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Margalit S, Tulpová Z, Detinis Zur T, Michaeli Y, Deek J, Nifker G, Haldar R, Gnatek Y, Omer D, Dekel B, Feldman HB, Grunwald A, Ebenstein Y. Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587463. [PMID: 38915648 PMCID: PMC11195078 DOI: 10.1101/2024.03.31.587463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Carcinogenesis often involves significant alterations in the cancer genome architecture, marked by large structural and copy number variations (SVs and CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping and nanopore sequencing are attractive technologies that bridge this resolution gap and offer enhanced performance for cytogenetic applications. These methods profile native, individual DNA molecules, thus capturing epigenetic information. We applied both techniques to characterize a clear cell renal cell carcinoma (ccRCC) tumor's structural and copy number landscape, highlighting the relative strengths of each method in the context of variant size and average read length. Additionally, we assessed their utility for methylome and hydroxymethylome profiling, emphasizing differences in epigenetic analysis applicability.
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Affiliation(s)
- Sapir Margalit
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Zuzana Tulpová
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
- Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Tahir Detinis Zur
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Jasline Deek
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Gil Nifker
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Rita Haldar
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yehudit Gnatek
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Dorit Omer
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
- Pediatric Nephrology Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, 52621 Ramat Gan, Israel
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Hagit Baris Feldman
- School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Assaf Grunwald
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
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Nogin Y, Sapir D, Zur TD, Weinberger N, Belinkov Y, Ebenstein Y, Shechtman Y. OM2Seq: learning retrieval embeddings for optical genome mapping. BIOINFORMATICS ADVANCES 2024; 4:vbae079. [PMID: 38915884 PMCID: PMC11194751 DOI: 10.1093/bioadv/vbae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/27/2024] [Accepted: 05/28/2024] [Indexed: 06/26/2024]
Abstract
Motivation Genomics-based diagnostic methods that are quick, precise, and economical are essential for the advancement of precision medicine, with applications spanning the diagnosis of infectious diseases, cancer, and rare diseases. One technology that holds potential in this field is optical genome mapping (OGM), which is capable of detecting structural variations, epigenomic profiling, and microbial species identification. It is based on imaging of linearized DNA molecules that are stained with fluorescent labels, that are then aligned to a reference genome. However, the computational methods currently available for OGM fall short in terms of accuracy and computational speed. Results This work introduces OM2Seq, a new approach for the rapid and accurate mapping of DNA fragment images to a reference genome. Based on a Transformer-encoder architecture, OM2Seq is trained on acquired OGM data to efficiently encode DNA fragment images and reference genome segments to a common embedding space, which can be indexed and efficiently queried using a vector database. We show that OM2Seq significantly outperforms the baseline methods in both computational speed (by 2 orders of magnitude) and accuracy. Availability and implementation https://github.com/yevgenin/om2seq.
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Affiliation(s)
- Yevgeni Nogin
- Russel Berrie Nanotechnology Institute, Technion, Haifa 320003, Israel
| | - Danielle Sapir
- Faculty of Electrical and Computer Engineering, Technion, Haifa 320003, Israel
| | - Tahir Detinis Zur
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Nir Weinberger
- Faculty of Electrical and Computer Engineering, Technion, Haifa 320003, Israel
| | | | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute, Technion, Haifa 320003, Israel
- Department of Biomedical Engineering, Technion, Haifa 320003, Israel
- Lorry I. Lokey Center for Life Sciences and Engineering, Technion, Haifa 320003, Israel
- Department of Mechanical Engineering, University of Texas at Austin, Austin, TX 78712, United States
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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LoTempio J, Delot E, Vilain E. Benchmarking long-read genome sequence alignment tools for human genomics applications. PeerJ 2023; 11:e16515. [PMID: 38130927 PMCID: PMC10734412 DOI: 10.7717/peerj.16515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/02/2023] [Indexed: 12/23/2023] Open
Abstract
Background The utility of long-read genome sequencing platforms has been shown in many fields including whole genome assembly, metagenomics, and amplicon sequencing. Less clear is the applicability of long reads to reference-guided human genomics, which is the foundation of genomic medicine. Here, we benchmark available platform-agnostic alignment tools on datasets from nanopore and single-molecule real-time platforms to understand their suitability in producing a genome representation. Results For this study, we leveraged publicly-available data from sample NA12878 generated on Oxford Nanopore and sample NA24385 on Pacific Biosciences platforms. We employed state of the art sequence alignment tools including GraphMap2, long-read aligner (LRA), Minimap2, CoNvex Gap-cost alignMents for Long Reads (NGMLR), and Winnowmap2. Minimap2 and Winnowmap2 were computationally lightweight enough for use at scale, while GraphMap2 was not. NGMLR took a long time and required many resources, but produced alignments each time. LRA was fast, but only worked on Pacific Biosciences data. Each tool widely disagreed on which reads to leave unaligned, affecting the end genome coverage and the number of discoverable breakpoints. No alignment tool independently resolved all large structural variants (1,001-100,000 base pairs) present in the Database of Genome Variants (DGV) for sample NA12878 or the truthset for NA24385. Conclusions These results suggest a combined approach is needed for LRS alignments for human genomics. Specifically, leveraging alignments from three tools will be more effective in generating a complete picture of genomic variability. It should be best practice to use an analysis pipeline that generates alignments with both Minimap2 and Winnowmap2 as they are lightweight and yield different views of the genome. Depending on the question at hand, the data available, and the time constraints, NGMLR and LRA are good options for a third tool. If computational resources and time are not a factor for a given case or experiment, NGMLR will provide another view, and another chance to resolve a case. LRA, while fast, did not work on the nanopore data for our cluster, but PacBio results were promising in that those computations completed faster than Minimap2. Due to its significant burden on computational resources and slow run time, Graphmap2 is not an ideal tool for exploration of a whole human genome generated on a long-read sequencing platform.
