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Herrmann MG, Durtschi JD, Wittwer CT, Voelkerding KV. Expanded Instrument Comparison of Amplicon DNA Melting Analysis for Mutation Scanning and Genotyping. Clin Chem 2020; 53:1544-8. [PMID: 17556647 DOI: 10.1373/clinchem.2007.088120] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Additional instruments have become available since instruments for DNA melting analysis of PCR products for genotyping and mutation scanning were compared. We assessed the performance of these new instruments for genotyping and scanning for mutations.
Methods: A 110-bp fragment of the β-globin gene including the sickle cell anemia locus (HBB c. 20A>T) was amplified by PCR in the presence of LCGreen Plus or SYBR Green I. Amplicons of 4 different genotypes [wild-type, homozygous, and heterozygous HBB c. 20A>T and double-heterozygote HBB c. (9C>T; 20A>T)] were melted on 7 different instruments [Applied Biosystems 7300, Corbett Life Sciences Rotor-Gene 6500HRM, Eppendorf Mastercycler RealPlex4S, Idaho Technology LightScanner (384 well), Roche LightCycler 480 (96 and 384 well) and Stratagene Mx3005p] at a rate of 0.61 °C/s or when this was not possible, at 0.50 °C steps. We evaluated the ability of each instrument to genotype by melting temperature (Tm) and to scan for heterozygotes by curve shape.
Results: The ability of most instruments to accurately genotype single-base changes by amplicon melting was limited by spatial temperature variation across the plate (SD of Tm = 0.020 to 0.264 °C). Other variables such as data density, signal-to-noise ratio, and melting rate also affected heterozygote scanning.
Conclusions: Different instruments vary widely in their ability to genotype homozygous variants and scan for heterozygotes by whole amplicon melting analysis. Instruments specifically designed for high-resolution melting, however, displayed the least variation, suggesting better genotyping accuracy and scanning sensitivity and specificity.
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Affiliation(s)
- Mark G Herrmann
- Institute for Clinical and Experimental Pathology, ARUP, Salt Lake City, UT 84108, USA.
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Elsayed Metawlly D, Noby Amer A, Mostafa Mostafa H, El Din Elsawaf G, Abd El Kader O. Low cost detection of hepatitis C virus RNA in HCV infected patients by SYBR Green I real-time PCR. ALEXANDRIA JOURNAL OF MEDICINE 2019. [DOI: 10.1016/j.ajme.2017.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
| | - Ahmed Noby Amer
- Department of Microbiology, Faculty of Pharmacy, University of Pharos, Egypt
| | - Hanan Mostafa Mostafa
- Department of Internal Medicine, Medical Research Institute, Alexandria University, Egypt
| | - Gamal El Din Elsawaf
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Ola Abd El Kader
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
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Grandi N, Tramontano E. Type W Human Endogenous Retrovirus (HERV-W) Integrations and Their Mobilization by L1 Machinery: Contribution to the Human Transcriptome and Impact on the Host Physiopathology. Viruses 2017; 9:v9070162. [PMID: 28653997 PMCID: PMC5537654 DOI: 10.3390/v9070162] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/08/2017] [Accepted: 06/20/2017] [Indexed: 01/07/2023] Open
Abstract
Human Endogenous Retroviruses (HERVs) are ancient infection relics constituting ~8% of our DNA. While HERVs’ genomic characterization is still ongoing, impressive amounts of data have been obtained regarding their general expression across tissues. Among HERVs, one of the most studied is the W group, which is the sole HERV group specifically mobilized by the long interspersed element-1 (LINE-1) machinery, providing a source of novel insertions by retrotransposition of HERV-W processed pseudogenes, and comprising a member encoding a functional envelope protein coopted for human placentation. The HERV-W group has been intensively investigated for its putative role in several diseases, such as cancer, inflammation, and autoimmunity. Despite major interest in the link between HERV-W expression and human pathogenesis, no conclusive correlation has been demonstrated so far. In general, (i) the absence of a proper identification of the specific HERV-W sequences expressed in a given condition; and (ii) the lack of studies attempting to connect the various observations in the same experimental conditions are the major problems preventing the definitive assessment of the HERV-W impact on human physiopathology. In this review, we summarize the current knowledge on the HERV-W group presence within the human genome and its expression in physiological tissues as well as in the main pathological contexts.
