1
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Gridina MM, Stepanchuk YK, Nurridinov MA, Lagunov TA, Torgunakov NY, Shadsky AA, Ryabova AI, Vasiliev NV, Vtorushin SV, Gerashchenko TS, Denisov EV, Travin MA, Korolev MA, Fishman VS. Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:637-652. [PMID: 38831501 DOI: 10.1134/s0006297924040047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 06/05/2024]
Abstract
Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development; it is also necessary for the choice of targeted therapy. The Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements, such as inversions and translocations. We propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. The developed protocol allows to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for the targeted therapy selection. The practical value of molecular genetic testing is its ability to influence the treatment strategies and to provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of the targeted therapies, which is a critical aspect of personalized medicine in oncology.
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Affiliation(s)
- Maria M Gridina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yana K Stepanchuk
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Miroslav A Nurridinov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Timofey A Lagunov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Nikita Yu Torgunakov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Artem A Shadsky
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Anastasia I Ryabova
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Nikolay V Vasiliev
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Sergey V Vtorushin
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
- Siberian State Medical University, Ministry of Health of Russia, Tomsk, 634050, Russia
| | - Tatyana S Gerashchenko
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Evgeny V Denisov
- Research Institute of Oncology, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - Mikhail A Travin
- Research Institute of Clinical and Experimental Lymphology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630117, Russia
| | - Maxim A Korolev
- Research Institute of Clinical and Experimental Lymphology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630117, Russia
| | - Veniamin S Fishman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
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2
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Chakraborty A, Wang JG, Ay F. dcHiC detects differential compartments across multiple Hi-C datasets. Nat Commun 2022; 13:6827. [PMID: 36369226 PMCID: PMC9652325 DOI: 10.1038/s41467-022-34626-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
The compartmental organization of mammalian genomes and its changes play important roles in distinct biological processes. Here, we introduce dcHiC, which utilizes a multivariate distance measure to identify significant changes in compartmentalization among multiple contact maps. Evaluating dcHiC on four collections of bulk and single-cell contact maps from in vitro mouse neural differentiation (n = 3), mouse hematopoiesis (n = 10), human LCLs (n = 20) and post-natal mouse brain development (n = 3 stages), we show its effectiveness and sensitivity in detecting biologically relevant changes, including those orthogonally validated. dcHiC reported regions with dynamically regulated genes associated with cell identity, along with correlated changes in chromatin states, subcompartments, replication timing and lamin association. With its efficient implementation, dcHiC enables high-resolution compartment analysis as well as standalone browser visualization, differential interaction identification and time-series clustering. dcHiC is an essential addition to the Hi-C analysis toolbox for the ever-growing number of bulk and single-cell contact maps. Available at: https://github.com/ay-lab/dcHiC .
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Affiliation(s)
- Abhijit Chakraborty
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.
| | - Jeffrey G Wang
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- The Bishop's School, La Jolla, CA, 92037, USA
- Harvard College, Cambridge, MA, 02138, USA
| | - Ferhat Ay
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
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3
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Yadav VK, Singh S, Yadav A, Agarwal N, Singh B, Jalmi SK, Yadav VK, Tiwari VK, Kumar V, Singh R, Sawant SV. Stress Conditions Modulate the Chromatin Interactions Network in Arabidopsis. Front Genet 2022; 12:799805. [PMID: 35069698 PMCID: PMC8766718 DOI: 10.3389/fgene.2021.799805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/15/2021] [Indexed: 11/26/2022] Open
Abstract
Stresses have been known to cause various responses like cellular physiology, gene regulation, and genome remodeling in the organism to cope and survive. Here, we assessed the impact of stress conditions on the chromatin-interactome network of Arabidopsis thaliana. We identified thousands of chromatin interactions in native as well as in salicylic acid treatment and high temperature conditions in a genome-wide fashion. Our analysis revealed the definite pattern of chromatin interactions and stress conditions could modulate the dynamics of chromatin interactions. We found the heterochromatic region of the genome actively involved in the chromatin interactions. We further observed that the establishment or loss of interactions in response to stress does not result in the global change in the expression profile of interacting genes; however, interacting regions (genes) containing motifs for known TFs showed either lower expression or no difference than non-interacting genes. The present study also revealed that interactions preferred among the same epigenetic state (ES) suggest interactions clustered the same ES together in the 3D space of the nucleus. Our analysis showed that stress conditions affect the dynamics of chromatin interactions among the chromatin loci and these interaction networks govern the folding principle of chromatin by bringing together similar epigenetic marks.
