1
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Mishra A, Pandey VP. CRISPR/Cas system: A revolutionary tool for crop improvement. Biotechnol J 2024; 19:e2300298. [PMID: 38403466 DOI: 10.1002/biot.202300298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
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Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, India
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2
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Kk S, Persson F, Fritzsche J, Beech JP, Tegenfeldt JO, Westerlund F. Fluorescence Microscopy of Nanochannel-Confined DNA. Methods Mol Biol 2024; 2694:175-202. [PMID: 37824005 DOI: 10.1007/978-1-0716-3377-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.
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Affiliation(s)
- Sriram Kk
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Jason P Beech
- NanoLund and Department of Physics, Lund University, Lund, Sweden
| | | | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
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3
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Sauvagère S, Siatka C. CRISPR-Cas: 'The Multipurpose Molecular Tool' for Gene Therapy and Diagnosis. Genes (Basel) 2023; 14:1542. [PMID: 37628594 PMCID: PMC10454384 DOI: 10.3390/genes14081542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Since the discovery of the CRISPR-Cas engineering system in 2012, several approaches for using this innovative molecular tool in therapeutic strategies and even diagnosis have been investigated. The use of this tool requires a global approach to DNA damage processes and repair systems in cells. The diversity in the functions of various Cas proteins allows for the use of this technology in clinical applications and trials. Wide variants of Cas12 and Cas13 are exploited using the collateral effect in many diagnostic applications. Even though this tool is well known, its use still raises real-world ethical and regulatory questions.
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4
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Uppuluri L, Wang Y, Young E, Wong JS, Abid HZ, Xiao M. Multiplex structural variant detection by whole-genome mapping and nanopore sequencing. Sci Rep 2022; 12:6512. [PMID: 35444207 PMCID: PMC9021263 DOI: 10.1038/s41598-022-10483-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/08/2022] [Indexed: 11/26/2022] Open
Abstract
Identification of structural variants (SVs) breakpoints is important in studying mutations, mutagenic causes, and functional impacts. Next-generation sequencing and whole-genome optical mapping are extensively used in SV discovery and characterization. However, multiple platforms and computational approaches are needed for comprehensive analysis, making it resource-intensive and expensive. Here, we propose a strategy combining optical mapping and cas9-assisted targeted nanopore sequencing to analyze SVs. Optical mapping can economically and quickly detect SVs across a whole genome but does not provide sequence-level information or precisely resolve breakpoints. Furthermore, since only a subset of all SVs is known to affect biology, we attempted to type a subset of all SVs using targeted nanopore sequencing. Using our approach, we resolved the breakpoints of five deletions, five insertions, and an inversion, in a single experiment.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA.,Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, USA
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jessica S Wong
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA. .,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA.
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5
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Waghchoure AP, Reddy JP, Bhosale RS. Fluorescence based miniaturized microfluidic and nanofluidic systems for biomedical applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:217-243. [PMID: 35033286 DOI: 10.1016/bs.pmbts.2021.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Over the last two decades miniaturized microfluidic and nanofluidic systems with fluorescence setup emerged as a powerful technological platform for diverse biomedical applications. Bio-macromolecules such as nucleic acids and proteins are the core cellular components, their single molecule analysis allow us to understand biological processes, disease creation and progression, and development of novel treatment policies. Design and development of foolproof treatment methods requires rigorously analysis of nucleic acids and proteins such as length quantifications, sequence profiling, sequence mapping, analysis of conformational changes, analysis and recognition of epigenetic changes, and their interactions with other biomolecules. Miniaturized microfluidic and nanofluidic systems with fluorescence spectroscopy enable worldwide researchers to perform nucleic acids and proteins extractions and single molecule analysis from the trace amount of biological samples. In the present chapter we mostly highlighted over one decade applications of microfluidic and nanofluidic systems for single cell micro ribonucleic acid (miRNA) isolation and detection, deoxyribonucleic acid (DNA) mapping, DNA barcoding, identification of epigenetic mark on single DNA molecule, DNA-protein interactions study, protein sensing, protein sequencing, protein binding kinetics and many other applications. We also presented the recently reported microfluidic platform for the preparation of reproducible unisize aggregation induced emission (AIE) active nanomaterials and their biological applications.
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Affiliation(s)
| | - J Prakasha Reddy
- Department of Chemistry, Indrashil University, Rajpur, Mehsana, Gujarat, India.
| | - Rajesh S Bhosale
- Department of Chemistry, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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6
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Wong JS, Jadhav T, Young E, Wang Y, Xiao M. Characterization of full-length LINE-1 insertions in 154 genomes. Genomics 2021; 113:3804-3810. [PMID: 34534648 DOI: 10.1016/j.ygeno.2021.09.011] [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: 05/17/2021] [Revised: 08/18/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Long interspersed nuclear elements (LINEs) are retrotransposons that contribute to genetic variation in the human genome. LINE-1 elements in larger-scale studies are challenging to identify using sequencing technologies due to cost and scalability. We developed an approach using optical mapping for detection of full-length LINE-1 insertions and 10× sequencing for confirmation. We found 51 true positive full-length LINE-1 insertions, of which 4 are novel insertions, in NA12878. Repeating our analysis on a larger sample set representing 26 populations, we identified 329 full-length LINE-1 elements, of which 123 are novel. 24.8% of these 329 LINE-1 insertions were shared amongst all 5 superpopulations (AFR, AMR, EUR, EAS, SAS). The African superpopulation has a higher percentage of population-specific LINE-1 insertions than any other superpopulation. These data indicate that our approach can provide high-speed, cost-effective, and increased accuracy for LINE-1 detection. These data also provide an insight into variations of LINE-1 elements between different populations.