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Affiliation(s)
- Jonathan LoTempio
- Institute for Clinical and Translational Science, University of California, Irvine, CA, United States of America
- International Research Laboratory (IRL2006) “Epigenetics, Data, Politics (EpiDaPo)”, Centre National de la Recherche Scientifique, Washington, DC, United States of America
| | - Emmanuele Delot
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, United States of America
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, United States of America
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, CA, United States of America
- International Research Laboratory (IRL2006) “Epigenetics, Data, Politics (EpiDaPo)”, Centre National de la Recherche Scientifique, Washington, DC, United States of America
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Avraham S, Schütz L, Käver L, Dankers A, Margalit S, Michaeli Y, Zirkin S, Torchinsky D, Gilat N, Bahr O, Nifker G, Koren-Michowitz M, Weinhold E, Ebenstein Y. Chemo-Enzymatic Fluorescence Labeling Of Genomic DNA For Simultaneous Detection Of Global 5-Methylcytosine And 5-Hydroxymethylcytosine. Chembiochem 2023; 24:e202300400. [PMID: 37518671 DOI: 10.1002/cbic.202300400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/05/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
5-Methylcytosine and 5-hydroxymethylcytosine are epigenetic modifications involved in gene regulation and cancer. We present a new, simple, and high-throughput platform for multi-color epigenetic analysis. The novelty of our approach is the ability to multiplex methylation and de-methylation signals in the same assay. We utilize an engineered methyltransferase enzyme that recognizes and labels all unmodified CpG sites with a fluorescent cofactor. In combination with the already established labeling of the de-methylation mark 5-hydroxymethylcytosine via enzymatic glycosylation, we obtained a robust platform for simultaneous epigenetic analysis of these marks. We assessed the global epigenetic levels in multiple samples of colorectal cancer and observed a 3.5-fold reduction in 5hmC levels but no change in DNA methylation levels between sick and healthy individuals. We also measured epigenetic modifications in chronic lymphocytic leukemia and observed a decrease in both modification levels (5-hydroxymethylcytosine: whole blood 30 %; peripheral blood mononuclear cells (PBMCs) 40 %. 5-methylcytosine: whole blood 53 %; PBMCs 48 %). Our findings propose using a simple blood test as a viable method for analysis, simplifying sample handling in diagnostics. Importantly, our results highlight the assay's potential for epigenetic evaluation of clinical samples, benefiting research and patient management.
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Affiliation(s)
- Sigal Avraham
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Larissa Käver
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Andreas Dankers
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Sapir Margalit
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shahar Zirkin
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Dmitry Torchinsky
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Noa Gilat
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Omer Bahr
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gil Nifker
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
| | | | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly SacklerFaculty of Exact Sciences, Department of Biomedical Engineering, Tel Aviv University Tel Aviv-Yafo, 6997801, Tel Aviv, Israel
- School of Chemistry,Ramat Aviv, Tel Aviv University, Tel Aviv, 6997801, Israel
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Detinis Zur T, Deek J, Ebenstein Y. Single-molecule approaches for DNA damage detection and repair: A focus on Repair Assisted Damage Detection (RADD). DNA Repair (Amst) 2023; 129:103533. [PMID: 37467630 PMCID: PMC10496029 DOI: 10.1016/j.dnarep.2023.103533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023]
Abstract
The human genome is continually exposed to various stressors, which can result in DNA damage, mutations, and diseases. Among the different types of DNA damage, single-strand lesions are commonly induced by external stressors and metabolic processes. Accurate detection and quantification of DNA damage are crucial for understanding repair mechanisms, assessing environmental impacts, and evaluating response to therapy. However, traditional techniques have limitations in sensitivity and the ability to detect multiple types of damage. In recent years, single-molecule fluorescence approaches have emerged as powerful tools for precisely localizing and quantifying DNA damage. Repair Assisted Damage Detection (RADD) is a single-molecule technique that employs specific repair enzymes to excise damaged bases and incorporates fluorescently labeled nucleotides to visualize the damage. This technique provides valuable insights into repair efficiency and sequence-specific damage. In this review, we discuss the principles and applications of RADD assays, highlighting their potential for enhancing our understanding of DNA damage and repair processes.