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Affiliation(s)
- Vikash Kumar Yadav
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Swadha Singh
- CSIR-National Botanical Research Institute, Lucknow, India.,School of Natural Sciences, University of California, Merced, Merced, CA, United States
| | - Amrita Yadav
- CSIR-National Botanical Research Institute, Lucknow, India
| | - Neha Agarwal
- CSIR-National Botanical Research Institute, Lucknow, India
| | - Babita Singh
- CSIR-National Botanical Research Institute, Lucknow, India
| | | | | | - Vipin Kumar Tiwari
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Verandra Kumar
- Department of Botany, Manyawar Kanshiram Government Degree College, Aligarh, India
| | | | - Samir Vishwanath Sawant
- CSIR-National Botanical Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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4
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Goel VY, Hansen AS. The macro and micro of chromosome conformation capture. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2021; 10:e395. [PMID: 32987449 PMCID: PMC8236208 DOI: 10.1002/wdev.395] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022]
Abstract
The 3D organization of the genome facilitates gene regulation, replication, and repair, making it a key feature of genomic function and one that remains to be properly understood. Over the past two decades, a variety of chromosome conformation capture (3C) methods have delineated genome folding from megabase-scale compartments and topologically associating domains (TADs) down to kilobase-scale enhancer-promoter interactions. Understanding the functional role of each layer of genome organization is a gateway to understanding cell state, development, and disease. Here, we discuss the evolution of 3C-based technologies for mapping 3D genome organization. We focus on genomics methods and provide a historical account of the development from 3C to Hi-C. We also discuss ChIP-based techniques that focus on 3D genome organization mediated by specific proteins, capture-based methods that focus on particular regions or regulatory elements, 3C-orthogonal methods that do not rely on restriction digestion and proximity ligation, and methods for mapping the DNA-RNA and RNA-RNA interactomes. We consider the biological discoveries that have come from these methods, examine the mechanistic contributions of CTCF, cohesin, and loop extrusion to genomic folding, and detail the 3D genome field's current understanding of nuclear architecture. Finally, we give special consideration to Micro-C as an emerging frontier in chromosome conformation capture and discuss recent Micro-C findings uncovering fine-scale chromatin organization in unprecedented detail. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics.
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Affiliation(s)
- Viraat Y. Goel
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Anders S. Hansen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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5
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Kundu S, Ray MD, Sharma A. Interplay between genome organization and epigenomic alterations of pericentromeric DNA in cancer. J Genet Genomics 2021; 48:184-197. [PMID: 33840602 DOI: 10.1016/j.jgg.2021.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/07/2021] [Accepted: 02/20/2021] [Indexed: 12/16/2022]
Abstract
In eukaryotic genome biology, the genomic organization inside the three-dimensional (3D) nucleus is highly complex, and whether this organization governs gene expression is poorly understood. Nuclear lamina (NL) is a filamentous meshwork of proteins present at the lining of inner nuclear membrane that serves as an anchoring platform for genome organization. Large chromatin domains termed as lamina-associated domains (LADs), play a major role in silencing genes at the nuclear periphery. The interaction of the NL and genome is dynamic and stochastic. Furthermore, many genes change their positions during developmental processes or under disease conditions such as cancer, to activate certain sorts of genes and/or silence others. Pericentromeric heterochromatin (PCH) is mostly in the silenced region within the genome, which localizes at the nuclear periphery. Studies show that several genes located at the PCH are aberrantly expressed in cancer. The interesting question is that despite being localized in the pericentromeric region, how these genes still manage to overcome pericentromeric repression. Although epigenetic mechanisms control the expression of the pericentromeric region, recent studies about genome organization and genome-nuclear lamina interaction have shed light on a new aspect of pericentromeric gene regulation through a complex and coordinated interplay between epigenomic remodeling and genomic organization in cancer.
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Affiliation(s)
- Subhadip Kundu
- Laboratory of Chromatin and Cancer Epigenetics, Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - M D Ray
- Department of Surgical Oncology, IRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ashok Sharma
- Laboratory of Chromatin and Cancer Epigenetics, Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India.
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6
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Gridina M, Mozheiko E, Valeev E, Nazarenko LP, Lopatkina ME, Markova ZG, Yablonskaya MI, Voinova VY, Shilova NV, Lebedev IN, Fishman V. A cookbook for DNase Hi-C. Epigenetics Chromatin 2021; 14:15. [PMID: 33743768 PMCID: PMC7981840 DOI: 10.1186/s13072-021-00389-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 03/08/2021] [Indexed: 12/23/2022] Open
Abstract
Background The Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation. Results In this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming. Conclusions We propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00389-5.