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Affiliation(s)
- Jessica S Wong
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Tanaya Jadhav
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Yilin Wang
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America; Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, United States of America.
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7
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Uppuluri L, Jadhav T, Wang Y, Xiao M. Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis. Anal Chem 2021; 93:9808-9816. [PMID: 34232611 PMCID: PMC9705121 DOI: 10.1021/acs.analchem.1c01373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Analysis of structural variations (SVs) is important to understand mutations underlying genetic disorders and pathogenic conditions. However, characterizing SVs using short-read, high-throughput sequencing technology is difficult. Although long-read sequencing technologies are being increasingly employed in characterizing SVs, their low throughput and high costs discourage widespread adoption. Sequence motif-based optical mapping in nanochannels is useful in whole-genome mapping and SV detection, but it is not possible to precisely locate the breakpoints or estimate the copy numbers. We present here a universal multicolor mapping strategy in nanochannels combining conventional sequence-motif labeling system with Cas9-mediated target-specific labeling of any 20-base sequences (20mers) to create custom labels and detect new features. The sequence motifs are labeled with green fluorophores and the 20mers are labeled with red fluorophores. Using this strategy, it is possible to not only detect the SVs but also utilize custom labels to interrogate the features not accessible to motif-labeling, locate breakpoints, and precisely estimate copy numbers of genomic repeats. We validated our approach by quantifying the D4Z4 copy numbers, a known biomarker for facioscapulohumeral muscular dystrophy (FSHD) and estimating the telomere length, a clinical biomarker for assessing disease risk factors in aging-related diseases and malignant cancers. We also demonstrate the application of our methodology in discovering transposable long non-interspersed Elements 1 (LINE-1) insertions across the whole genome.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Tanaya Jadhav
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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8
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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9
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Uppuluri L, Varapula D, Young E, Riethman H, Xiao M. Single-molecule telomere length characterization by optical mapping in nano-channel array: Perspective and review on telomere length measurement. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 82:103562. [PMID: 33310082 PMCID: PMC8500550 DOI: 10.1016/j.etap.2020.103562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 05/11/2023]
Abstract
In humans, the telomere consists of tandem 5'TTAGGG3' DNA repeats on both ends of all 46 chromosomes. Telomere shortening has been linked to aging and age-related diseases. Similarly, telomere length changes have been associated with chemical exposure, molecular-level DNA damage, and tumor development. Telomere elongation has been associated to tumor development, caused due to chemical exposure and molecular-level DNA damage. The methods used to study these effects mostly rely on average telomere length as a biomarker. The mechanisms regulating subtelomere-specific and haplotype-specific telomere lengths in humans remain understudied and poorly understood, primarily because of technical limitations in obtaining these data for all chromosomes. Recent studies have shown that it is the short telomeres that are crucial in preserving chromosome stability. The identity and frequency of specific critically short telomeres potentially is a useful biomarker for studying aging, age-related diseases, and cancer. Here, we will briefly review the role of telomere length, its measurement, and our recent single-molecule telomere length measurement assay. With this assay, one can measure individual telomere lengths as well as identify their physically linked subtelomeric DNA. This assay can also positively detect telomere loss, characterize novel subtelomeric variants, haplotypes, and previously uncharacterized recombined subtelomeres. We will also discuss its applications in aging cells and cancer cells, highlighting the utility of the single molecule telomere length assay.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Harold Riethman
- Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA, USA.
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA; Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, USA.
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10
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Abid HZ, Young E, McCaffrey J, Raseley K, Varapula D, Wang HY, Piazza D, Mell J, Xiao M. Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs. Nucleic Acids Res 2021; 49:e8. [PMID: 33231685 PMCID: PMC7826249 DOI: 10.1093/nar/gkaa1088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR-Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR-Cas9 DNA labeling. We first design a CRISPR-Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR-Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR-Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.