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Affiliation(s)
- Tahir Detinis Zur
- 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
| | - Jasline Deek
- 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
| | - 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.
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Lee JH, Chiu JHC, Ginga NJ, Ahmed T, Thouless MD, Liu Y, Takayama S. Super-resolution imaging of linearized chromatin in tunable nanochannels. NANOSCALE HORIZONS 2023; 8:1043-1053. [PMID: 37221952 DOI: 10.1039/d3nh00096f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nanofluidic linearization and optical mapping of naked DNA have been reported in the research literature, and implemented in commercial instruments. However, the resolution with which DNA features can be resolved is still inherently limited by both Brownian motion and diffraction-limited optics. Direct analysis of native chromatin is further hampered by difficulty in electrophoretic manipulation, which is routinely used for DNA analysis. This paper describes the development of a three-layer, tunable, nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Furthermore, through careful selection of self-blinking fluorescent dyes and the design of the nanochannel system, we achieve direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging of the linearized chromatin. As an initial demonstration, rDNA chromatin extracted from Tetrahymena is analyzed by multi-color imaging of total DNA, newly synthesized DNA, and newly synthesized histone H3. Our analysis reveals a relatively even distribution of newly synthesized H3 across two halves of the rDNA chromatin with palindromic symmetry, supporting dispersive nucleosome segregation. As a proof-of-concept study, our work achieves super-resolution imaging of native chromatin fibers linearized and immobilized in tunable nanochannels. It opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.
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Affiliation(s)
- Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joyce Han-Ching Chiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas J Ginga
- Department of Mechanical and Aerospace Engineering, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Tasdiq Ahmed
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - M D Thouless
- Department of Mechanical Engineering and Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifan Liu
- Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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Malikėnas M, Masevičius V, Klimašauskas S. Synthesis of S-Adenosyl-L-Methionine Analogs with Extended Transferable Groups for Methyltransferase-Directed Labeling of DNA and RNA. Curr Protoc 2023; 3:e799. [PMID: 37327316 DOI: 10.1002/cpz1.799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
S-Adenosyl-L-methionine (AdoMet) is a ubiquitous methyl donor for a variety of biological methylation reactions catalyzed by methyltransferases (MTases). AdoMet analogs with extended propargylic chains replacing the sulfonium-bound methyl group can serve as surrogate cofactors for many DNA and RNA MTases, enabling covalent derivatization and subsequent labeling of their cognate target sites in DNA or RNA. Although AdoMet analogs with saturated aliphatic chains are less popular than propargylic ones, they can be useful for dedicated studies that require certain chemical derivatization. Here we describe synthetic procedures for the preparation of two AdoMet analogs, one with a transferable 6-azidohex-2-ynyl group (carrying an activating C≡C triple bond and a terminal azide functionality), and the other one with a transferable ethyl-2,2,2-d3 group (an isotope-labeled aliphatic moiety). Our synthetic approach is based on direct chemoselective alkylation of S-adenosyl-L-homocysteine at sulfur with a corresponding nosylate or triflate, respectively, under acidic conditions. We also describe synthetic routes to 6-azidohex-2-yn-1-ol and conversion of the alcohols to corresponding nosylate and triflate alkylators. Using these protocols, the synthetic AdoMet analogs can be prepared within 1 to 2 weeks. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 6-azidohex-2-yn-1-ol Basic Protocol 2: Synthesis of 4-nitrobenzenesulfonate Basic Protocol 3: Synthesis of trifluoromethanesulfonates Basic Protocol 4: S-Alkylation of AdoHcy with sulfonates Basic Protocol 5: Purification and characterization of AdoMet analogs.
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Affiliation(s)
- Martynas Malikėnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Institute of Chemistry, Department of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Institute of Chemistry, Department of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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10
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Nifker G, Grunwald A, Margalit S, Tulpova Z, Michaeli Y, Har-Gil H, Maimon N, Roichman E, Schütz L, Weinhold E, Ebenstein Y. Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays. ACS NANO 2023; 17:9178-9187. [PMID: 37154345 DOI: 10.1021/acsnano.2c12755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.