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Affiliation(s)
- Maria Gridina
- Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia
| | - Evgeniy Mozheiko
- Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia
| | - Emil Valeev
- Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia.,Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia
| | - Ludmila P Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Kooperativny Str, 5, Tomsk, Russia
| | - Maria E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Kooperativny Str, 5, Tomsk, Russia
| | - Zhanna G Markova
- Research Centre for Medical Genetics, Moskvorechie str., 1, Moscow, Russia
| | - Maria I Yablonskaya
- Clinical Research Institute of Pediatrics Named After Acad. Y.E. Veltischev, Moscow, Russia
| | - Viktoria Yu Voinova
- Clinical Research Institute of Pediatrics Named After Acad. Y.E. Veltischev, Moscow, Russia
| | - Nadezhda V Shilova
- Research Centre for Medical Genetics, Moskvorechie str., 1, Moscow, Russia
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Kooperativny Str, 5, Tomsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia. .,Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia.
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7
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Zhang Q, Xu Z, Lai Y. An Empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data. Stat Appl Genet Mol Biol 2021; 20:1-15. [PMID: 33544558 DOI: 10.1515/sagmb-2020-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 01/06/2021] [Indexed: 11/15/2022]
Abstract
Hi-C experiments have become very popular for studying the 3D genome structure in recent years. Identification of long-range chromosomal interaction, i.e., peak detection, is crucial for Hi-C data analysis. But it remains a challenging task due to the inherent high dimensionality, sparsity and the over-dispersion of the Hi-C count data matrix. We propose EBHiC, an empirical Bayes approach for peak detection from Hi-C data. The proposed framework provides flexible over-dispersion modeling by explicitly including the "true" interaction intensities as latent variables. To implement the proposed peak identification method (via the empirical Bayes test), we estimate the overall distributions of the observed counts semiparametrically using a Smoothed Expectation Maximization algorithm, and the empirical null based on the zero assumption. We conducted extensive simulations to validate and evaluate the performance of our proposed approach and applied it to real datasets. Our results suggest that EBHiC can identify better peaks in terms of accuracy, biological interpretability, and the consistency across biological replicates. The source code is available on Github (https://github.com/QiZhangStat/EBHiC).
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Affiliation(s)
- Qi Zhang
- Department of Mathematics and Statistics, University of New Hampshire, Durham, NH03824, USA
| | - Zheng Xu
- Department of Mathematics and Statistics, Wright State University, Dayton, OH45435, USA
| | - Yutong Lai
- ClinChoice, Fort Washington, PA19034, USA
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8
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Cameron CJF, Dostie J, Blanchette M. HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution. Genome Biol 2020; 21:11. [PMID: 31937349 PMCID: PMC6961295 DOI: 10.1186/s13059-019-1913-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 12/05/2019] [Indexed: 12/31/2022] Open
Abstract
Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C's resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces researchers to artificially reduce the resolution of Hi-C matrices at a loss of biological interpretability. We present the Hi-C Interaction Frequency Inference (HIFI) algorithms that accurately estimate restriction-fragment resolution Hi-C matrices by exploiting dependencies between neighboring fragments. Cross-validation experiments and comparisons to 5C data and known regulatory interactions demonstrate HIFI's superiority to existing approaches. In addition, HIFI's restriction-fragment resolution reveals a new role for active regulatory regions in structuring topologically associating domains.
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Affiliation(s)
- Christopher JF Cameron
- School of Computer Science, McGill University, Montreal, Canada
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Canada
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Canada
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9
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Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Methods 2020; 170:61-68. [PMID: 31536770 PMCID: PMC6949367 DOI: 10.1016/j.ymeth.2019.09.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/13/2019] [Indexed: 12/31/2022] Open
Abstract
The highly dynamic nature of chromosome conformation and three-dimensional (3D) genome organization leads to cell-to-cell variability in chromatin interactions within a cell population, even if the cells of the population appear to be functionally homogeneous. Hence, although Hi-C is a powerful tool for mapping 3D genome organization, this heterogeneity of chromosome higher order structure among individual cells limits the interpretive power of population based bulk Hi-C assays. Moreover, single-cell studies have the potential to enable the identification and characterization of rare cell populations or cell subtypes in a heterogeneous population. However, it may require surveying relatively large numbers of single cells to achieve statistically meaningful observations in single-cell studies. By applying combinatorial cellular indexing to chromosome conformation capture, we developed single-cell combinatorial indexed Hi-C (sci-Hi-C), a high throughput method that enables mapping chromatin interactomes in large number of single cells. We demonstrated the use of sci-Hi-C data to separate cells by karytoypic and cell-cycle state differences and to identify cellular variability in mammalian chromosomal conformation. Here, we provide a detailed description of method design and step-by-step working protocols for sci-Hi-C.