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MESH Headings
- Alleles
- Base Sequence
- Benzoxazoles/analysis
- CRISPR-Cas Systems
- Chromosome Mapping/methods
- Chromosomes, Bacterial/genetics
- Computer Simulation
- Conserved Sequence/genetics
- DNA-Directed RNA Polymerases
- Drug Resistance, Bacterial/genetics
- Fluorescent Dyes/analysis
- Gene Editing/methods
- Genome, Bacterial
- Genome, Human
- Haemophilus influenzae/drug effects
- Haemophilus influenzae/genetics
- Haplotypes/genetics
- Humans
- Lab-On-A-Chip Devices
- Nalidixic Acid/pharmacology
- Novobiocin/pharmacology
- Nucleotide Motifs/genetics
- Polymorphism, Single Nucleotide
- Quinolinium Compounds/analysis
- RNA, Guide, CRISPR-Cas Systems/chemical synthesis
- RNA, Guide, CRISPR-Cas Systems/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Staining and Labeling/methods
- Viral Proteins
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Affiliation(s)
- Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Hung-Yi Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Danielle Piazza
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
| | - Joshua Mell
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
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11
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Xing WQ, Ma SY, Liu YY, Xia QY. CRISPR/dCas9-mediated imaging of endogenous genomic loci in living Bombyx mori cells. INSECT SCIENCE 2020; 27:1360-1364. [PMID: 31476099 DOI: 10.1111/1744-7917.12722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/31/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Wei-Qing Xing
- Biological Science Research Center, Southwest University, Chongqing, China
| | - San-Yuan Ma
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Yuan-Yuan Liu
- Biological Science Research Center, Southwest University, Chongqing, China
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qing-You Xia
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
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12
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Bouwens A, Deen J, Vitale R, D’Huys L, Goyvaerts V, Descloux A, Borrenberghs D, Grussmayer K, Lukes T, Camacho R, Su J, Ruckebusch C, Lasser T, Van De Ville D, Hofkens J, Radenovic A, Frans Janssen KP. Identifying microbial species by single-molecule DNA optical mapping and resampling statistics. NAR Genom Bioinform 2020; 2:lqz007. [PMID: 33575560 PMCID: PMC7671359 DOI: 10.1093/nargab/lqz007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022] Open
Abstract
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.
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Affiliation(s)
- Arno Bouwens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jochem Deen
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Raffaele Vitale
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Laurens D’Huys
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Vince Goyvaerts
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Adrien Descloux
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Kristin Grussmayer
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Tomas Lukes
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rafael Camacho
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Jia Su
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cyril Ruckebusch
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Theo Lasser
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Dimitri Van De Ville
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department of Radiology and Medical Informatics, Université de Genève, 1205 Genève, Switzerland
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Aleksandra Radenovic
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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13
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Zrehen A, Huttner D, Meller A. On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA. ACS NANO 2019; 13:14388-14398. [PMID: 31756076 PMCID: PMC6933818 DOI: 10.1021/acsnano.9b07873] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/22/2019] [Indexed: 05/22/2023]
Abstract
Solid-state nanopore sensing of ultralong genomic DNA molecules has remained challenging, as the DNA must be controllably delivered by its leading end for efficient entry into the nanopore. Herein, we introduce a nanopore sensor device designed for electro-optical detection and sorting of ultralong (300+ kilobase pair) genomic DNA. The fluidic device, fabricated in-silicon and anodically bonded to glass, uses pressure-induced flow and an embedded pillar array for controllable DNA stretching and delivery. Extremely low concentrations (50 fM) and sample volumes (∼1 μL) of DNA can be processed. The low height profile of the device permits high numerical aperture, high magnification imaging of DNA molecules, which remain in focus over extended distances. We demonstrate selective DNA sorting based on sequence-specific nick translation labeling and imaging at high camera frame rates. Nanopores are fabricated directly in the assembled device by laser etching. We show that uncoiling and stretching of the ultralong DNA molecules permits efficient nanopore capture and threading, which is simultaneously and synchronously imaged and electrically measured. Furthermore, our technique provides key insights into the translocation behavior of ultralong DNA and promotes the development of all-in-one micro/nanofluidic platforms for nanopore sensing of biomolecules.
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Affiliation(s)
- Adam Zrehen
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Diana Huttner
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Amit Meller
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
- Russell
Berrie Nanotechnology Institute, Technion
− IIT, Haifa 32000, Israel
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14
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Müller V, Dvirnas A, Andersson J, Singh V, Kk S, Johansson P, Ebenstein Y, Ambjörnsson T, Westerlund F. Enzyme-free optical DNA mapping of the human genome using competitive binding. Nucleic Acids Res 2019; 47:e89. [PMID: 31165870 PMCID: PMC6735870 DOI: 10.1093/nar/gkz489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/22/2019] [Indexed: 01/24/2023] Open
Abstract
Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - John Andersson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kk
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Pegah Johansson
- Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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15
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Leung AKY, Liu MCJ, Li L, Lai YYY, Chu C, Kwok PY, Ho PL, Yip KY, Chan TF. OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps. Gigascience 2019; 8:giz079. [PMID: 31289833 PMCID: PMC6615982 DOI: 10.1093/gigascience/giz079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 01/13/2019] [Accepted: 06/16/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Optical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1 Mb) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples. FINDINGS We present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g., multiple haplotypes, copy number variations, and subtelomeric structures when applied to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains. CONCLUSIONS With the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools.