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Affiliation(s)
- Gil Nifker
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Assaf Grunwald
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Sapir Margalit
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Zuzana Tulpova
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Hagai Har-Gil
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Noy Maimon
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Elad Roichman
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
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11
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Erdmann H, Scharf F, Gehling S, Benet-Pagès A, Jakubiczka S, Becker K, Seipelt M, Kleefeld F, Knop KC, Prott EC, Hiebeler M, Montagnese F, Gläser D, Vorgerd M, Hagenacker T, Walter MC, Reilich P, Neuhann T, Zenker M, Holinski-Feder E, Schoser B, Abicht A. Methylation of the 4q35 D4Z4 repeat defines disease status in facioscapulohumeral muscular dystrophy. Brain 2023; 146:1388-1402. [PMID: 36100962 DOI: 10.1093/brain/awac336] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/06/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic diagnosis of facioscapulohumeral muscular dystrophy (FSHD) remains a challenge in clinical practice as it cannot be detected by standard sequencing methods despite being the third most common muscular dystrophy. The conventional diagnostic strategy addresses the known genetic parameters of FSHD: the required presence of a permissive haplotype, a size reduction of the D4Z4 repeat of chromosome 4q35 (defining FSHD1) or a pathogenic variant in an epigenetic suppressor gene (consistent with FSHD2). Incomplete penetrance and epistatic effects of the underlying genetic parameters as well as epigenetic parameters (D4Z4 methylation) pose challenges to diagnostic accuracy and hinder prediction of clinical severity. In order to circumvent the known limitations of conventional diagnostics and to complement genetic parameters with epigenetic ones, we developed and validated a multistage diagnostic workflow that consists of a haplotype analysis and a high-throughput methylation profile analysis (FSHD-MPA). FSHD-MPA determines the average global methylation level of the D4Z4 repeat array as well as the regional methylation of the most distal repeat unit by combining bisulphite conversion with next-generation sequencing and a bioinformatics pipeline and uses these as diagnostic parameters. We applied the diagnostic workflow to a cohort of 148 patients and compared the epigenetic parameters based on FSHD-MPA to genetic parameters of conventional genetic testing. In addition, we studied the correlation of repeat length and methylation level within the most distal repeat unit with age-corrected clinical severity and age at disease onset in FSHD patients. The results of our study show that FSHD-MPA is a powerful tool to accurately determine the epigenetic parameters of FSHD, allowing discrimination between FSHD patients and healthy individuals, while simultaneously distinguishing FSHD1 and FSHD2. The strong correlation between methylation level and clinical severity indicates that the methylation level determined by FSHD-MPA accounts for differences in disease severity among individuals with similar genetic parameters. Thus, our findings further confirm that epigenetic parameters rather than genetic parameters represent FSHD disease status and may serve as a valuable biomarker for disease status.
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Affiliation(s)
- Hannes Erdmann
- Medical Genetics Center (MGZ), 80335 Munich, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | | | | | - Anna Benet-Pagès
- Medical Genetics Center (MGZ), 80335 Munich, Germany
- Institute of Neurogenomics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Sibylle Jakubiczka
- Institute of Human Genetics, Universitätsklinikum Magdeburg, Otto-von-Guericke Universität, 39120 Magdeburg, Germany
| | | | - Maria Seipelt
- Department of Neurology, Universitätsklinikum Marburg, Philipps-University Marburg, 35043 Marburg, Germany
| | - Felix Kleefeld
- Department of Neurology and Experimental Neurology, Charité Berlin, 10117 Berlin, Germany
| | | | | | - Miriam Hiebeler
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | - Federica Montagnese
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | | | - Matthias Vorgerd
- Department of Neurology, Berufgenossenschaftliches Universitätsklinikum Bergmannsheil, Ruhr-Universität Bochum, 44789 Bochum, Germany
| | - Tim Hagenacker
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, 45147 Essen, Germany
| | - Maggie C Walter
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | - Peter Reilich
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | | | - Martin Zenker
- Institute of Human Genetics, Universitätsklinikum Magdeburg, Otto-von-Guericke Universität, 39120 Magdeburg, Germany
| | - Elke Holinski-Feder
- Medical Genetics Center (MGZ), 80335 Munich, Germany
- Department of Medicine IV, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
| | - Angela Abicht
- Medical Genetics Center (MGZ), 80335 Munich, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, 80336 Munich, Germany
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12
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Cornelissen NV, Hoffmann A, Rentmeister A. DNA‐Methyltransferasen und AdoMet‐Analoga als Werkzeuge für die Molekularbiologie und Biotechnologie. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Nicolas V. Cornelissen
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Arne Hoffmann
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
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13
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Iqbal W, Zhou W. Computational Methods for Single-cell DNA Methylome Analysis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:48-66. [PMID: 35718270 PMCID: PMC10372927 DOI: 10.1016/j.gpb.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022]
Abstract
Dissecting intercellular epigenetic differences is key to understanding tissue heterogeneity. Recent advances in single-cell DNA methylome profiling have presented opportunities to resolve this heterogeneity at the maximum resolution. While these advances enable us to explore frontiers of chromatin biology and better understand cell lineage relationships, they pose new challenges in data processing and interpretation. This review surveys the current state of computational tools developed for single-cell DNA methylome data analysis. We discuss critical components of single-cell DNA methylome data analysis, including data preprocessing, quality control, imputation, dimensionality reduction, cell clustering, supervised cell annotation, cell lineage reconstruction, gene activity scoring, and integration with transcriptome data. We also highlight unique aspects of single-cell DNA methylome data analysis and discuss how techniques common to other single-cell omics data analyses can be adapted to analyze DNA methylomes. Finally, we discuss existing challenges and opportunities for future development.