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Affiliation(s)
- Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SS554, 09042 Monserrato, Cagliari, Italy.
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SS554, 09042 Monserrato, Cagliari, Italy.
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Cagliari, Italy.
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Otto S, Scholz N, Behnke T, Resch-Genger U, Heinze K. Thermo-Chromium: A Contactless Optical Molecular Thermometer. Chemistry 2017; 23:12131-12135. [DOI: 10.1002/chem.201701726] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Sven Otto
- Institute of Inorganic Chemistry and Analytical Chemistry; Johannes Gutenberg-University of Mainz; Duesbergweg 10-14 55128 Mainz Germany
- Graduate School Materials Science in Mainz; Staudingerweg 9 55128 Mainz Germany
| | - Norman Scholz
- Division 1.10; Federal Institute for Materials Research and Testing (BAM); Richard-Willstätter-Strasse 11 12489 Berlin Germany
| | - Thomas Behnke
- Division 1.10; Federal Institute for Materials Research and Testing (BAM); Richard-Willstätter-Strasse 11 12489 Berlin Germany
| | - Ute Resch-Genger
- Division 1.10; Federal Institute for Materials Research and Testing (BAM); Richard-Willstätter-Strasse 11 12489 Berlin Germany
| | - Katja Heinze
- Institute of Inorganic Chemistry and Analytical Chemistry; Johannes Gutenberg-University of Mainz; Duesbergweg 10-14 55128 Mainz Germany
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Fidan Z, Wende A, Resch-Genger U. Visible and red emissive molecular beacons for optical temperature measurements and quality control in diagnostic assays utilizing temperature-dependent amplification reactions. Anal Bioanal Chem 2016; 409:1519-1529. [DOI: 10.1007/s00216-016-0088-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/31/2016] [Accepted: 11/07/2016] [Indexed: 12/11/2022]
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6
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Li F, Karlsson H. Expression and regulation of human endogenous retrovirus W elements. APMIS 2016; 124:52-66. [PMID: 26818262 DOI: 10.1111/apm.12478] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 10/12/2015] [Indexed: 01/06/2023]
Abstract
Human endogenous retroviruses (HERV) comprise 8% of the human genome and can be classified into at least 31 families. A typical HERV provirus consists of internal gag, pol and env genes, flanked by two long terminal repeats (LTRs). No single provirus is capable of engendering infectious particles. HERV are by nature repetitive and have with few notable exceptions lost their protein-coding capacity. Therefore, HERV have consistently been excluded from array-based expression studies and hence little is known of their expression, regulation, and potential functional significance. An increasing number of studies have, however, observed expression of the W family of HERV in various human tissues and cells, predominantly in placenta. HERV-W LTRs act as promoters in directing transcription of HERV-W members, contribute to their tissue-specific and highly diversified expression pattern. Furthermore, leaky transcription originating from adjacent genes plays a role in the transcription initiation of HERV-W psudoelements. It has been reported that HERV-W elements, including ERVWE1 (the so far only known HERV-W locus harboring a gene (env) functionally adopted by the human host to critically participate in placenta biogenesis), can become transactivated in a range of human non-placental cell-lines during exogenous virus infections. Aberrant expression of HERV-W has been associated with human diseases, such as cancer, multiple sclerosis, and schizophrenia. Based on published reports, transcriptional activities of HERV-W appear to be influenced by several mechanisms; binding of transcription factors to LTR promoters and enhancers outside of LTRs, genetic variation and alteration in DNA methylation and histone modification. Emerging mechanistic studies support the notion that HERV-W represents a potential marker or mediator of environmental exposures (e.g., virus infection) in the development of chronic complex diseases.