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Affiliation(s)
| | - Melissa Chun-Jiao Liu
- Carol Yu Center for Infection and Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Le Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yvonne Yuk-Yin Lai
- Cardiovascular Research Institute, University of California, San Francisco, CA 94153, USA
- Institute of Human Genetics, University of California, San Francisco, CA 94153, USA
| | - Catherine Chu
- Cardiovascular Research Institute, University of California, San Francisco, CA 94153, USA
- Institute of Human Genetics, University of California, San Francisco, CA 94153, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, CA 94153, USA
- Institute of Human Genetics, University of California, San Francisco, CA 94153, USA
| | - Pak-Leung Ho
- Carol Yu Center for Infection and Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
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16
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Nguyen K, Broucqsault N, Chaix C, Roche S, Robin JD, Vovan C, Gerard L, Mégarbané A, Urtizberea JA, Bellance R, Barnérias C, David A, Eymard B, Fradin M, Manel V, Sacconi S, Tiffreau V, Zagnoli F, Cuisset JM, Salort-Campana E, Attarian S, Bernard R, Lévy N, Magdinier F. Deciphering the complexity of the 4q and 10q subtelomeres by molecular combing in healthy individuals and patients with facioscapulohumeral dystrophy. J Med Genet 2019; 56:590-601. [PMID: 31010831 DOI: 10.1136/jmedgenet-2018-105949] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/28/2019] [Accepted: 03/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Subtelomeres are variable regions between telomeres and chromosomal-specific regions. One of the most studied pathologies linked to subtelomeric imbalance is facioscapulohumeral dystrophy (FSHD). In most cases, this disease involves shortening of an array of D4Z4 macrosatellite elements at the 4q35 locus. The disease also segregates with a specific A-type haplotype containing a degenerated polyadenylation signal distal to the last repeat followed by a repetitive array of β-satellite elements. This classification applies to most patients with FSHD. A subset of patients called FSHD2 escapes this definition and carries a mutation in the SMCHD1 gene. We also recently described patients carrying a complex rearrangement consisting of a cis-duplication of the distal 4q35 locus identified by molecular combing. METHODS Using this high-resolution technology, we further investigated the organisation of the 4q35 region linked to the disease and the 10q26 locus presenting with 98% of homology in controls and patients. RESULTS Our analyses reveal a broad variability in size of the different elements composing these loci highlighting the complexity of these subtelomeres and the difficulty for genomic assembly. Out of the 1029 DNA samples analysed in our centre in the last 7 years, we also identified 54 cases clinically diagnosed with FSHD carrying complex genotypes. This includes mosaic patients, patients with deletions of the proximal 4q region and 23 cases with an atypical chromosome 10 pattern, infrequently found in the control population and never reported before. CONCLUSION Overall, this work underlines the complexity of these loci challenging the diagnosis and genetic counselling for this disease.
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Affiliation(s)
- Karine Nguyen
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Natacha Broucqsault
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Charlene Chaix
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Stephane Roche
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Catherine Vovan
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Laurene Gerard
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | | | - Jon Andoni Urtizberea
- Pôle Soins de suite et réadaptation handicaps lourds et maladies rares neurologiques, Hôpital Marin, Assistance publique des hopitaux de Paris, Hendaye, France
| | - Remi Bellance
- Hopital Pierre Zobda-Quitman, Fort-de-France, France
| | - Christine Barnérias
- Service de Neurologie infantile, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.,Centre de Référence de Maladies Neuromusculaires Garches-Necker-Mondor-Hendaye (GNMH), Réseau National Français de la Filière Neuromusculaire (FILNEMUS), Paris, France
| | | | - Bruno Eymard
- Assistance Publique - Hopitaux de Paris, Paris, Île-de-France, France
| | - Melanie Fradin
- Service de Génétique Médicale, Centre De Référence Anomalies du Développement, CHU de Rennes, Rennes, France
| | - Véronique Manel
- Centre référent maladies neuromusculaires rares, Hospices Civils de Lyon, Hôpital Femme Mère Enfant, Bron, France
| | - Sabrina Sacconi
- Peripheral Nervous System, Muscle and ALS Department, Université Côte d'Azur, Nice, France.,Institute for Research on Cancer and Aging of Nice, Université Côte d'Azur, Faculty of Medicine, Nice, France
| | - Vincent Tiffreau
- Centre de Référence des Maladies Neuromusculaires, service de Médecine Physique et de Réadaptation, Centre hospitalier régionale de Lille, Lille, France
| | - Fabien Zagnoli
- Centre de Référence des Maladies Neuromusculaires, CHU Morvan, Brest, France
| | | | - Emmanuelle Salort-Campana
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France.,Centre de reference des maladies neuromusculaires, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France.,Centre de reference des maladies neuromusculaires, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Rafaëlle Bernard
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Nicolas Lévy
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Frederique Magdinier
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
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17
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Genome maps across 26 human populations reveal population-specific patterns of structural variation. Nat Commun 2019; 10:1025. [PMID: 30833565 PMCID: PMC6399254 DOI: 10.1038/s41467-019-08992-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/12/2019] [Indexed: 01/10/2023] Open
Abstract
Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome. Large structural variants (SV) are understudied in human genetics research because of the difficulty to detect them in the routinely generated short-read sequencing data. Here, the authors generate optical genome maps of 154 individuals from 26 populations that allow comprehensive examination of large SVs.
