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Feng K, Costa J, Edwards JS. Next-generation sequencing library construction on a surface. BMC Genomics 2018; 19:416. [PMID: 29848309 PMCID: PMC5975494 DOI: 10.1186/s12864-018-4797-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/14/2018] [Indexed: 11/10/2022] Open
Abstract
Background Next-generation sequencing (NGS) has revolutionized almost all fields of biology, agriculture and medicine, and is widely utilized to analyse genetic variation. Over the past decade, the NGS pipeline has been steadily improved, and the entire process is currently relatively straightforward. However, NGS instrumentation still requires upfront library preparation, which can be a laborious process, requiring significant hands-on time. Herein, we present a simple but robust approach to streamline library preparation by utilizing surface bound transposases to construct DNA libraries directly on a flowcell surface. Results The surface bound transposases directly fragment genomic DNA while simultaneously attaching the library molecules to the flowcell. We sequenced and analysed a Drosophila genome library generated by this surface tagmentation approach, and we showed that our surface bound library quality was comparable to the quality of the library from a commercial kit. In addition to the time and cost savings, our approach does not require PCR amplification of the library, which eliminates potential problems associated with PCR duplicates. Conclusions We described the first study to construct libraries directly on a flowcell. We believe our technique could be incorporated into the existing Illumina sequencing pipeline to simplify the workflow, reduce costs, and improve data quality.
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Affiliation(s)
- Kuan Feng
- Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Justin Costa
- Special Projects, Centrillion Technologies, Palo Alto, CA, 94303, USA
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, 87131, USA. .,Internal Medicine, Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA. .,University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87131, USA. .,University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
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Chen Y, Li M, Islam I, You L, Wang Y, Li Z, Ling L, Zeng B, Xu J, Huang Y, Tan A. Allelic-specific expression in relation to Bombyx mori resistance to Bt toxin. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 54:53-60. [PMID: 25123097 DOI: 10.1016/j.ibmb.2014.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 06/03/2023]
Abstract
Understanding the mechanism of Bt resistance is one of the key elements of the effective application of Bt in pest control. The lepidopteran model insect, the silkworm, demonstrates qualities that make it an ideal species to use in achieving this understanding. We screened 45 strains of silkworm (Bombyx mori) using a Cry1Ab toxin variant. The sensitivity levels of the strains varied over a wide range. A resistant strain (P50) and a phylogenetically related susceptible strain (Dazao) were selected to profile the expressions of 12 Bt resistance-related genes. The SNPs in these genes were detected based on EST analysis and were validated by allelic-specific PCR. A comparison of allelic-specific expression between P50 and Dazao showed that the transcript levels of heterozygous genes containing two alleles rather than an imbalanced allelic expression contribute more to the resistance of P50 against Bt. The responses of the allelic-specific expression to Bt in hybrid larvae were then investigated. The results showed that the gene expression pattern of an ATP-binding cassette transporter C2 (ABCC2) and an aminopeptidase N (APN3), changed in an allelic-specific manner, with the increase of the resistant allele expression correlated with larval survival. The results suggest that a trans-regulatory mechanism in ABCC2 and APN3 allelic-specific expression is involved in the insect's response to the Bt toxin. The potential role of allelic-specific gene regulation in insect resistance to Bt toxins is discussed.
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Affiliation(s)
- Yazhou Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Muwang Li
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhengjiang 212018, Jiangsu, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhengjiang 212018, Jiangsu, China
| | - Iftakher Islam
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lang You
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yueqiang Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhiqian Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lin Ling
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Baosheng Zeng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Anjiang Tan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Ruegger PM, Bent E, Li W, Jeske DR, Cui X, Braun J, Jiang T, Borneman J. Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology. J Microbiol Methods 2012; 90:235-40. [PMID: 22640891 PMCID: PMC3404216 DOI: 10.1016/j.mimet.2012.05.013] [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: 03/20/2012] [Revised: 05/20/2012] [Accepted: 05/20/2012] [Indexed: 10/28/2022]
Abstract
Improvements to oligonucleotide fingerprinting of rRNA genes (OFRG) were obtained by implementing polony microarray technology. OFRG is an array-based method for analyzing microbial community composition. Polonies are discrete clusters of DNA, produced by solid-phase PCR in hydrogels, and derived from individual, spatially isolated DNA molecules. The advantages of a polony-based OFRG method include higher throughput and reductions in the PCR-induced errors and compositional skew inherent in all other PCR-based community composition methods, including high-throughput sequencing of rRNA genes. Given the similarities between polony microarrays and certain aspects of sequencing methods such as the Illumina platform, we suggest that if concepts presented in this study were implemented in high-throughput sequencing protocols, a reduction of PCR-induced errors and compositional skew may be realized.
