical significance of chromatin complexes, and identify topological domains and frequent inter-domain contacts. On chromatin immunoprecipitation (ChIP)-enriched data, MIA-Sig can clearly distinguish the protein-associated interactions from the non-specific topological domains. Together, MIA-Sig represents a novel algorithmic framework for multiplex chromatin interaction analysis.
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Affiliation(s)
- Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Meizhen Zheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA.
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25
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Zhang Y, Ruan Y, Li G. The 5th International 3D Genomics Workshop 2018: conference report. Epigenomics 2019; 11:1353-1357. [PMID: 31571508 DOI: 10.2217/epi-2019-0185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The International 3D Genomics Workshop is an annual international scientific conference focused on the research of the 3D structure of the genome in the nucleus. The 5th International 3D Genomics Workshop 2018 was held at the International Academic Center of Huazhong Agricultural University on the 13th-14th of October 2018. It attracted >150 international and local participants, including leading researchers in the field of the 3D genomics and editors from top journals. The main topic of the conference was the research achievements newly published or unpublished on the 3D genome area. The invited speakers shared their works on the topic of the new detection technologies on the 3D genome, the advanced computational analysis algorithms or suites, the nucleus microimaging technique, the simulation modeling method, the application on the biological research in different species (human, animals, plants, microorganisms, etc.) and the applications of 3D genome on medicine and agriculture. The workshop provided a forum to discuss the latest scientific news and ideas from the field of 3D genome research on various aspects of interesting topics.
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Affiliation(s)
- Yan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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26
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Huang J, Jiang Y, Zheng H, Ji X. BAT Hi-C maps global chromatin interactions in an efficient and economical way. Methods 2019; 170:38-47. [PMID: 31442560 DOI: 10.1016/j.ymeth.2019.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/15/2019] [Indexed: 11/18/2022] Open
Abstract
Chromosome Conformation Capture (3C)-based technologies, such as Hi-C, have represented a significant breakthrough in investigating the structure and function of higher-order genome architecture. However, the mapping of global chromatin interactions remains challenging across many biological conditions due to high background noise and financial constraints, especially for small laboratories. Here, we describe the Bridge linker-Alul-Tn5 Hi-C (BAT Hi-C) method, which is a simple and efficient method for delineating chromatin conformational features of mouse embryonic stem (mES) cells and uncover DNA loops. This protocol combines Alul fragmentation and biotinylated linker-mediated proximity ligation to obtain kilobase (kb) resolution with a marked increase in the amount of unique read pairs. The protocol also includes chromatin isolation to reduce background noise and Tn5 tagmentation to cut down on preparation time. Importantly, with only one-third sequencing depth, our method revealed the same spectrum of chromatin contacts as in situ Hi-C. BAT Hi-C is an economical (i.e., approximately $40 for library preparation) and straightforward (total hands-on time of 3 days) tool that is ideal for the in-depth analysis of long-range chromatin looping events in a genome-wide fashion.
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Affiliation(s)
- Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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27
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Abstract
Hi-C is a commonly used technology in 3D genomics which can depict global chromatin interactions across eukaryotic genome. Integrating with different datasets, it can also be applied to studying various biological questions, such as nuclear organization, gene transcription regulation, spatiotemporal development, genome assembly, and cancer genomics. During the last decade, the development and application of Hi-C have dramatically changed the view of genome architecture, chromatin conformation, and gene interaction. So far, Hi-C-related studies remain vivacious and controversial; thus, a unified standard of library construction and bioinformatics analysis are urgently needed. In this review, we have summarized its history, development, methodologies, advances, applications, shortages, and future perspectives. We discuss a few limitations of the current Hi-C technologies and future directions for improvement and highlight how Hi-C can bridge 3D structure to gene function. This review will be helpful for scientists who want to engage in the 3D genomics field; it also shows some future tracks.
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Affiliation(s)
- Siyuan Kong
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng District, 518120, Shenzhen, People's Republic of China
| | - Yubo Zhang
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng District, 518120, Shenzhen, People's Republic of China.
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Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst 2018; 6:256-258.e1. [PMID: 29428417 PMCID: PMC6047755 DOI: 10.1016/j.cels.2018.01.001] [Citation(s) in RCA: 201] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/22/2017] [Accepted: 12/30/2017] [Indexed: 11/22/2022]
Abstract
Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute. The web app also makes it possible to create interactive figures online that can complement or replace ordinary journal figures. When combined with Juicer, this makes the entire process of data analysis transparent, insofar as every step from raw reads to published figure is publicly available as open source code.
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Affiliation(s)
- James T Robinson
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Douglass Turner
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The 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 77030, USA; Department of Computer Science, Rice University, Houston, TX 77030, USA
| | | | - Jill P Mesirov
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92037, USA
| | - Erez Lieberman Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The 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 77030, USA; Department of Computer Science, Rice University, Houston, TX 77030, USA.
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