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Affiliation(s)
- Fang Li
- Department of Basic Medical Science, Changsha Medical University, Changsha, China.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Håkan Karlsson
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Transcriptional derepression of the ERVWE1 locus following influenza A virus infection. J Virol 2014; 88:4328-37. [PMID: 24478419 DOI: 10.1128/jvi.03628-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Syncytin-1, a fusogenic protein encoded by a human endogenous retrovirus of the W family (HERV-W) element (ERVWE1), is expressed in the syncytiotrophoblast layer of the placenta. This locus is transcriptionally repressed in adult tissues through promoter CpG methylation and suppressive histone modifications. Whereas syncytin-1 appears to be crucial for the development and functioning of the human placenta, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. We previously reported on the transactivation of HERV-W elements, including ERVWE1, during influenza A/WSN/33 virus infection in a range of human cell lines. Here we report the results of quantitative PCR analyses of transcripts encoding syncytin-1 in both cell lines and primary fibroblast cells. We observed that spliced ERVWE1 transcripts and those encoding the transcription factor glial cells missing 1 (GCM1), acting as an enhancer element upstream of ERVWE1, are prominently upregulated in response to influenza A/WSN/33 virus infection in nonplacental cells. Knockdown of GCM1 by small interfering RNA followed by infection suppressed the transactivation of ERVWE1. While the infection had no influence on CpG methylation in the ERVWE1 promoter, chromatin immunoprecipitation assays detected decreased H3K9 trimethylation (H3K9me3) and histone methyltransferase SETDB1 levels along with influenza virus proteins associated with ERVWE1 and other HERV-W loci in infected CCF-STTG1 cells. The present findings suggest that an exogenous influenza virus infection can transactivate ERVWE1 by increasing transcription of GCM1 and reducing H3K9me3 in this region and in other regions harboring HERV-W elements. IMPORTANCE Syncytin-1, a protein encoded by the env gene in the HERV-W locus ERVWE1, appears to be crucial for the development and functioning of the human placenta and is transcriptionally repressed in nonplacental tissues. Nevertheless, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. In the present paper, we report findings suggesting that an exogenous influenza A virus infection can transactivate ERVWE1 by increasing the transcription of GCM1 and reducing the repressive histone mark H3K9me3 in this region and in other regions harboring HERV-W elements. These observations have implications of potential relevance for viral pathogenesis and for conditions associated with the aberrant transcription of HERV-W loci.
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You Y, Tataurov AV, Owczarzy R. Measuring thermodynamic details of DNA hybridization using fluorescence. Biopolymers 2011; 95:472-86. [PMID: 21384337 PMCID: PMC3082624 DOI: 10.1002/bip.21615] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 01/31/2011] [Accepted: 02/21/2011] [Indexed: 11/11/2022]
Abstract
Modern real-time PCR systems make it easy to monitor fluorescence while temperature is varied for hundreds of samples in parallel, permitting high-throughput studies. We employed such system to investigate melting transitions of ordered nucleic acid structures into disordered random coils. Fluorescent dye and quencher were attached to oligonucleotides in such a way that changes of fluorescence intensity with temperature indicated progression of denaturation. When fluorescence melting data were compared with traditional ultraviolet optical experiments, commonly used dye/quencher combinations, like fluorescein and tetramethylrhodamine, showed substantial discrepancies. We have therefore screened 22 commercially available fluorophores and quenchers for their ability to reliably report annealing and melting transitions. Dependence of fluorescence on temperature and pH was also investigated. The optimal performance was observed using Texas Red or ROX dyes with Iowa Black RQ or Black Hole quenchers. These labels did not alter two-state nature of duplex melting process and provided accurate melting temperatures, free energies, enthalpies, and entropies. We also suggest a new strategy for determination of DNA duplex thermodynamics where concentration of a dye-labeled strand is kept constant and its complementary strand modified with a quencher is added at increasing excess. These methodological improvements will help build predictive models of nucleic acid hybridization. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 472–486, 2011.