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Affiliation(s)
- Paul M. Ruegger
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | - Elizabeth Bent
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | - Wei Li
- Department of Computer Science, University of California, Riverside, CA, USA
| | - Daniel R. Jeske
- Department of Statistics, University of California, Riverside, CA, USA
| | - Xinping Cui
- Department of Statistics, University of California, Riverside, CA, USA
| | - Jonathan Braun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, USA
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
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Atrazhev A, Manage DP, Stickel AJ, Crabtree HJ, Pilarski LM, Acker JP. In-gel technology for PCR genotyping and pathogen detection. Anal Chem 2011; 82:8079-87. [PMID: 20809605 DOI: 10.1021/ac1013157] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This work describes the use of polyacrylamide gel and PCR reagents photopolymerized in a mold to create an array of semisolid posts that serve as reaction vessels for parallel PCR amplification of an externally added template. DNA amplification occurred in a cylindrical, self-standing 9 × 9 array of gel posts each less than 1 μL in volume. Photopolymerization of the gel with an intercalating dye added prior to polymerization permitted acquisition of real-time PCR data and melting curve analysis data without the need for any type of post-PCR staining procedures. PCR was equally efficient and reproducible when template DNA was polymerized within the gel or when exogenous template was added atop precast gel posts. PCR amplification occurred with template from purified DNA or from raw urine of patients with BK viruria. Multiple primer sets can be utilized per gel post array with no detectable cross contamination. As few as 34 BK virus templates were consistently detected by PCR in an individual gel post. Amplification of HPA1 and FGFR2 genes in human genomic DNA (gDNA) required as little as 2-5 ng of gDNA template/gel post. The device prototype includes a Peltier element for PCR thermal cycling and a CCD camera to capture fluorescence for product detection. Our technology is amenable to integration in point of care microdevices.
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Affiliation(s)
- Alexey Atrazhev
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
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Chetverina EV, Chetverin AB. Nanocolonies and diagnostics of oncological diseases associated with chromosomal translocations. BIOCHEMISTRY (MOSCOW) 2011; 75:1667-91. [DOI: 10.1134/s0006297910130109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Zhang C, Xing D. Single-Molecule DNA Amplification and Analysis Using Microfluidics. Chem Rev 2010; 110:4910-47. [DOI: 10.1021/cr900081z] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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7
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Chetverina HV, Chetverin AB. Nanocolonies: Detection, cloning, and analysis of individual molecules. BIOCHEMISTRY (MOSCOW) 2009; 73:1361-87. [DOI: 10.1134/s0006297908130014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, Huntley JJ, Luo S, Zhang L, van Velkinburgh JC, Farmer AD, Lewis S, Beavis WD, Schilkey FD, Virk SM, Black CF, Myers MK, Mader LC, Langley RJ, Utsey JP, Kim RW, Roberts RC, Khalsa SK, Garcia M, Ambriz-Griffith V, Harlan R, Czika W, Martin S, Wolfinger RD, Perrone-Bizzozero NI, Schroth GP, Kingsmore SF. Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One 2008; 3:e3625. [PMID: 18985160 PMCID: PMC2576459 DOI: 10.1371/journal.pone.0003625] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 10/10/2008] [Indexed: 02/06/2023] Open
Abstract
Schizophrenia (SCZ) is a common, disabling mental illness with high heritability but complex, poorly understood genetic etiology. As the first phase of a genomic convergence analysis of SCZ, we generated 16.7 billion nucleotides of short read, shotgun sequences of cDNA from post-mortem cerebellar cortices of 14 patients and six, matched controls. A rigorous analysis pipeline was developed for analysis of digital gene expression studies. Sequences aligned to approximately 33,200 transcripts in each sample, with average coverage of 450 reads per gene. Following adjustments for confounding clinical, sample and experimental sources of variation, 215 genes differed significantly in expression between cases and controls. Golgi apparatus, vesicular transport, membrane association, Zinc binding and regulation of transcription were over-represented among differentially expressed genes. Twenty three genes with altered expression and involvement in presynaptic vesicular transport, Golgi function and GABAergic neurotransmission define a unifying molecular hypothesis for dysfunction in cerebellar cortex in SCZ.