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Affiliation(s)
- Waleed Iqbal
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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14
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Koppikar P, Shenoy S, Guruju N, Hegde M. Testing for Facioscapulohumeral Muscular Dystrophy with Optical Genome Mapping. Curr Protoc 2023; 3:e629. [PMID: 36648278 DOI: 10.1002/cpz1.629] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The introduction of optical genome mapping has improved time constraints and a lack of specificity from previous methodologies when performing genome-wide analyses of samples. Optical genome mapping allows for the detection of structural variations, aberrations, and functionality traits from a single stained molecule of DNA. Though the preparation time is increased compared to previously utilized visualization techniques, optical genome mapping significantly reduces the time needed for analysis. Specifically, individual disease pipelines have been developed to rapidly analyze prepared samples. One of these diseases, Facioscapulohumeral Muscular Dystrophy (FSHD), is detected through quantification of the D4Z4 repeat array on chromosome 4q35. Optical genome mapping, with the ability to enumerate the repeats of the D4Z4 array, has demonstrated the capability to precisely diagnose FSHD. In this protocol, the preparation of samples and subsequent loading and analysis in an optical genome mapping system is discussed for the detection and analysis of FSHD. These methods should prove highly useful in FSHD analyses and beyond with the development of further disease analysis pipelines within the instrument. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Genomic DNA isolation, labeling, and staining Basic Protocol 2: Mapping and analysis with the Bionano Saphyr® system.
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Affiliation(s)
| | | | - Naga Guruju
- PerkinElmer Genomics, Pittsburgh, Pennsylvania, USA
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15
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MGMT and Whole-Genome DNA Methylation Impacts on Diagnosis, Prognosis and Therapy of Glioblastoma Multiforme. Int J Mol Sci 2022; 23:ijms23137148. [PMID: 35806153 PMCID: PMC9266959 DOI: 10.3390/ijms23137148] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022] Open
Abstract
Epigenetic changes in DNA methylation contribute to the development of many diseases, including cancer. In glioblastoma multiforme, the most prevalent primary brain cancer and an incurable tumor with a median survival time of 15 months, a single epigenetic modification, the methylation of the O6-Methylguanine-DNA Methyltransferase (MGMT) gene, is a valid biomarker for predicting response to therapy with alkylating agents and also, independently, prognosis. More recently, the progress from single gene to whole-genome analysis of DNA methylation has allowed a better subclassification of glioblastomas. Here, we review the clinically relevant information that can be obtained by studying MGMT gene and whole-genome DNA methylation changes in glioblastomas, also highlighting benefits, including those of liquid biopsy, and pitfalls of the different detection methods. Finally, we discuss how changes in DNA methylation, especially in glioblastomas bearing mutations in the Isocitrate Dehydrogenase (IDH) 1 and 2 genes, can be exploited as targets for tailoring therapy.
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16
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Gabrieli T, Michaeli Y, Avraham S, Torchinsky D, Margalit S, Schütz L, Juhasz M, Coruh C, Arbib N, Zhou ZS, Law JA, Weinhold E, Ebenstein Y. Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping. Nucleic Acids Res 2022; 50:e92. [PMID: 35657088 PMCID: PMC9458417 DOI: 10.1093/nar/gkac460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/12/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022] Open
Abstract
DNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and significant epigenetic modification. Here we developed a chemoenzymatic procedure to fluorescently label non-methylated cytosines in CpG context, allowing epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs. We used a CpG methyltransferase with a synthetic S-adenosyl-l-methionine cofactor analog to transfer an azide to cytosines instead of the natural methyl group. A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. We found that labeling efficiency was increased up to 2-fold by the addition of a nucleosidase, presumably by degrading the inactive by-product of the cofactor after labeling, preventing its inhibitory effect. We used the method to determine the decline in global DNA methylation in a chronic lymphocytic leukemia patient and then performed whole-genome methylation mapping of the model plant Arabidopsis thaliana. Our genome maps show high concordance with published bisulfite sequencing methylation maps. Although mapping resolution is limited by optical detection to 500–1000 bp, the labeled DNA molecules produced by this approach are hundreds of thousands of base pairs long, allowing access to long repetitive and structurally variable genomic regions.
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Affiliation(s)
- Tslil Gabrieli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Michaeli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sigal Avraham
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dmitry Torchinsky
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sapir Margalit
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Matyas Juhasz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nissim Arbib
- Department of Obstetrics and Gynecology, Meir Hospital, Kfar Saba, Israel & Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, and Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts02115, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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17
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Bu L, Luo T, Yan J, Li G, Huang J. Single-molecule analysis of genome-wide DNA methylation by fiber FISH coupled with atomic force microscopy. Analyst 2022; 147:1559-1566. [DOI: 10.1039/d2an00216g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A straightforward single-molecule approach was developed for identifying whole-genome DNA methylation through fiber-FISH coupled with AFM. This method has advantages of low DNA input, reproduction, long reads and low cost.