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Affiliation(s)
- Yong You
- Department of Molecular Genetics and Biophysics, Integrated DNA Technologies, Coralville, IA, USA
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Li F, Nellåker C, Yolken RH, Karlsson H. A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation. BMC Genomics 2011; 12:22. [PMID: 21226900 PMCID: PMC3031232 DOI: 10.1186/1471-2164-12-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 01/12/2011] [Indexed: 12/19/2022] Open
Abstract
Background One member of the W family of human endogenous retroviruses (HERV) appears to have been functionally adopted by the human host. Nevertheless, a highly diversified and regulated transcription from a range of HERV-W elements has been observed in human tissues and cells. Aberrant expression of members of this family has also been associated with human disease such as multiple sclerosis (MS) and schizophrenia. It is not known whether this broad expression of HERV-W elements represents transcriptional leakage or specific transcription initiated from the retroviral promoter in the long terminal repeat (LTR) region. Therefore, potential influences of genomic context, structure and orientation on the expression levels of individual HERV-W elements in normal human tissues were systematically investigated. Results Whereas intronic HERV-W elements with a pseudogene structure exhibited a strong anti-sense orientation bias, intronic elements with a proviral structure and solo LTRs did not. Although a highly variable expression across tissues and elements was observed, systematic effects of context, structure and orientation were also observed. Elements located in intronic regions appeared to be expressed at higher levels than elements located in intergenic regions. Intronic elements with proviral structures were expressed at higher levels than those elements bearing hallmarks of processed pseudogenes or solo LTRs. Relative to their corresponding genes, intronic elements integrated on the sense strand appeared to be transcribed at higher levels than those integrated on the anti-sense strand. Moreover, the expression of proviral elements appeared to be independent from that of their corresponding genes. Conclusions Intronic HERV-W provirus integrations on the sense strand appear to have elicited a weaker negative selection than pseudogene integrations of transcripts from such elements. Our current findings suggest that the previously observed diversified and tissue-specific expression of elements in the HERV-W family is the result of both directed transcription (involving both the LTR and internal sequence) and leaky transcription of HERV-W elements in normal human tissues.
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Affiliation(s)
- Fang Li
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Nellåker C, Li F, Uhrzander F, Tyrcha J, Karlsson H. Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues. BMC Genomics 2009; 10:532. [PMID: 19919688 PMCID: PMC2779825 DOI: 10.1186/1471-2164-10-532] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 11/17/2009] [Indexed: 01/12/2023] Open
Abstract
Background Human endogenous retroviruses (HERV) constitute approximately 8% of the human genome and have long been considered "junk". The sheer number and repetitive nature of these elements make studies of their expression methodologically challenging. Hence, little is known of transcription of genomic regions harboring such elements. Results Applying a recently developed technique for obtaining high resolution melting temperature data, we examined the frequency distributions of HERV-W gag element into 13 Tm categories in human tissues. Transcripts containing HERV-W gag sequences were expressed in non-random patterns with extensive variations in the expression between both tissues, including different brain regions, and individuals. Furthermore, the patterns of such transcripts varied more between individuals in brain regions than other tissues. Conclusion Thus, regulated expression of non-coding regions of the human genome appears to include the HERV-W family of repetitive elements. Although it remains to be established whether such expression patterns represent leakage from transcription of functional regions or specific transcription, the current approach proves itself useful for studying detailed expression patterns of repetitive regions.
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Affiliation(s)
- Christoffer Nellåker
- Department of Neuroscience, Karolinska Institutet, Retzius Väg 8 B2:5, 17177 Stockholm, Sweden.