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Affiliation(s)
- Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Neil A. Miller
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | | | - Ingrid E. Lindquist
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Gregory D. May
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Jim J. Huntley
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Shujun Luo
- Illumina Inc., Hayward, California, United States of America
| | - Lu Zhang
- Illumina Inc., Hayward, California, United States of America
| | | | - Andrew D. Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Sharon Lewis
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - William D. Beavis
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Faye D. Schilkey
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Selene M. Virk
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - C. Forrest Black
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - M. Kathy Myers
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Lar C. Mader
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Ray J. Langley
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - John P. Utsey
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Ryan W. Kim
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Rosalinda C. Roberts
- Department of Psychiatry, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Sat Kirpal Khalsa
- Northern New Mexico College, Española, New Mexico, United States of America
| | - Meredith Garcia
- Northern New Mexico College, Española, New Mexico, United States of America
| | | | - Richard Harlan
- Northern New Mexico College, Española, New Mexico, United States of America
| | - Wendy Czika
- SAS Institute, Cary, North Carolina, United States of America
| | - Stanton Martin
- SAS Institute, Cary, North Carolina, United States of America
| | | | - Nora I. Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Gary P. Schroth
- Illumina Inc., Hayward, California, United States of America
| | - Stephen F. Kingsmore
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
- * E-mail:
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Chetverin AB, Chetverina HV. Molecular Colony Technique: A New Tool for Biomedical Research and Clinical Practice. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2008; 82:219-55. [DOI: 10.1016/s0079-6603(08)00007-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Cai F, Chen H, Hicks CB, Bartlett JA, Zhu J, Gao F. Detection of minor drug-resistant populations by parallel allele-specific sequencing. Nat Methods 2007; 4:123-5. [PMID: 17206150 DOI: 10.1038/nmeth995] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 11/09/2006] [Indexed: 01/06/2023]
Abstract
We developed a highly sensitive parallel allele-specific sequencing (PASS) assay to simultaneously analyze a large number of viral genomes and detect minor drug-resistant populations at approximately 0.1-0.01% levels. Using this assay on samples from individuals infected with human immunodeficiency viruses (HIV), we successfully detected and quantified minor populations of drug-resistant viruses and performed linkage analysis of multiple-drug resistance mutations. This assay may serve as a useful tool to study drug resistance in HIV and other infectious agents.
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Affiliation(s)
- Fangping Cai
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
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12
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Fredlake CP, Hert DG, Mardis ER, Barron AE. What is the future of electrophoresis in large-scale genomic sequencing? Electrophoresis 2006; 27:3689-702. [PMID: 17031784 DOI: 10.1002/elps.200600408] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.
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Affiliation(s)
- Christopher P Fredlake
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
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Bray NJ, O'Donovan MC. Investigating cis-acting regulatory variation using assays of relative allelic expression. Psychiatr Genet 2006; 16:173-7. [PMID: 16829785 DOI: 10.1097/01.ypg.0000218612.35139.84] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Assays of relative allelic expression offer a powerful means of exploring the influence of cis-acting regulatory variation. In this article, we provide a general assay protocol and discuss practical and theoretical considerations for the design and interpretation of relative allelic expression analysis.
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Affiliation(s)
- Nicholas J Bray
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK.
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Abstract
Conventional and real time polymerase chain reaction-based tests have been developed for the diagnosis of anthelmintic resistance (AR) in populations of several small and large ruminant as well as horse gastro-intestinal nematode species. To date, molecular markers that correlate well with AR are available only for the detection of benzimidazole resistance. Recently, however, a single nucleotide polymorphism was found in vitro to be of functional relevance for reduced drug efficacy to macrocylic lactones. The focus of the present review, therefore, is the molecular mechanism of action of these two drug classes and potential applications of this knowledge to the diagnosis of AR. It is argued that a prerequisite for future molecular diagnosis will be tests providing reliable and exact quantification of resistance related alleles in DNA extracted from representative pools of parasites.