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Affiliation(s)
- Lingli Bu
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Tao Luo
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jiangyu Yan
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Guorui Li
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Huang
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
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18
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DNA Labeling Using DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:535-562. [DOI: 10.1007/978-3-031-11454-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Jia FF, Drew AP, Nicholson GA, Corbett A, Kumar KR. Facioscapulohumeral muscular dystrophy type 2: an update on the clinical, genetic, and molecular findings. Neuromuscul Disord 2021; 31:1101-1112. [PMID: 34711481 DOI: 10.1016/j.nmd.2021.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 11/25/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a common genetic disease of the skeletal muscle with a characteristic pattern of weakness. Facioscapulohumeral muscular dystrophy type 2 (FSHD2) accounts for approximately 5% of all cases of FSHD and describes patients without a D4Z4 repeat contraction on chromosome 4. Phenotypically FSHD2 shows virtually no difference from FSHD1 and both forms of FSHD arise via a common downstream mechanism of epigenetic derepression of the transcription factor DUX4 in skeletal muscle cells. This results in expression of DUX4 and target genes leading to skeletal muscle toxicity. Over the past decade, major progress has been made in our understanding of the genetic and epigenetic architecture that underlies FSHD2 pathogenesis, as well as the clinical manifestations and disease progression. These include the finding that FSHD2 is a digenic disease and that mutations in the genes SMCHD1, DNMT3B, and more recently LRIF1, can cause FSHD2. FSHD2 is complex and it is important that clinicians keep abreast of recent developments; this review aims to serve as an update of the clinical, genetic, and molecular research into this condition.
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Affiliation(s)
- Fangzhi Frank Jia
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia.
| | - Alexander P Drew
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.
| | - Garth Alexander Nicholson
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Alastair Corbett
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Kishore Raj Kumar
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
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20
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Délot EC, Vilain E. Towards improved genetic diagnosis of human differences of sex development. Nat Rev Genet 2021; 22:588-602. [PMID: 34083777 PMCID: PMC10598994 DOI: 10.1038/s41576-021-00365-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/05/2023]
Abstract
Despite being collectively among the most frequent congenital developmental conditions worldwide, differences of sex development (DSD) lack recognition and research funding. As a result, what constitutes optimal management remains uncertain. Identification of the individual conditions under the DSD umbrella is challenging and molecular genetic diagnosis is frequently not achieved, which has psychosocial and health-related repercussions for patients and their families. New genomic approaches have the potential to resolve this impasse through better detection of protein-coding variants and ascertainment of under-recognized aetiology, such as mosaic, structural, non-coding or epigenetic variants. Ultimately, it is hoped that better outcomes data, improved understanding of the molecular causes and greater public awareness will bring an end to the stigma often associated with DSD.
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Affiliation(s)
- Emmanuèle C Délot
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.
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21
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Precise Epigenetic Analysis Using Targeted Bisulfite Genomic Sequencing Distinguishes FSHD1, FSHD2, and Healthy Subjects. Diagnostics (Basel) 2021; 11:diagnostics11081469. [PMID: 34441403 PMCID: PMC8393475 DOI: 10.3390/diagnostics11081469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/01/2021] [Accepted: 08/11/2021] [Indexed: 12/16/2022] Open
Abstract
The true prevalence of facioscapulohumeral muscular dystrophy (FSHD) is unknown due to difficulties with accurate clinical evaluation and the complexities of current genetic diagnostics. Interestingly, all forms of FSHD are linked to epigenetic changes in the chromosome 4q35 D4Z4 macrosatellite, suggesting that epigenetic analysis could provide an avenue for sequence-based FSHD diagnostics. However, studies assessing DNA methylation at the FSHD locus have produced conflicting results; thus, the utility of this technique as an FSHD diagnostic remains controversial. Here, we critically compared two protocols for epigenetic analysis of the FSHD region using bisulfite genomic sequencing: Jones et al., that contends to be individually diagnostic for FSHD1 and FSHD2, and Gaillard et al., that can identify some changes in DNA methylation levels between groups of clinically affected FSHD and healthy subjects, but is not individually diagnostic for any form of FSHD. We performed both sets of assays on the same genetically confirmed samples and showed that this discrepancy was due strictly to differences in amplicon specificity. We propose that the epigenetic status of the FSHD-associated D4Z4 arrays, when accurately assessed, is a diagnostic for genetic FSHD and can readily distinguish between healthy, FSHD1 and FSHD2. Thus, epigenetic diagnosis of FSHD, which can be performed on saliva DNA, will greatly increase accessibility to FSHD diagnostics for populations around the world.
