1
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Dagva O, Thibessard A, Lorenzi JN, Labat V, Piotrowski E, Rouhier N, Myllykallio H, Leblond P, Bertrand C. Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS. Nucleic Acids Res 2024; 52:5033-5047. [PMID: 38444149 PMCID: PMC11109965 DOI: 10.1093/nar/gkae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/19/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
The linear chromosome of Streptomyces exhibits a highly compartmentalized structure with a conserved central region flanked by variable arms. As double strand break (DSB) repair mechanisms play a crucial role in shaping the genome plasticity of Streptomyces, we investigated the role of EndoMS/NucS, a recently characterized endonuclease involved in a non-canonical mismatch repair (MMR) mechanism in archaea and actinobacteria, that singularly corrects mismatches by creating a DSB. We showed that Streptomyces mutants lacking NucS display a marked colonial phenotype and a drastic increase in spontaneous mutation rate. In vitro biochemical assays revealed that NucS cooperates with the replication clamp to efficiently cleave G/T, G/G and T/T mismatched DNA by producing DSBs. These findings are consistent with the transition-shifted mutational spectrum observed in the mutant strains and reveal that NucS-dependent MMR specific task is to eliminate G/T mismatches generated by the DNA polymerase during replication. Interestingly, our data unveil a crescent-shaped distribution of the transition frequency from the replication origin towards the chromosomal ends, shedding light on a possible link between NucS-mediated DSBs and Streptomyces genome evolution.
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Affiliation(s)
- Oyut Dagva
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | | | | | - Victor Labat
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Emilie Piotrowski
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Nicolas Rouhier
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Hannu Myllykallio
- Ecole Polytechnique, INSERM U696-CNRS UMR 7645 LOB, 91128 Palaiseau, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Claire Bertrand
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
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2
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Brunderová M, Havlíček V, Matyašovský J, Pohl R, Poštová Slavětínská L, Krömer M, Hocek M. Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases. Nat Commun 2024; 15:3054. [PMID: 38594306 PMCID: PMC11004144 DOI: 10.1038/s41467-024-47444-9] [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: 10/28/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Innovative approaches to controlled nucleobase-modified RNA synthesis are urgently needed to support RNA biology exploration and to synthesize potential RNA therapeutics. Here we present a strategy for enzymatic construction of nucleobase-modified RNA based on primer-dependent engineered thermophilic DNA polymerases - SFM4-3 and TGK. We demonstrate introduction of one or several different base-modified nucleotides in one strand including hypermodified RNA containing all four modified nucleotides bearing four different substituents, as well as strategy for primer segment removal. We also show facile site-specific or segmented introduction of fluorophores or other functional groups at defined positions in variety of RNA molecules, including structured or long mRNA. Intriguing translation efficacy of single-site modified mRNAs underscores the necessity to study isolated modifications placed at designer positions to disentangle their biological effects and enable development of improved mRNA therapeutics. Our toolbox paves the way for more precise dissecting RNA structures and functions, as well as for construction of diverse types of base-functionalized RNA for therapeutic applications and diagnostics.
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Affiliation(s)
- Mária Brunderová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Vojtěch Havlíček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- The Rosalind Franklin Institute, Harwell Campus, Didcot, Oxfordshire, UK.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic.
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3
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Hernández-Rollán C, Ehrmann AK, Vlassis A, Kandasamy V, Nørholm MHH. Neq2X7: a multi-purpose and open-source fusion DNA polymerase for advanced DNA engineering and diagnostics PCR. BMC Biotechnol 2024; 24:17. [PMID: 38566117 PMCID: PMC10988834 DOI: 10.1186/s12896-024-00844-7] [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: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Thermostable DNA polymerases, such as Taq isolated from the thermophilic bacterium Thermus aquaticus, enable one-pot exponential DNA amplification known as polymerase chain reaction (PCR). However, properties other than thermostability - such as fidelity, processivity, and compatibility with modified nucleotides - are important in contemporary molecular biology applications. Here, we describe the engineering and characterization of a fusion between a DNA polymerase identified in the marine archaea Nanoarchaeum equitans and a DNA binding domain from the thermophile Sulfolobus solfataricus. The fusion creates a highly active enzyme, Neq2X7, capable of amplifying long and GC-rich DNA, unaffected by replacing dTTP with dUTP in PCR, and tolerant to various known PCR inhibitors. This makes it an attractive DNA polymerase for use, e.g., with uracil excision (USER) DNA assembly and for contamination-free diagnostics. Using a magnification via nucleotide imbalance fidelity assay, Neq2X7 was estimated to have an error rate lower than 2 ∙ 10-5 bp-1 and an approximately 100x lower fidelity than the parental variant Neq2X, indicating a trade-off between fidelity and processivity - an observation that may be of importance for similarly engineered DNA polymerases. Neq2X7 is easy to produce for routine application in any molecular biology laboratory, and the expression plasmid is made freely available.