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Samatov TR, Chetverina HV, Chetverin AB. Expressible molecular colonies. Nucleic Acids Res 2005; 33:e145. [PMID: 16204448 PMCID: PMC1243806 DOI: 10.1093/nar/gni153] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Revised: 09/19/2005] [Accepted: 09/19/2005] [Indexed: 12/19/2022] Open
Abstract
Carrying out polymerase chain reaction in a gel layer generates a 2-D pattern of DNA colonies comprising pure genetic clones. Here we demonstrate that transcription, translation and protein folding can be performed in the same gel. The resulting nucleoprotein colonies mimic living cells by serving as compartments in which the synthesized RNAs and proteins co-localize with their templates. Yet, due to the absence of penetration barriers, such a molecular colony display allows cloned genes to be directly tested for the encoded functions. Now, the results imply that virtually any manipulations with genes and their expression products can be accomplished in vitro.
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Affiliation(s)
- Timur R. Samatov
- Institute of Protein Research, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
| | - Helena V. Chetverina
- Institute of Protein Research, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
| | - Alexander B. Chetverin
- Institute of Protein Research, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
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Merritt J, Butz JA, Ogunnaike BA, Edwards JS. Parallel analysis of mutant human glucose 6-phosphate dehydrogenase in yeast using PCR colonies. Biotechnol Bioeng 2005; 92:519-31. [PMID: 16193512 DOI: 10.1002/bit.20726] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We demonstrate a highly parallel strategy to analyze the impact of single nucleotide mutations on protein function. Using our method, it is possible to screen a population and quickly identify a subset of functionally interesting mutants. Our method utilizes a combination of yeast functional complementation, growth competition of mutant pools, and polymerase colonies. A defined mutant human glucose-6-phosphate-dehydrogenase library was constructed which contains all possible single nucleotide missense mutations in the eight-residue glucose-6-phosphate binding peptide of the enzyme. Mutant human enzymes were expressed in a zwf1 (gene encoding yeast homologue) deletion strain of Saccharomyces cerevisiae. Growth rates of the 54 mutant strains arising from this library were measured in parallel in conditions selective for active hG6PD. Several residues were identified which tolerated no mutations (Asp200, His201 and Lys205) and two (Ile199 and Leu203) tolerated several substitutions. Arg198, Tyr202, and Gly204 tolerated only 1-2 specific substitutions. Generalizing from the positions of tolerated and non-tolerated amino acid substitutions, hypotheses were generated about the functional role of specific residues, which could, potentially, be tested using higher resolution/lower throughput methods.
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Affiliation(s)
- Joshua Merritt
- Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
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Ding C, Maier E, Roscher AA, Braun A, Cantor CR. Simultaneous quantitative and allele-specific expression analysis with real competitive PCR. BMC Genet 2004; 5:8. [PMID: 15128429 PMCID: PMC411033 DOI: 10.1186/1471-2156-5-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Accepted: 05/05/2004] [Indexed: 11/17/2022] Open
Abstract
Background For a diploid organism such as human, the two alleles of a particular gene can be expressed at different levels due to X chromosome inactivation, gene imprinting, different local promoter activity, or mRNA stability. Recently, imbalanced allelic expression was found to be common in human and can follow Mendelian inheritance. Here we present a method that employs real competitive PCR for allele-specific expression analysis. Results A transcribed mutation such as a single nucleotide polymorphism (SNP) is used as the marker for allele-specific expression analysis. A synthetic mutation created in the competitor is close to a natural mutation site in the cDNA sequence. PCR is used to amplify the two cDNA sequences from the two alleles and the competitor. A base extension reaction with a mixture of ddNTPs/dNTP is used to generate three oligonucleotides for the two cDNAs and the competitor. The three products are identified and their ratios are calculated based on their peak areas in the MALDI-TOF mass spectrum. Several examples are given to illustrate how allele-specific gene expression can be applied in different biological studies. Conclusions This technique can quantify the absolute expression level of each individual allele of a gene with high precision and throughput.
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Affiliation(s)
- Chunming Ding
- Bioinformatics Program and Center for Advanced Biotechnology, Boston University, Boston, MA 02215 USA
| | - Esther Maier
- Children's Hospital, University of Munich, Lindwurmstrasse 4, 80337 Munich, Germany
| | - Adelbert A Roscher
- Children's Hospital, University of Munich, Lindwurmstrasse 4, 80337 Munich, Germany
| | | | - Charles R Cantor
- Bioinformatics Program and Center for Advanced Biotechnology, Boston University, Boston, MA 02215 USA
- SEQUENOM, Inc., San Diego, CA 92121 USA
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