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22
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Margalit S, Abramson Y, Sharim H, Manber Z, Bhattacharya S, Chen YW, Vilain E, Barseghyan H, Elkon R, Sharan R, Ebenstein Y. Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. Bioinformatics 2021; 37:i327-i333. [PMID: 34252972 PMCID: PMC8275347 DOI: 10.1093/bioinformatics/btab306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION While promoter methylation is associated with reinforcing fundamental tissue identities, the methylation status of distant enhancers was shown by genome-wide association studies to be a powerful determinant of cell-state and cancer. With recent availability of long reads that report on the methylation status of enhancer-promoter pairs on the same molecule, we hypothesized that probing these pairs on the single-molecule level may serve the basis for detection of rare cancerous transformations in a given cell population. We explore various analysis approaches for deconvolving cell-type mixtures based on their genome-wide enhancer-promoter methylation profiles. RESULTS To evaluate our hypothesis we examine long-read optical methylome data for the GM12878 cell line and myoblast cell lines from two donors. We identified over 100 000 enhancer-promoter pairs that co-exist on at least 30 individual DNA molecules. We developed a detailed methodology for mixture deconvolution and applied it to estimate the proportional cell compositions in synthetic mixtures. Analysis of promoter methylation, as well as enhancer-promoter pairwise methylation, resulted in very accurate estimates. In addition, we show that pairwise methylation analysis can be generalized from deconvolving different cell types to subtle scenarios where one wishes to resolve different cell populations of the same cell-type. AVAILABILITY AND IMPLEMENTATION The code used in this work to analyze single-molecule Bionano Genomics optical maps is available via the GitHub repository https://github.com/ebensteinLab/Single_molecule_methylation_in_EP.
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Affiliation(s)
- Sapir Margalit
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yotam Abramson
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Sharim
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Zohar Manber
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Ran Elkon
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roded Sharan
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,School of Computer Science, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Yuval Ebenstein
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
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23
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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 DOI: 10.1021/acs.analchem.1c01373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [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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24
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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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25
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Bhattacharya S, Barseghyan H, Délot EC, Vilain E. nanotatoR: a tool for enhanced annotation of genomic structural variants. BMC Genomics 2021; 22:10. [PMID: 33407088 PMCID: PMC7789800 DOI: 10.1186/s12864-020-07182-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/22/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. RESULTS We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient's phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR's annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. CONCLUSIONS The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.
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Affiliation(s)
- Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, 20010, USA
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, 20010, USA.,Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20052, USA.,Bionano Genomics Inc, San Diego, CA, 92121, USA
| | - Emmanuèle C Délot
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, 20010, USA.,Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20052, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, 20010, USA. .,Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20052, USA.
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26
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Heck C, Torchinsky D, Nifker G, Gularek F, Michaeli Y, Weinhold E, Ebenstein Y. Label as you fold: methyltransferase-assisted functionalization of DNA nanostructures. NANOSCALE 2020; 12:20287-20291. [PMID: 33001091 DOI: 10.1039/d0nr03694c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Non-DNA labels are key components for the construction of functional DNA nanostructures. Here, we present a method to graft covalent labels onto DNA origami nanostructures in an enzymatic one-pot reaction. The DNA methyltransferase M.TaqI labels the DNA nanostructures with azide groups, which serve as universal attachment points via click chemistry. Direct labeling with fluorescent dyes is also demonstrated. The procedure yields structures with high fluorescence intensities and narrow intensity distributions. In combination with UV crosslinking it enables the creation of temperature-stable, intense fluorescent beacons.
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Affiliation(s)
- Christian Heck
- School of Chemistry/Center for Nanoscience and Nanotechnology/Center for Light-Matter Interaction, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
| | - Dmitry Torchinsky
- School of Chemistry/Center for Nanoscience and Nanotechnology/Center for Light-Matter Interaction, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
| | - Gil Nifker
- School of Chemistry/Center for Nanoscience and Nanotechnology/Center for Light-Matter Interaction, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
| | - Felix Gularek
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Yael Michaeli
- School of Chemistry/Center for Nanoscience and Nanotechnology/Center for Light-Matter Interaction, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Yuval Ebenstein
- School of Chemistry/Center for Nanoscience and Nanotechnology/Center for Light-Matter Interaction, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
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27
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Yuan Y, Chung CYL, Chan TF. Advances in optical mapping for genomic research. Comput Struct Biotechnol J 2020; 18:2051-2062. [PMID: 32802277 PMCID: PMC7419273 DOI: 10.1016/j.csbj.2020.07.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.
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Key Words
- 3D, three-dimensional
- DBG, de Bruijn graph
- DLS, direct label and strain
- DNA, deoxyribonucleic acid
- Genome assembly
- Hi-C, high-throughput chromosome conformation capture
- Mb, million base pair
- Next generation sequencing
- OLC, overlap-layout-consensus
- Optical mapping
- PCR, polymerase chain reaction
- PacBio, Pacific Biosciences
- SRS, short-read sequencing
- SV, structural variation
- Structural variation
- bp, base pair
- kb, kilobase pair
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Affiliation(s)
- Yuxuan Yuan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire Yik-Lok Chung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
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28
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Singh V, Johansson P, Torchinsky D, Lin YL, Öz R, Ebenstein Y, Hammarsten O, Westerlund F. Quantifying DNA damage induced by ionizing radiation and hyperthermia using single DNA molecule imaging. Transl Oncol 2020; 13:100822. [PMID: 32652469 PMCID: PMC7350159 DOI: 10.1016/j.tranon.2020.100822] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 11/19/2022] Open
Abstract
Ionizing radiation (IR) is a common mode of cancer therapy, where DNA damage is the major reason of cell death. Here, we use an assay based on fluorescence imaging of single damaged DNA molecules isolated from radiated lymphocytes, to quantify IR induced DNA damage. The assay uses a cocktail of DNA-repair enzymes that recognizes and excises DNA lesions and then a polymerase and a ligase incorporate fluorescent nucleotides at the damage sites, resulting in a fluorescent “spot” at each site. The individual fluorescent spots can then be counted along single stretched DNA molecules and the global level of DNA damage can be quantified. Our results demonstrate that inclusion of the human apurinic/apyrimidinic endonuclease 1 (APE1) in the enzyme cocktail increases the sensitivity of the assay for detection of IR induced damage significantly. This optimized assay also allowed detection of a cooperative increase in DNA damage when IR was combined with mild hyperthermia, which is sometimes used as an adjuvant in IR therapy. Finally, we discuss how the method may be used to identify patients that are sensitive to IR and other types of DNA damaging agents.