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Affiliation(s)
- Cristina Hernández-Rollán
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark
| | - Anja K Ehrmann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark
| | - Arsenios Vlassis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark
| | - Vijayalakshmi Kandasamy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby, 2800, Denmark.
- Mycropt ApS, Kongens Lyngby, 2800, Denmark.
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4
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:ijms24119331. [PMID: 37298280 DOI: 10.3390/ijms24119331] [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] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
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5
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Wanchai V, Jenjaroenpun P, Leangapichart T, Arrey G, Burnham CM, Tümmler MC, Delgado-Calle J, Regenberg B, Nookaew I. CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences. Brief Bioinform 2022; 23:bbac422. [PMID: 36198068 PMCID: PMC10144670 DOI: 10.1093/bib/bbac422] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL's performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL's capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.
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Affiliation(s)
- Visanu Wanchai
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thongpan Leangapichart
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Gerard Arrey
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Charles M Burnham
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Maria C Tümmler
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesus Delgado-Calle
- Department of Physiology and Cell Biology, College of Medicine, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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6
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AlJanahi AA, Lazzarotto CR, Chen S, Shin TH, Cordes S, Fan X, Jabara I, Zhou Y, Young DJ, Lee BC, Yu KR, Li Y, Toms B, Tunc I, Hong SG, Truitt LL, Klermund J, Andrieux G, Kim MY, Cathomen T, Gill S, Tsai SQ, Dunbar CE. Prediction and validation of hematopoietic stem and progenitor cell off-target editing in transplanted rhesus macaques. Mol Ther 2022; 30:209-222. [PMID: 34174439 PMCID: PMC8753565 DOI: 10.1016/j.ymthe.2021.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/18/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
The programmable nuclease technology CRISPR-Cas9 has revolutionized gene editing in the last decade. Due to the risk of off-target editing, accurate and sensitive methods for off-target characterization are crucial prior to applying CRISPR-Cas9 therapeutically. Here, we utilized a rhesus macaque model to compare the predictive values of CIRCLE-seq, an in vitro off-target prediction method, with in silico prediction (ISP) based solely on genomic sequence comparisons. We use AmpliSeq HD error-corrected sequencing to validate off-target sites predicted by CIRCLE-seq and ISP for a CD33 guide RNA (gRNA) with thousands of off-target sites predicted by ISP and CIRCLE-seq. We found poor correlation between the sites predicted by the two methods. When almost 500 sites predicted by each method were analyzed by error-corrected sequencing of hematopoietic cells following transplantation, 19 off-target sites revealed insertion or deletion mutations. Of these sites, 8 were predicted by both methods, 8 by CIRCLE-seq only, and 3 by ISP only. The levels of cells with these off-target edits exhibited no expansion or abnormal behavior in vivo in animals followed for up to 2 years. In addition, we utilized an unbiased method termed CAST-seq to search for translocations between the on-target site and off-target sites present in animals following transplantation, detecting one specific translocation that persisted in blood cells for at least 1 year following transplantation. In conclusion, neither CIRCLE-seq or ISP predicted all sites, and a combination of careful gRNA design, followed by screening for predicted off-target sites in target cells by multiple methods, may be required for optimizing safety of clinical development.
