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Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM. cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches. Nucleic Acids Res 2017; 45:11559-11569. [PMID: 29036576 PMCID: PMC5714207 DOI: 10.1093/nar/gkx814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/04/2017] [Indexed: 11/14/2022] Open
Abstract
DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome. Herein, we present customised Reduced Representation Bisulfite Sequencing (cuRRBS), a novel and easy-to-use computational method that solves this problem. By computing the optimal enzymatic digestions and size selection steps required, cuRRBS generalises the traditional MspI-based Reduced Representation Bisulfite Sequencing (RRBS) protocol to all restriction enzyme combinations. In addition, cuRRBS estimates the fold-reduction in sequencing costs and provides a robustness value for the personalised RRBS protocol, allowing users to tailor the protocol to their experimental needs. Moreover, we show in silico that cuRRBS-defined restriction enzymes consistently out-perform MspI digestion in many biological systems, considering both CpG and CHG contexts. Finally, we have validated the accuracy of cuRRBS predictions for single and double enzyme digestions using two independent experimental datasets.
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Affiliation(s)
- Daniel E Martin-Herranz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Thomas M Stubbs
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
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Roszik J, Fenyőfalvi G, Halász L, Karányi Z, Székvölgyi L. In Silico Restriction Enzyme Digests to Minimize Mapping Bias in Genomic Sequencing. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 6:66-67. [PMID: 28695155 PMCID: PMC5485759 DOI: 10.1016/j.omtm.2017.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
| | - György Fenyőfalvi
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen 4032, Hungary
| | - László Halász
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen 4032, Hungary.,Department of Biochemistry and Molecular Biology, University of Debrecen, Egyetem sq. 1, Debrecen 4032, Hungary
| | - Zsolt Karányi
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen 4032, Hungary
| | - Lóránt Székvölgyi
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Research Centre for Molecular Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen 4032, Hungary.,Department of Biochemistry and Molecular Biology, University of Debrecen, Egyetem sq. 1, Debrecen 4032, Hungary
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Suryawanshi GW, Xu S, Xie Y, Chou T, Kim N, Chen ISY, Kim S. Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow. J Vis Exp 2017. [PMID: 28654067 DOI: 10.3791/55812] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral gene therapy studies, IS assays, in combination with next-generation sequencing, have been used as a cell-tracking tool to characterize clonal stem cell populations sharing the same IS. For the accurate comparison of repopulating stem cell clones within and across different samples, the detection sensitivity, data reproducibility, and high-throughput capacity of the assay are among the most important assay qualities. This work provides a detailed protocol and data analysis workflow for bidirectional IS analysis. The bidirectional assay can simultaneously sequence both upstream and downstream vector-host junctions. Compared to conventional unidirectional IS sequencing approaches, the bidirectional approach significantly improves IS detection rates and the characterization of integration events at both ends of the target DNA. The data analysis pipeline described here accurately identifies and enumerates identical IS sequences through multiple steps of comparison that map IS sequences onto the reference genome and determine sequencing errors. Using an optimized assay procedure, we have recently published the detailed repopulation patterns of thousands of Hematopoietic Stem Cell (HSC) clones following transplant in rhesus macaques, demonstrating for the first time the precise time point of HSC repopulation and the functional heterogeneity of HSCs in the primate system. The following protocol describes the step-by-step experimental procedure and data analysis workflow that accurately identifies and quantifies identical IS sequences.
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Affiliation(s)
- Gajendra W Suryawanshi
- UCLA AIDS Institute, University of California at Los Angeles (UCLA); Department of Microbiology, Immunology, & Molecular Genetics, University of California at Los Angeles (UCLA)
| | - Song Xu
- Departments of Biomathematics and Mathematics, University of California at Los Angeles (UCLA)
| | - Yiming Xie
- UCLA AIDS Institute, University of California at Los Angeles (UCLA)
| | - Tom Chou
- Departments of Biomathematics and Mathematics, University of California at Los Angeles (UCLA)
| | - Namshin Kim
- Personalized Genomic Medicine Research Center, Division of Strategic Research Groups, Korea Research Institute of Bioscience and Biotechnology
| | - Irvin S Y Chen
- UCLA AIDS Institute, University of California at Los Angeles (UCLA); Department of Medicine, University of California at Los Angeles (UCLA);
| | - Sanggu Kim
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University (OSU);
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4
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Kirschner SA, Hunewald O, Mériaux SB, Brunnhoefer R, Muller CP, Turner JD. Focussing reduced representation CpG sequencing through judicious restriction enzyme choice. Genomics 2016; 107:109-19. [PMID: 26945642 DOI: 10.1016/j.ygeno.2016.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 01/01/2023]
Abstract
Current restriction enzyme based reduced representation methylation analyses aim for limited, but unbiased, methylome coverage. As the current best estimate suggests that only ~20% of CpGs are dynamically regulated, we characterised the CpG and genomic context surrounding all suitable restriction enzyme sites to identify those that were located in regions rich in dynamically methylated CpGs. The restriction-site distributions for MspI, BstUI, and HhaI were non-random. CpGs in CGI and shelf+shore could be enriched, particularly in gene bodies for all genomic regions, promoters (TSS1500, TSS200), intra- (1st exon, gene body, 3'UTR, 5'UTR) and inter-genic regions. HpyCH4IV enriched CpG elements in the open sea for all genomic elements. Judicious restriction enzyme choice improves the focus of reduced representation approaches by avoiding the monopolization of read coverage by genomic regions that are irrelevant, unwanted or difficult to map, and only sequencing the most informative fraction of CpGs.
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Affiliation(s)
- Sophie A Kirschner
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg; Department of Immunology, Research Institute of Psychobiology, University of Trier, D-54290, Germany
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Sophie B Mériaux
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Regina Brunnhoefer
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg; Department of Immunology, Research Institute of Psychobiology, University of Trier, D-54290, Germany
| | - Jonathan D Turner
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), House of Bio-Health 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Grand Duchy of Luxembourg.
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