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18
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Basak R, Liu F, Qureshi S, Gupta N, Zhang C, de Vries R, van Kan JA, Dheen ST, van der Maarel JRC. Linearization and Labeling of Single-Stranded DNA for Optical Sequence Analysis. J Phys Chem Lett 2019; 10:316-321. [PMID: 30615463 DOI: 10.1021/acs.jpclett.8b03465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic profiling would benefit from linearization of ssDNA through the exposure of the unpaired bases to gene-targeting probes. This is compromised by ssDNA's high flexibility and tendency to form self-annealed structures. Here, we demonstrate that self-annealing can be avoided through controlled coating with a cationic-neutral diblock polypeptide copolymer. Coating does not preclude site-specific binding of fluorescence labeled oligonucleotides. Bottlebrush-coated ssDNA can be linearized by confinement inside a nanochannel or molecular combing. A stretch of 0.32 nm per nucleotide is achieved inside a channel with a cross-section of 100 nm and a 2-fold excess of polypeptide with respect to DNA charge. With combing, the complexes are stretched to a similar extent. Atomic force microscopy of dried complexes on silica revealed that the contour and persistence lengths are close to those of dsDNA in the B-form. Labeling is based on hybridization and not limited by restriction enzymes. Enzyme-free labeling offers new opportunities for the detection of specific sequences.
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Affiliation(s)
- Rajib Basak
- Department of Physics , National University of Singapore , Singapore 117542
| | - Fan Liu
- Department of Physics , National University of Singapore , Singapore 117542
| | - Sarfraz Qureshi
- Department of Physics , National University of Singapore , Singapore 117542
| | - Neelima Gupta
- Department of Anatomy , National University of Singapore , Singapore 117594
| | - Ce Zhang
- Institute of Photonics and Photon-Technology , Northwest University , Xi'an , China 710069
| | - Renko de Vries
- Laboratory of Physical Chemistry and Colloid Science , Wageningen University , 6708 Wageningen , The Netherlands
| | - Jeroen A van Kan
- Department of Physics , National University of Singapore , Singapore 117542
| | - S Thameem Dheen
- Department of Anatomy , National University of Singapore , Singapore 117594
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19
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Liu Q, Georgieva DC, Egli D, Wang K. NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data. BMC Genomics 2019; 20:78. [PMID: 30712508 PMCID: PMC6360650 DOI: 10.1186/s12864-018-5372-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Recent advances in single-molecule sequencing techniques, such as Nanopore sequencing, improved read length, increased sequencing throughput, and enabled direct detection of DNA modifications through the analysis of raw signals. These DNA modifications include naturally occurring modifications such as DNA methylations, as well as modifications that are introduced by DNA damage or through synthetic modifications to one of the four standard nucleotides. METHODS To improve the performance of detecting DNA modifications, especially synthetically introduced modifications, we developed a novel computational tool called NanoMod. NanoMod takes raw signal data on a pair of DNA samples with and without modified bases, extracts signal intensities, performs base error correction based on a reference sequence, and then identifies bases with modifications by comparing the distribution of raw signals between two samples, while taking into account of the effects of neighboring bases on modified bases ("neighborhood effects"). RESULTS We evaluated NanoMod on simulation data sets, based on different types of modifications and different magnitudes of neighborhood effects, and found that NanoMod outperformed other methods in identifying known modified bases. Additionally, we demonstrated superior performance of NanoMod on an E. coli data set with 5mC (5-methylcytosine) modifications. CONCLUSIONS In summary, NanoMod is a flexible tool to detect DNA modifications with single-base resolution from raw signals in Nanopore sequencing, and will facilitate large-scale functional genomics experiments that use modified nucleotides.
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Affiliation(s)
- Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Daniela C. Georgieva
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032 USA
| | - Dieter Egli
- Department of Pediatrics, Columbia University, New York, NY 10032 USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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20
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Bocklandt S, Hastie A, Cao H. Bionano Genome Mapping: High-Throughput, Ultra-Long Molecule Genome Analysis System for Precision Genome Assembly and Haploid-Resolved Structural Variation Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:97-118. [DOI: 10.1007/978-981-13-6037-4_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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21
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Raper AT, Stephenson AA, Suo Z. Sharpening the Scissors: Mechanistic Details of CRISPR/Cas9 Improve Functional Understanding and Inspire Future Research. J Am Chem Soc 2018; 140:11142-11152. [PMID: 30160947 DOI: 10.1021/jacs.8b05469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interest in CRISPR/Cas9 remains high level as new applications of the revolutionary gene-editing tool continue to emerge. While key structural and biochemical findings have illuminated major steps in the enzymatic mechanism of Cas9, several important details remain unidentified or poorly characterized that may contribute to known functional limitations. Here we describe the foundation of research that has led to a fundamental understanding of Cas9 and address mechanistic uncertainties that restrict continued development of this gene-editing platform, including specificity for the protospacer adjacent motif, propensity for off-target binding and cleavage, as well as interactions with cellular components during gene editing. Discussion of these topics and considerations should inspire future research to hone this remarkable technology and advance CRISPR/Cas9 to new heights.