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Barilero T, Le Saux T, Gosse C, Jullien L. Fluorescent Thermometers for Dual-Emission-Wavelength Measurements: Molecular Engineering and Application to Thermal Imaging in a Microsystem. Anal Chem 2009; 81:7988-8000. [DOI: 10.1021/ac901027f] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- T. Barilero
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS-ENS-UPMC Paris 6 8640 Pasteur, 24, Rue Lhomond, 75005 Paris, France, and Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Route de Nozay, 91460 Marcoussis, France
| | - T. Le Saux
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS-ENS-UPMC Paris 6 8640 Pasteur, 24, Rue Lhomond, 75005 Paris, France, and Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Route de Nozay, 91460 Marcoussis, France
| | - C. Gosse
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS-ENS-UPMC Paris 6 8640 Pasteur, 24, Rue Lhomond, 75005 Paris, France, and Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Route de Nozay, 91460 Marcoussis, France
| | - L. Jullien
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS-ENS-UPMC Paris 6 8640 Pasteur, 24, Rue Lhomond, 75005 Paris, France, and Laboratoire de Photonique et de Nanostructures, LPN-CNRS, Route de Nozay, 91460 Marcoussis, France
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Nellåker C, Uhrzander F, Tyrcha J, Karlsson H. Mixture models for analysis of melting temperature data. BMC Bioinformatics 2008; 9:370. [PMID: 18786251 PMCID: PMC2567994 DOI: 10.1186/1471-2105-9-370] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 09/11/2008] [Indexed: 11/10/2022] Open
Abstract
Background In addition to their use in detecting undesired real-time PCR products, melting temperatures are useful for detecting variations in the desired target sequences. Methodological improvements in recent years allow the generation of high-resolution melting-temperature (Tm) data. However, there is currently no convention on how to statistically analyze such high-resolution Tm data. Results Mixture model analysis was applied to Tm data. Models were selected based on Akaike's information criterion. Mixture model analysis correctly identified categories in Tm data obtained for known plasmid targets. Using simulated data, we investigated the number of observations required for model construction. The precision of the reported mixing proportions from data fitted to a preconstructed model was also evaluated. Conclusion Mixture model analysis of Tm data allows the minimum number of different sequences in a set of amplicons and their relative frequencies to be determined. This approach allows Tm data to be analyzed, classified, and compared in an unbiased manner.
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Affiliation(s)
- Christoffer Nellåker
- Department of Neuroscience, Karolinska Institutet, Retzius Väg, Stockholm, Sweden.
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Gundry CN, Dobrowolski SF, Martin YR, Robbins TC, Nay LM, Boyd N, Coyne T, Wall MD, Wittwer CT, Teng DHF. Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons. Nucleic Acids Res 2008; 36:3401-8. [PMID: 18448472 PMCID: PMC2425497 DOI: 10.1093/nar/gkn204] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genotyping by high-resolution melting analysis of small amplicons is homogeneous and simple. However, this approach can be limited by physical and chemical components of the system that contribute to intersample melting variation. It is challenging for this method to distinguish homozygous G::C from C::G or A::T from T::A base-pair neutral variants, which comprise ∼16% of all human single nucleotide polymorphisms (SNPs). We used internal oligonucleotide calibrators and custom analysis software to improve small amplicon (42–86 bp) genotyping on the LightScanner®. Three G/C (PAH c.1155C>G, CHK2 c.1-3850G>C and candidate gene BX647987 c.261+22,290C>G) and three T/A (CPS1 c.3405-29A>T, OTC c.299-8T>A and MSH2 c.1511-9A>T) human single nucleotide variants were analyzed. Calibration improved homozygote genotyping accuracy from 91.7 to 99.7% across 1105 amplicons from 141 samples for five of the six targets. The average Tm standard deviations of these targets decreased from 0.067°C before calibration to 0.022°C after calibration. We were unable to generate a small amplicon that could discriminate the BX647987 c.261+22,290C>G (rs1869458) SNP, despite reducing standard deviations from 0.086°C to 0.032°C. Two of the sites contained symmetric nearest neighbors adjacent to the SNPs. Unexpectedly, we were able to distinguish these homozygotes by Tm even though current nearest neighbor models predict that the two homozygous alleles would be identical.
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Affiliation(s)
- Cameron N Gundry
- Idaho Technology Inc., 390 Wakara Way and Department of Pathology, University of Utah School of Medicine, 50 North Medical Drive 5B426, Salt Lake City, Utah 84108, USA
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