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High-resolution melting for accurate assessment of DNA methylation.

Methylation of cytosine in DNA is an epigenetic mark that is important for genome stability, transcriptional regulation of endogenous genes, and permanent silencing of transposable elements and viral sequences. Methylcytosine, sometimes referred to as the 5th base of DNA, constitutes 3%-6% of all cytosines in the human genome and occurs almost exclusively within the context of CpG dinucleotides (1). DNA methylation patterns have been shown to correlate with various disease states, including inherited disorders and cancer, and the identification of aberrantly methylated genes is a promising strategy in research, diagnostics, and therapeutics (2). In the current issue of Clinical Chemistry, White et al. (3) report a simple closed-tube PCR assay that combines amplification of bisulfite-treated DNA with high-resolution amplicon melting for sensitive and high-throughput assessment of DNA methylation.

One major problem inherent in gene-specific DNA methylation analysis is that methylation marks are erased during conventional PCR and cloning procedures because methylcytosine is replaced with cytosine. To circumvent this problem, DNA can be treated with sodium bisulfite, which converts unmethylated cytosines to uracil, whereas methylcytosine is protected against this modification (4). The bisulfite-modified DNA can be used as template in a standard PCR to amplify specific DNA sequences and examine their methylation content. The most accurate methylation profiling can be achieved by sequence analysis of the PCR products, which display methylcytosine as cytosine and unmethylated cytosine as thymine (4). High-resolution mapping of individual CpG sites by bisulfite genomic sequencing may still be technically challenging and labor-intensive, however, and may not always be the most rational approach to methylation analysis. A large number of simpler PCR-based assays have been developed that use bisulfite-converted DNA as a template and provide information on DNA methylation with varying sensitivity, specificity, and extent of detection (5, 6). One of these assays, methylation-specific melting curve analysis, was first described by Worm et al. (7) in 2001 and has now been further developed on a high-resolution melting platform by White et al. (3). The principle of this method is that PCR products generated from bisulfite-treated DNA templates with different contents of methylcytosine show differences in melting temperature ([T.sub.m]), which can be resolved by melting analysis in a thermal cycler coupled with a fluorometer (7-9).

DNA melting is the cooperative unwinding of the double-helical structure into single-stranded random coils. The [T.sub.m] of a DNA molecule can be determined by gradual heating of the DNA in aqueous solution, and it is highly dependent on the nucleotide sequence; a single-base substitution may change the [T.sub.m] of a PCR product by up to 1 [degrees]C, depending on the length of the amplified sequence and the type of substitution. In melting experiments dating back 25 years, single-base mutations were detected in a spectrophotometer by monitoring ultraviolet absorbance of DNA solutions near or at 260 nm while slowly increasing the temperature (10). Now, a new generation of PCR cyclers has paved the way for successful high-throughput, in-tube melting analysis. Inclusion in the reaction of a PCR-compatible fluorescent dye that specifically binds to double-stranded DNA allows the melting properties of a PCR product to be examined immediately after amplification (11). During a linear temperature transition, an abrupt decrease in fluorescence reflects the cooperative melting of the PCR product. This feature was introduced as a simple means to distinguish between specific and nonspecific PCR products, but detection of single-base substitutions has now become possible with the use of instruments specifically designed for high-resolution melting in combination with special saturation dyes (12).

Resolution of DNA methylation by melting analysis relies on the fact that the [T.sub.m] of a PCR product generated from bisulfite-treated DNA reflects the methylation status of the original DNA template (8). Because unmethylated cytosines will be converted into uracil during bisulfite treatment and subsequently amplified as thymine, whereas methylcytosines will remain as methylcytosine and be amplified as cytosine, the methylated sequence will have a higher G:C content, and hence a higher [T.sub.m], than the corresponding unmethylated sequence. After amplification with primers that will not differentiate between methylated and unmethylated molecules, the melting properties of the PCR products can be examined in the thermal cycler by slowly elevating the temperature under continuous or step-wise fluorescence acquisition. The melting curves or derived melting peaks provide a profile of the methylation status of the entire pool of DNA molecules in the sample (7, 8).