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Affiliation(s)
- Austin T Raper
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Anthony A Stephenson
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Zucai Suo
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States.,The James Comprehensive Cancer Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Department of Biomedical Sciences , College of Medicine, Florida State University , Tallahassee , Florida 32306 , United States
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22
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Chen X, Kozhaya L, Tastan C, Placek L, Dogan M, Horne M, Abblett R, Karhan E, Vaeth M, Feske S, Unutmaz D. Functional Interrogation of Primary Human T Cells via CRISPR Genetic Editing. THE JOURNAL OF IMMUNOLOGY 2018; 201:1586-1598. [PMID: 30021769 DOI: 10.4049/jimmunol.1701616] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 06/28/2018] [Indexed: 12/21/2022]
Abstract
Developing precise and efficient gene editing approaches using CRISPR in primary human T cell subsets would provide an effective tool in decoding their functions. Toward this goal, we used lentiviral CRISPR/Cas9 systems to transduce primary human T cells to stably express the Cas9 gene and guide RNAs that targeted either coding or noncoding regions of genes of interest. We showed that multiple genes (CD4, CD45, CD95) could be simultaneously and stably deleted in naive, memory, effector, or regulatory T cell (Treg) subsets at very high efficiency. Additionally, nuclease-deficient Cas9, associated with a transcriptional activator or repressor, can downregulate or increase expression of genes in T cells. For example, expression of glycoprotein A repetitions predominant (GARP), a gene that is normally and exclusively expressed on activated Tregs, could be induced on non-Treg effector T cells by nuclease-deficient Cas9 fused to transcriptional activators. Further analysis determined that this approach could be used in mapping promoter sequences involved in gene transcription. Through this CRISPR/Cas9-mediated genetic editing we also demonstrated the feasibility of human T cell functional analysis in several examples: 1) CD95 deletion inhibited T cell apoptosis upon reactivation; 2) deletion of ORAI1, a Ca2+ release-activated channel, abolished Ca2+ influx and cytokine secretion, mimicking natural genetic mutations in immune-deficient patients; and 3) transcriptional activation of CD25 or CD127 expression enhanced cytokine signaling by IL-2 or IL-7, respectively. Taken together, application of the CRISPR toolbox to human T cell subsets has important implications for decoding the mechanisms of their functional outputs.
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Affiliation(s)
- Xin Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032.,Department of Immunology, University of Connecticut School of Medicine, Farmington, CT 06030; and
| | - Lina Kozhaya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
| | - Cihan Tastan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032.,Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Lindsey Placek
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
| | - Mikail Dogan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
| | - Meghan Horne
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
| | - Rebecca Abblett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032.,Department of Immunology, University of Connecticut School of Medicine, Farmington, CT 06030; and
| | - Ece Karhan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
| | - Martin Vaeth
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Stefan Feske
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Derya Unutmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032; .,Department of Immunology, University of Connecticut School of Medicine, Farmington, CT 06030; and
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23
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Baliou S, Adamaki M, Kyriakopoulos AM, Spandidos DA, Panayiotidis M, Christodoulou I, Zoumpourlis V. CRISPR therapeutic tools for complex genetic disorders and cancer (Review). Int J Oncol 2018; 53:443-468. [PMID: 29901119 PMCID: PMC6017271 DOI: 10.3892/ijo.2018.4434] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
One of the fundamental discoveries in the field of biology is the ability to modulate the genome and to monitor the functional outputs derived from genomic alterations. In order to unravel new therapeutic options, scientists had initially focused on inducing genetic alterations in primary cells, in established cancer cell lines and mouse models using either RNA interference or cDNA overexpression or various programmable nucleases [zinc finger nucleases (ZNF), transcription activator-like effector nucleases (TALEN)]. Even though a huge volume of data was produced, its use was neither cheap nor accurate. Therefore, the clustered regularly interspaced short palindromic repeats (CRISPR) system was evidenced to be the next step in genome engineering tools. CRISPR-associated protein 9 (Cas9)-mediated genetic perturbation is simple, precise and highly efficient, empowering researchers to apply this method to immortalized cancerous cell lines, primary cells derived from mouse and human origins, xenografts, induced pluripotent stem cells, organoid cultures, as well as the generation of genetically engineered animal models. In this review, we assess the development of the CRISPR system and its therapeutic applications to a wide range of complex diseases (particularly distinct tumors), aiming at personalized therapy. Special emphasis is given to organoids and CRISPR screens in the design of innovative therapeutic approaches. Overall, the CRISPR system is regarded as an eminent genome engineering tool in therapeutics. We envision a new era in cancer biology during which the CRISPR-based genome engineering toolbox will serve as the fundamental conduit between the bench and the bedside; nonetheless, certain obstacles need to be addressed, such as the eradication of side-effects, maximization of efficiency, the assurance of delivery and the elimination of immunogenicity.
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Affiliation(s)
- Stella Baliou
- National Hellenic Research Foundation, 11635 Athens, Greece
| | - Maria Adamaki
- National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion 71003, Greece
| | - Mihalis Panayiotidis
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, NE1 8ST, UK
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24
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Cui Y, Xu J, Cheng M, Liao X, Peng S. Review of CRISPR/Cas9 sgRNA Design Tools. Interdiscip Sci 2018; 10:455-465. [PMID: 29644494 DOI: 10.1007/s12539-018-0298-z] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/02/2018] [Accepted: 04/04/2018] [Indexed: 12/22/2022]
Abstract
The adaptive immunity system in bacteria and archaea, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associate (CRISPR/Cas), has been adapted as a powerful gene editing tool and got a broad application in genome research field due to its ease of use and cost-effectiveness. The performance of CRISPR/Cas relies on well-designed single-guide RNA (sgRNA), so a lot of bioinformatic tools have been developed to assist the design of highly active and specific sgRNA. These tools vary in design specifications, parameters, genomes and so on. To help researchers to choose their proper tools, we reviewed various sgRNA design tools, mainly focusing on their on-target efficiency prediction model and off-target detection algorithm.