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Affiliation(s)
- Aisha A AlJanahi
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biology, Georgetown University, Washington, DC 20057, USA
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shirley Chen
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Tae-Hoon Shin
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Stefan Cordes
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Xing Fan
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Isabel Jabara
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - David J Young
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Byung-Chul Lee
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Kyung-Rok Yu
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA; Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yuesheng Li
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | | | - Ilker Tunc
- Bioinformatics and Computational Biology Laboratory, NHLBI, NIH, Bethesda, MD 20892, USA
| | - So Gun Hong
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Lauren L Truitt
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Geoffroy Andrieux
- Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Miriam Y Kim
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Saar Gill
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, NHLBI, NIH, Building 10-CRC, 5E-3332, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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7
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Lähnemann D, Köster J, Fischer U, Borkhardt A, McHardy AC, Schönhuth A. Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo. Nat Commun 2021; 12:6744. [PMID: 34795237 PMCID: PMC8602313 DOI: 10.1038/s41467-021-26938-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/22/2021] [Indexed: 01/14/2023] Open
Abstract
Accurate single cell mutational profiles can reveal genomic cell-to-cell heterogeneity. However, sequencing libraries suitable for genotyping require whole genome amplification, which introduces allelic bias and copy errors. The resulting data violates assumptions of variant callers developed for bulk sequencing. Thus, only dedicated models accounting for amplification bias and errors can provide accurate calls. We present ProSolo for calling single nucleotide variants from multiple displacement amplified (MDA) single cell DNA sequencing data. ProSolo probabilistically models a single cell jointly with a bulk sequencing sample and integrates all relevant MDA biases in a site-specific and scalable-because computationally efficient-manner. This achieves a higher accuracy in calling and genotyping single nucleotide variants in single cells in comparison to state-of-the-art tools and supports imputation of insufficiently covered genotypes, when downstream tools cannot handle missing data. Moreover, ProSolo implements the first approach to control the false discovery rate reliably and flexibly. ProSolo is implemented in an extendable framework, with code and usage at: https://github.com/prosolo/prosolo.
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Affiliation(s)
- David Lähnemann
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106, Braunschweig, Germany
- Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Algorithms for Reproducible Bioinformatics, Institute of Human Genetics, University of Duisburg-Essen, 45147, Essen, Germany
| | - Johannes Köster
- Algorithms for Reproducible Bioinformatics, Institute of Human Genetics, University of Duisburg-Essen, 45147, Essen, Germany
- Genome Data Science, Life Sciences Group, Centrum Wiskunde & Informatica, 1098 XG, Amsterdam, The Netherlands
| | - Ute Fischer
- Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Arndt Borkhardt
- Department of Paediatric Oncology, Haematology and Immunology, University Hospital, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Alice C McHardy
- Department for Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106, Braunschweig, Germany.
- Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Alexander Schönhuth
- Genome Data Science, Life Sciences Group, Centrum Wiskunde & Informatica, 1098 XG, Amsterdam, The Netherlands.
- Genome Data Science, Faculty of Technology, Bielefeld University, 33615, Bielefeld, Germany.
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8
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Bhan N, Callisto A, Strutz J, Glaser J, Kalhor R, Boyden ES, Church G, Kording K, Tyo KEJ. Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis. J Am Chem Soc 2021; 143:16630-16640. [PMID: 34591459 PMCID: PMC8982284 DOI: 10.1021/jacs.1c07331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Employing DNA as a high-density data storage medium has paved the way for next-generation digital storage and biosensing technologies. However, the multipart architecture of current DNA-based recording techniques renders them inherently slow and incapable of recording fluctuating signals with subhour frequencies. To address this limitation, we developed a simplified system employing a single enzyme, terminal deoxynucleotidyl transferase (TdT), to transduce environmental signals into DNA. TdT adds nucleotides to the 3'-ends of single-stranded DNA (ssDNA) in a template-independent manner, selecting bases according to inherent preferences and environmental conditions. By characterizing TdT nucleotide selectivity under different conditions, we show that TdT can encode various physiologically relevant signals such as Co2+, Ca2+, and Zn2+ concentrations and temperature changes in vitro. Further, by considering the average rate of nucleotide incorporation, we show that the resulting ssDNA functions as a molecular ticker tape. With this method we accurately encode a temporal record of fluctuations in Co2+ concentration to within 1 min over a 60 min period. Finally, we engineer TdT to allosterically turn off in the presence of a physiologically relevant concentration of calcium. We use this engineered TdT in concert with a reference TdT to develop a two-polymerase system capable of recording a single-step change in the Ca2+ signal to within 1 min over a 60 min period. This work expands the repertoire of DNA-based recording techniques by developing a novel DNA synthesis-based system that can record temporal environmental signals into DNA with a resolution of minutes.