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Affiliation(s)
- Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, WA, United States.
| | - Xinxian Deng
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Christine M Disteche
- Department of Pathology, University of Washington, Seattle, WA, United States; Department of Medicine, University of Washington, Seattle, WA, United States
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, United States; Howard Hughes Medical Institute, Seattle, WA, United States.
| | - Zhijun Duan
- Division of Hematology, University of Washington School of Medicine, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States.
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10
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Kempfer R, Pombo A. Methods for mapping 3D chromosome architecture. Nat Rev Genet 2019; 21:207-226. [PMID: 31848476 DOI: 10.1038/s41576-019-0195-2] [Citation(s) in RCA: 281] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Determining how chromosomes are positioned and folded within the nucleus is critical to understanding the role of chromatin topology in gene regulation. Several methods are available for studying chromosome architecture, each with different strengths and limitations. Established imaging approaches and proximity ligation-based chromosome conformation capture (3C) techniques (such as DNA-FISH and Hi-C, respectively) have revealed the existence of chromosome territories, functional nuclear landmarks (such as splicing speckles and the nuclear lamina) and topologically associating domains. Improvements to these methods and the recent development of ligation-free approaches, including GAM, SPRITE and ChIA-Drop, are now helping to uncover new aspects of 3D genome topology that confirm the nucleus to be a complex, highly organized organelle.
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Affiliation(s)
- Rieke Kempfer
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
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11
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Corbett-Detig RB, Said I, Calzetta M, Genetti M, McBroome J, Maurer NW, Petrarca V, Della Torre A, Besansky NJ. Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing. Genetics 2019; 213:1495-1511. [PMID: 31666292 PMCID: PMC6893396 DOI: 10.1534/genetics.119.302385] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/21/2019] [Indexed: 11/18/2022] Open
Abstract
Chromosomal inversions are fundamental drivers of genome evolution. In the main Afrotropical malaria vector species, belonging to the Anopheles gambiae species complex, inversions play an important role in local adaptation and have a rich history of cytological study. Despite the importance and ubiquity of some chromosomal inversions across the species complex, inversion breakpoints are often challenging to map molecularly due to the presence of large repetitive regions. Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions. We demonstrate that this approach is robust and likely to be widely applicable for both identification and fine-mapping inversion breakpoints in species whose inversions have heretofore been challenging to characterize. We apply our method to interrogate the previously unknown inversion breakpoints of 2Rbc and 2Rd in An. coluzzii We found that inversion breakpoints occur in large repetitive regions, and, strikingly, among three inversions analyzed, two breakpoints appear to be reused in two separate inversions. These breakpoint-adjacent regions are strongly enriched for the presence of a 30 bp satellite repeat sequence. Because low frequency inversion breakpoints are not correlated with genomic regions containing this satellite, we suggest that interrupting this particular repeat may result in arrangements with higher relative fitness. Additionally, we use heterozygous individuals to quantitatively investigate the impacts of somatic pairing in the regions immediately surrounding inversion breakpoints. Finally, we discuss important considerations for possible applications of this approach for inversion breakpoint identification in a range of organisms.
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Affiliation(s)
- Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
- Genomics Institute, University of California Santa Cruz, California 95064
| | - Iskander Said
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Maria Calzetta
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Max Genetti
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Vincenzo Petrarca
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Nora J Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Indiana 46556
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12
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Mozheiko EA, Fishman VS. Detection of Point Mutations and Chromosomal Translocations Based on Massive Parallel Sequencing of Enriched 3C Libraries. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Li T, Jia L, Cao Y, Chen Q, Li C. OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks. Genome Biol 2018; 19:54. [PMID: 29690904 PMCID: PMC5926533 DOI: 10.1186/s13059-018-1430-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 03/30/2018] [Indexed: 01/26/2023] Open
Abstract
We develop a method called open chromatin enrichment and network Hi-C (OCEAN-C) for antibody-independent mapping of global open chromatin interactions. By integrating FAIRE-seq and Hi-C, OCEAN-C detects open chromatin interactions enriched by active cis-regulatory elements. We identify more than 10,000 hubs of open chromatin interactions (HOCIs) in human cells, which are mainly active promoters and enhancers bound by many DNA-binding proteins and form interaction networks crucial for gene transcription. In addition to identifying large-scale topological structures, including topologically associated domains and A/B compartments, OCEAN-C can detect HOCI-mediated chromatin interactions that are strongly associated with gene expression, super-enhancers, and broad H3K4me3 domains.
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Affiliation(s)
- Tingting Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China.,State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Lumeng Jia
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yong Cao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China. .,Center for Statistical Science; Center for Bioinformatics, Peking University, Beijing, 100871, China.
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