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Affiliation(s)
- Yingbo Cui
- College of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Jiaming Xu
- College of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Minxia Cheng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Xiangke Liao
- College of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Shaoliang Peng
- College of Computer, National University of Defense Technology, Changsha, 410073, China.
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
- National Supercomputing Center in Changsha, Changsha, 410082, China.
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25
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Klompe SE, Sternberg SH. Harnessing "A Billion Years of Experimentation": The Ongoing Exploration and Exploitation of CRISPR-Cas Immune Systems. CRISPR J 2018; 1:141-158. [PMID: 31021200 PMCID: PMC6636882 DOI: 10.1089/crispr.2018.0012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The famed physicist-turned-biologist, Max Delbrück, once remarked that, for physicists, "the field of bacterial viruses is a fine playground for serious children who ask ambitious questions." Early discoveries in that playground helped establish molecular genetics, and half a century later, biologists delving into the same field have ushered in the era of precision genome engineering. The focus has of course shifted-from bacterial viruses and their mechanisms of infection to the bacterial hosts and their mechanisms of immunity-but it is the very same evolutionary arms race that continues to awe and inspire researchers worldwide. In this review, we explore the remarkable diversity of CRISPR-Cas adaptive immune systems, describe the molecular components that mediate nucleic acid targeting, and outline the use of these RNA-guided machines for biotechnology applications. CRISPR-Cas research has yielded far more than just Cas9-based genome-editing tools, and the wide-reaching, innovative impacts of this fascinating biological playground are sure to be felt for years to come.
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Affiliation(s)
- Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
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26
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Abstract
The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard “foreign” contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.
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27
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Abstract
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.
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28
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Mikheikin A, Olsen A, Leslie K, Russell-Pavier F, Yacoot A, Picco L, Payton O, Toor A, Chesney A, Gimzewski JK, Mishra B, Reed J. DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle. Nat Commun 2017; 8:1665. [PMID: 29162844 PMCID: PMC5698298 DOI: 10.1038/s41467-017-01891-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/24/2017] [Indexed: 01/26/2023] Open
Abstract
Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new “nanomapping” method to detect and map precisely BCL2–IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM “nanomapping” technique can be complementary to both sequencing and other physical mapping approaches. Physical mapping of DNA can be used to detect structural variants and for whole-genome haplotype assembly. Here, the authors use CRISPR-Cas9 and high-speed atomic force microscopy to ‘nanomap’ single molecules of DNA.
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Affiliation(s)
- Andrey Mikheikin
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Anita Olsen
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Kevin Leslie
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Freddie Russell-Pavier
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK.,Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Andrew Yacoot
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK
| | - Loren Picco
- Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Oliver Payton
- Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Amir Toor
- Department of Internal Medicine, VCU School of Medicine, Richmond, 23284, VA, USA.,VCU Massey Cancer Center, Richmond, 23284, VA, USA
| | - Alden Chesney
- VCU Massey Cancer Center, Richmond, 23284, VA, USA.,Department of Pathology, VCU School of Medicine, Richmond, 23284, VA, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, 90095, CA, USA
| | - Bud Mishra
- Departments of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, 10012, NY, USA
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA. .,VCU Massey Cancer Center, Richmond, 23284, VA, USA.
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29
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McCaffrey J, Young E, Lassahn K, Sibert J, Pastor S, Riethman H, Xiao M. High-throughput single-molecule telomere characterization. Genome Res 2017; 27:1904-1915. [PMID: 29025896 PMCID: PMC5668947 DOI: 10.1101/gr.222422.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/11/2017] [Indexed: 12/21/2022]
Abstract
We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7-bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG)n tract length at the end of each large telomere-terminal DNA segment. The methodology also permits subtelomere and haplotype-resolved analyses of SRE organization and variation, providing a window into the population dynamics and potential functions of these complex and structurally variant telomere-adjacent DNA regions. At its current stage of development, the assay can be used to identify and characterize telomere length distributions of 30–35 discrete telomeres simultaneously and accurately. The assay's utility is demonstrated using early versus late passage and senescent human diploid fibroblasts, documenting the anticipated telomere attrition on a global telomere-by-telomere basis as well as identifying subtelomere-specific biases for critically short telomeres. Similarly, we present the first global single-telomere-resolved analyses of two cancer cell lines.
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Affiliation(s)
- Jennifer McCaffrey
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - Katy Lassahn
- Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Justin Sibert
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - Steven Pastor
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - Harold Riethman
- Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA.,Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, Pennsylvania 19129, USA
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30
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Chen K, Juhasz M, Gularek F, Weinhold E, Tian Y, Keyser UF, Bell NAW. Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores. NANO LETTERS 2017; 17:5199-5205. [PMID: 28829136 PMCID: PMC5599873 DOI: 10.1021/acs.nanolett.7b01009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5'-TCGA-3' sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Matyas Juhasz
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Felix Gularek
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Yu Tian
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail:
| | - Nicholas A. W. Bell
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail: . Fax: +44 (0)1223 337000
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31
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Young E, Pastor S, Rajagopalan R, McCaffrey J, Sibert J, Mak ACY, Kwok PY, Riethman H, Xiao M. High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres. Nucleic Acids Res 2017; 45:e73. [PMID: 28180280 PMCID: PMC5605236 DOI: 10.1093/nar/gkx017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 02/07/2017] [Indexed: 01/22/2023] Open
Abstract
Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG)n repeat tracts. We establish detailed maps for subtelomere gap regions in the human reference sequence, detect many new large subtelomeric variants and demonstrate the feasibility of long-range haplotyping through segmentally duplicated subtelomere regions. These features make the method a uniquely valuable new tool for improving the quality of genome assemblies in complex DNA regions. Based on single molecule mapping of telomere-terminal DNA fragments, we provide proof of principle for a novel method to estimate telomere lengths linked to distinguishable telomeric haplotypes; this single-telomere genotyping method may ultimately enable delineation of human cis elements involved in telomere length regulation.