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Affiliation(s)
- Vandana Singh
- Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pegah Johansson
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Dmitry Torchinsky
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Israel
| | - Yii-Lih Lin
- Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Robin Öz
- Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Israel
| | - Ola Hammarsten
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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29
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Kraft F, Kurth I. Long-read sequencing to understand genome biology and cell function. Int J Biochem Cell Biol 2020; 126:105799. [PMID: 32629027 DOI: 10.1016/j.biocel.2020.105799] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023]
Abstract
Determining the sequence of DNA and RNA molecules has a huge impact on the understanding of cell biology and function. Recent advancements in next-generation short-read sequencing (NGS) technologies, drops in cost and a resolution down to the single-cell level shaped our current view on genome structure and function. Third-generation sequencing (TGS) methods further complete the knowledge about these processes based on long reads and the ability to analyze DNA or RNA at single molecule level. Long-read sequencing provides additional possibilities to study genome architecture and the composition of highly complex regions and to determine epigenetic modifications of nucleotide bases at a genome-wide level. We discuss the principles and advancements of long-read sequencing and its applications in genome biology.
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Affiliation(s)
- Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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30
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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31
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Abstract
Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity, relationship to disease and possible effects on biological mechanisms. Given the variability in SV type and size, along with unique detection biases of emerging genomic platforms, multiplatform discovery is necessary to resolve the full spectrum of variation. Here, we review modern approaches for investigating SVs and proffer that, moving forwards, studies integrating biological information with detection will be necessary to comprehensively understand the impact of SV in the human genome.
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Affiliation(s)
- Steve S Ho
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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32
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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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33
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Torchinsky D, Michaeli Y, Gassman NR, Ebenstein Y. Simultaneous detection of multiple DNA damage types by multi-colour fluorescent labelling. Chem Commun (Camb) 2019; 55:11414-11417. [PMID: 31482872 DOI: 10.1039/c9cc05198h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Herein we present an assay allowing concurrent detection of oxidative DNA damage and photoproducts. We apply DNA repair enzymes specific for each lesion type to incorporate spectrally distinct fluorescent nucleotides, enabling simultaneous quantification of the lesions on individual DNA molecules. We follow the repair of both damage types in skin cells exposed to artificial sunlight.
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Affiliation(s)
- Dmitry Torchinsky
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.
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34
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Jain N, Shahal T, Gabrieli T, Gilat N, Torchinsky D, Michaeli Y, Vogel V, Ebenstein Y. Global modulation in DNA epigenetics during pro-inflammatory macrophage activation. Epigenetics 2019; 14:1183-1193. [PMID: 31262215 DOI: 10.1080/15592294.2019.1638700] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DNA methylation patterns create distinct gene-expression profiles. These patterns are maintained after cell division, thus enabling the differentiation and maintenance of multiple cell types from the same genome sequence. The advantage of this mechanism for transcriptional control is that chemical-encoding allows to rapidly establish new epigenetic patterns 'on-demand' through enzymatic methylation and demethylation of DNA. Here we show that this feature is associated with the fast response of macrophages during their pro-inflammatory activation. By using a combination of mass spectroscopy and single-molecule imaging to quantify global epigenetic changes in the genomes of primary macrophages, we followed three distinct DNA marks (methylated, hydroxymethylated and unmethylated), involved in establishing new DNA methylation patterns during pro-inflammatory activation. The observed epigenetic modulation together with gene-expression data generated for the involved enzymatic machinery may suggest that de-methylation upon LPS-activation starts with oxidation of methylated CpGs, followed by excision-repair of these oxidized bases and their replacement with unmodified cytosine.
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Affiliation(s)
- Nikhil Jain
- Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology, Institute of Translational Medicine, ETH Zurich , Zurich , Switzerland
| | - Tamar Shahal
- Sagol Center for the Epigenetics of Metabolism and Aging, Tel Aviv Sourasky Medical Center , Tel Aviv , Israel.,Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv , Israel
| | - Tslil Gabrieli
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv , Israel
| | - Noa Gilat
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv , Israel
| | - Dmitry Torchinsky
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv , Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv , Israel
| | - Viola Vogel
- Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology, Institute of Translational Medicine, ETH Zurich , Zurich , Switzerland
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv , Israel
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