White et al. (3) have established a simple diagnostic assay for Prader-Willi syndrome and Angelman syndrome. Both syndromes are neurodevelopmental disorders caused by genomic abnormalities at an imprinted region on chromosome 15g11.2, leading to methylation changes at the small nuclear ribonucleoprotein polypeptide N (SNRPN) locus (13). After bisulfite conversion of DNA, an approximately 240-bp sequence of the SNRPN promoter containing 21 CpG sites was amplified and subjected to high-resolution melting. Melting curves and difference plots clearly showed a biphasic melting profile for samples from healthy individuals, representing the unmethylated and methylated SNRPN alleles. In contrast, samples from individuals with Angelman syndrome showed a monophasic low-melting profile consistent with an unmethylated SNRPN promoter, and samples from individuals with Prader-Willi syndrome showed a monophasic high-melting profile consistent with a hyper-methylated SNRPN promoter. Use of the automated genotyping facility of the thermal cycler resulted in correct typing of 97.6% of the 165 test samples, and the methylation data were consistent with data obtained with methylation-specific PCR (14). The high-resolution melting assay was even efficient in detecting mosaicism at the SNRPN promoter (3).

The report by White et al. (3) and a recent report by Wojdacz and Dobrovic (15) clearly illustrate the great potential of melting analysis for sensitive and high-throughput assessment of DNA methylation in inherited disorders and cancer. Compared with current gel-based assays (6), melting analysis has the important advantage of the closed-tube format, which simplifies the procedure, decreases the risk of PCR contamination, and decreases analysis time. In addition, melting analysis resolves heterogeneous methylation, detects methylated and unmethylated alleles in the same reaction, and requires only standard, inexpensive PCR reagents. In addition, the design of individual assays is simple (7-9). Although many methylation applications can be performed using the melting facility of conventional real-time PCR instruments, analysis on high-resolution platforms may allow assessment of single CpG sites and detection of low-abundance methylated DNA (down to 0.1%-1%). In the near future, we may expect an increasing number of applications for which melting analysis provides an attractive alternative or supplement to existing methods for characterizing the methylation status of specific genes.

Grant/funding support: P.G. is supported by grants from the Danish Cancer Society, the Neye Foundation, and the Danish Medical Research Council.

Financial disclosures: Aspects of methylation-sensitive melting analyses are covered by issued and pending patents owned by P.G.

DOI: 10.1373/clinchem.2007.094854

References

(1.) Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007;8:286-98.

(2.) Egger G, Liang G, Aparicio A, Jones PA. Epigenetics in human disease and prospects for epigenetic therapy. Nature 2004;429:457-63.

(3.) White HE, Hall VJ, Cross NCP. Methylation sensitive high resolution melt curve analysis of the SNRPN gene as a diagnostic screen for Prader-Willi and Angelman syndromes. Clin Chem 2007.

(4.) Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994;22:2990-7.

(5.) Fraga MF, Esteller M. DNA methylation: a profile of methods and applications. Biotechniques 2002;33:632-49.

(6.) Dahl C, Guldberg P. DNA methylation analysis techniques. Biogerontology 2003;4:233-50.

(7.) Worm J, Aggerholm A, Guldberg P. In-tube DNA methylation profiling by fluorescence melting curve analysis. Clin Chem 2001;47:1183-9.

(8.) Guldberg P, Worm J, Gronbaek K. Profiling DNA methylation by melting analysis. Methods 2002;27:121-7.

(9.) Dahl C, Gronskov K, Larsen LA, Guldberg P, Brondum-Nielsen K. A homogeneous assay for analysis of FMR1 promoter methylation in patients with fragile X syndrome. Clin Chem 2007;53:790-3.

(10.) Schaeffer F, Kolb A, Buc H. Point mutations change the thermal denaturation profile of a short DNA fragment containing the lactose control elements: comparison between experiment and theory. EMBO J 1982;1: 99-105.

(11.) Withver CT, Herrmann MG, Moss AA, Rasmussen RP. Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 1997;22: 130-8.

(12.) Herrmann MG, Durtschi JD, Bromley LK, Withver CT, Voelkerding KV. Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clin Chem 2006;52: 494-503.

(13.) Horsthemke B, Buiting K. Imprinting defects on human chromosome 15. Cytogenet Genome Res 2006;113:292-9.

(14.) Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A 1996;93:9821-6.

(15.) Wojdacz TK, Dobrovic A. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 2007;35:e41.

Christina Dahl Per Guldberg *

Institute of Cancer Biology Danish Cancer Society Copenhagen, Denmark

* Address correspondence to this author at: Institute of Cancer Biology, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark. Fax 45-3525-7721; e-mail perg@cancer.dk.
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Title Annotation:Editorial
Author:Dahl, Christina; Guldberg, Per
Publication:Clinical Chemistry
Date:Nov 1, 2007
Words:1517
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