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Affiliation(s)
- Eleanor Young
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Steven Pastor
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | | | - Jennifer McCaffrey
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Justin Sibert
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Angel C Y Mak
- Cardiovascular Research Institute, University of California, San Francisco, CA, 94158 USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, CA, 94158 USA
| | - Harold Riethman
- Old Dominion University, Medical Diagnostic and Translational Sciences, Norfolk, VA, 23529 USA
| | - Ming Xiao
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA.,Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, 19102 USA
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32
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Abstract
Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.
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33
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Müller V, Westerlund F. Optical DNA mapping in nanofluidic devices: principles and applications. LAB ON A CHIP 2017; 17:579-590. [PMID: 28098301 DOI: 10.1039/c6lc01439a] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Optical DNA mapping has over the last decade emerged as a very powerful tool for obtaining long range sequence information from single DNA molecules. In optical DNA mapping, intact large single DNA molecules are labeled, stretched out, and imaged using a fluorescence microscope. This means that sequence information ranging over hundreds of kilobasepairs (kbp) can be obtained in one single image. Nanochannels offer homogeneous and efficient stretching of DNA that is crucial to maximize the information that can be obtained from optical DNA maps. In this review, we highlight progress in the field of optical DNA mapping in nanochannels. We discuss the different protocols for sequence specific labeling and divide them into two main categories, enzymatic labeling and affinity-based labeling. Examples are highlighted where optical DNA mapping is used to gain information on length scales that would be inaccessible with traditional techniques. Enzymatic labeling has been commercialized and is mainly used in human genetics and assembly of complex genomes, while the affinity-based methods have primarily been applied in bacteriology, for example for rapid analysis of plasmids encoding antibiotic resistance. Next, we highlight how the design of nanofluidic channels can been altered in order to obtain the desired information and discuss how recent advances in the field make it possible to retrieve information beyond DNA sequence. In the outlook section, we discuss future directions of optical DNA mapping, such as fully integrated devices and portable microscopes.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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34
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Guha TK, Wai A, Hausner G. Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering. Comput Struct Biotechnol J 2017; 15:146-160. [PMID: 28179977 PMCID: PMC5279741 DOI: 10.1016/j.csbj.2016.12.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 12/26/2022] Open
Abstract
Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break. In order to reduce potential toxic effects of genome editing reagents, it might be desirable to control the in vitro or in vivo activity of these reagents by incorporating regulatory switches that can reduce off-target activities and/or allow for these reagents to be turned on or off. This review will outline the various genome editing tools that are currently available and describe the strategies that have so far been employed for regulating these editing reagents. In addition, this review will examine potential regulatory switches/strategies that can be employed in the future in order to provide temporal control for these reagents.
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Affiliation(s)
| | | | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
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35
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Müller V, Rajer F, Frykholm K, Nyberg LK, Quaderi S, Fritzsche J, Kristiansson E, Ambjörnsson T, Sandegren L, Westerlund F. Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping. Sci Rep 2016; 6:37938. [PMID: 27905467 PMCID: PMC5131345 DOI: 10.1038/srep37938] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/01/2016] [Indexed: 12/03/2022] Open
Abstract
Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrika Rajer
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Karolin Frykholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lena K. Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Saair Quaderi
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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36
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Rems L, Kawale D, Lee LJ, Boukany PE. Flow of DNA in micro/nanofluidics: From fundamentals to applications. BIOMICROFLUIDICS 2016; 10:043403. [PMID: 27493701 PMCID: PMC4958106 DOI: 10.1063/1.4958719] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 05/26/2023]
Abstract
Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new single-molecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena, which were previously unachievable with conventional methods such as bulk rheometry tests. For instance, the field of polymer rheology is at a turning point to relate the complex molecular conformations to the nonlinear viscoelasticity of polymeric fluids (such as coil-stretch transition, shear thinning, and stress overshoot in startup shear). In addition, nanofluidic devices provided a starting point for manipulating single DNA molecules by applying basic principles of polymer physics, which is highly relevant to numerous processes in biosciences. In this article, we review recent progress regarding the flow and deformation of DNA in micro/nanofluidic systems from both fundamental and application perspectives. We particularly focus on advances in the understanding of polymer rheology and identify the emerging research trends and challenges, especially with respect to future applications of nanofluidics in the biomedical field.
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Affiliation(s)
- Lea Rems
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - Durgesh Kawale
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - L James Lee
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, Ohio 43210, USA
| | - Pouyan E Boukany
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
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