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Affiliation(s)
- Namita Bhan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Mitolab, Cambridge, Massachusetts 02139, United States
| | - Alec Callisto
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Jonathan Strutz
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua Glaser
- Center for Theoretical Neuroscience, Columbia University, New York, New York 10027, United States
| | - Reza Kalhor
- Department of Biomedical Engineering, Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Edward S Boyden
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George Church
- Department of Biomedical Engineering, Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Konrad Kording
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
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9
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Li QS, Shu YG, Ou-Yang ZC, Li M. Kinetic assays of DNA polymerase fidelity: A theoretical perspective beyond Michaelis-Menten kinetics. Phys Rev E 2021; 104:014408. [PMID: 34412358 DOI: 10.1103/physreve.104.014408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 06/23/2021] [Indexed: 11/07/2022]
Abstract
The high fidelity of DNA polymerase (DNAP) is critical for the faithful replication of DNA. There are several quantitative approaches to measure DNAP fidelity. Directly counting the error frequency in the replication products gives the true fidelity but it turns out very hard to implement in practice. Two biochemical kinetic approaches, the steady-state assay and the transient-state assay, were then suggested and widely adopted. In these assays, the error frequency is indirectly estimated by using kinetic theories combined with the measured apparent kinetic rates. However, whether it is equivalent to the true fidelity has never been clarified theoretically, and in particular there are different strategies using these assays to quantify the proofreading efficiency of DNAP but often lead to inconsistent results. In this paper, we make a comprehensive examination on the theoretical foundation of the two kinetic assays, based on the theory of DNAP fidelity recently proposed by us. Our studies show that while the conventional kinetic assays are generally valid to quantify the discrimination efficiency of DNAP, they are valid to quantify the proofreading efficiency of DNAP only when the kinetic parameters satisfy some constraints which will be given explicitly in this paper. These results may inspire more carefully-designed experiments to quantify DNAP fidelity.
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Affiliation(s)
- Qiu-Shi Li
- School of Physical Science, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 101400, People's Republic of China
| | - Yao-Gen Shu
- Wenzhou Institute, University of Chinese Academy of Sciences, No 1, Jinlian Road, Longwan District, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Zhong-Can Ou-Yang
- Institute of Theoretical Physics, Chinese Academy of Sciences, Zhong Guan Cun East Street 55, P. O. Box 2735, Beijing 100190, People's Republic of China
| | - Ming Li
- School of Physical Science, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 101400, People's Republic of China
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Dual Deep Sequencing Improves the Accuracy of Low-Frequency Somatic Mutation Detection in Cancer Gene Panel Testing. Int J Mol Sci 2020; 21:ijms21103530. [PMID: 32429412 PMCID: PMC7278996 DOI: 10.3390/ijms21103530] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer gene panel testing requires accurate detection of somatic mosaic mutations, as the test sample consists of a mixture of cancer cells and normal cells; each minor clone in the tumor also has different somatic mutations. Several studies have shown that the different types of software used for variant calling for next generation sequencing (NGS) can detect low-frequency somatic mutations. However, the accuracy of these somatic variant callers is unknown. We performed cancer gene panel testing in duplicate experiments using three different high-fidelity DNA polymerases in pre-capture amplification steps and analyzed by three different variant callers, Strelka2, Mutect2, and LoFreq. We selected six somatic variants that were detected in both experiments with more than two polymerases and by at least one variant caller. Among them, five single nucleotide variants were verified by CEL nuclease-mediated heteroduplex incision with polyacrylamide gel electrophoresis and silver staining (CHIPS) and Sanger sequencing. In silico analysis indicated that the FBXW7 and MAP3K1 missense mutations cause damage at the protein level. Comparing three somatic variant callers, we found that Strelka2 detected more variants than Mutect2 and LoFreq. We conclude that dual sequencing with Strelka2 analysis is useful for detection of accurate somatic mutations in cancer gene panel testing.
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Abbasi I, Nasereddin A, Warburg A. Development of a next generation DNA sequencing-based multi detection assay for detecting and identifying Leishmania parasites, blood sources, plant meals and intestinal microbiome in phlebotomine sand flies. Acta Trop 2019; 199:105101. [PMID: 31361989 DOI: 10.1016/j.actatropica.2019.105101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 02/06/2023]
Abstract
Leishmaniasis is a disease caused by Leishmania parasites transmitted by phlebotomine sand flies (Diptera: Psychodidae). Human infections with different Leishmania species cause characteristic clinical manifestations; cutaneous or visceral leishmaniasis. Here we describe the development and application of a Miseq Next GenerationSequencing (NGS)-based Multi Detection Assay (MDA) designed to characterize metagenomics parameters pertinent to the sand fly vectors which may affect their vectorial capacity for Leishmania. For this purpose, we developed a MDA by which, DNA fragments were amplified through polymerase chain reactions (PCR) and then sequenced by MiSeq/NGS. PCR amplification was achieved using some published and some new primers designed specifically for identifying Leishmania spp. (ITS1), sand fly spp. (cytochrome oxidase I), vertebrate blood (Cytochrome b), plant DNA ribulose-1,5-bisphosphate carboxylase large subunit gene (rbcL), and prokaryotic micobiome (16 s rRNA). This MDA/NGS analysis was performed on two species of wild-caught sand flies that transmit different Leishmania spp. in two ecologically distinct, but geographically neighboring locations. The results were analyzed to identify, quantitate and correlate the measured parameters in order to assess their putative importance in the transmission dynamics of leishmaniasis.
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Affiliation(s)
- Ibrahim Abbasi
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada (IMRIC), The Kuvin Centre for the Study of Infectious and Tropical Diseases, The Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
| | - Abdelmajeed Nasereddin
- The Genomics Applications Laboratory, The Core Research Facility, The Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Alon Warburg
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada (IMRIC), The Kuvin Centre for the Study of Infectious and Tropical Diseases, The Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
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Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019; 17:561-569. [PMID: 31049166 PMCID: PMC6482431 DOI: 10.1016/j.csbj.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023] Open
Abstract
Deep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants. Variant calling, distinguishing between true mutations and experimental errors, is a central task of genomic analysis and often requires sophisticated statistical, computational, and/or heuristic techniques. Although variant callers seek to overcome noise inherent in biological experiments, variant calling can be significantly affected by outside factors including those used to prepare, store, and analyze samples. The goal of this review is to discuss known experimental features, such as sample preparation, library preparation, and sequencing, alongside diverse biological and clinical variables, and evaluate their effect on variant caller selection and optimization.
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Sen O, Saurin AT, Higgins JMG. The live cell DNA stain SiR-Hoechst induces DNA damage responses and impairs cell cycle progression. Sci Rep 2018; 8:7898. [PMID: 29785044 PMCID: PMC5962532 DOI: 10.1038/s41598-018-26307-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022] Open
Abstract
SiR-Hoechst (SiR-DNA) is a far-red fluorescent DNA probe being used widely for time-lapse imaging of living cells that is reported to be minimally toxic at concentrations as high as 10-25 µM. However, measuring nuclear import of Cyclin B1, inhibition of mitotic entry, and the induction of γH2AX foci in cultured human cells reveals that SiR-Hoechst induces DNA damage responses and G2 arrest at concentrations well below 1 µM. SiR-Hoechst is useful for live cell imaging, but it should be used with caution and at the lowest practicable concentration.
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Affiliation(s)
- Onur Sen
- Cell Division Biology Group, Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Adrian T Saurin
- Division of Cancer Research, School of Medicine, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Jonathan M G Higgins
- Cell Division Biology Group, Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
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