Bisulfite sequencing
Bisulfite
Treatment of DNA with bisulfite converts cytosine residues to
Methods
Bisulfite sequencing applies routine sequencing methods on bisulfite-treated genomic DNA to determine methylation status at CpG dinucleotides. Other non-sequencing strategies are also employed to interrogate the methylation at specific loci or at a
Methodologies to analyze bisulfite-treated DNA are continuously being developed. To summarize these rapidly evolving methodologies, numerous review articles have been written.[2][3][4][5]
The methodologies can be generally divided into strategies based on methylation-specific PCR (MSP) (Figure 4), and strategies employing polymerase chain reaction (PCR) performed under non-methylation-specific conditions (Figure 3). Microarray-based methods use PCR based on non-methylation-specific conditions also.
Non-methylation-specific PCR based methods
Direct sequencing
The first reported method of methylation analysis using bisulfite-treated DNA utilized PCR and standard dideoxynucleotide
All subsequent DNA methylation analysis techniques using bisulfite-treated DNA is based on this report by Frommer et al. (Figure 2).[6] Although most other modalities are not true sequencing-based techniques, the term "bisulfite sequencing" is often used to describe bisulfite-conversion DNA methylation analysis techniques in general.
Pyrosequencing
Pyrosequencing has also been used to analyze bisulfite-treated DNA without using methylation-specific PCR.[7][8] Following PCR amplification of the region of interest, pyrosequencing is used to determine the bisulfite-converted sequence of specific CpG sites in the region. The ratio of C-to-T at individual sites can be determined quantitatively based on the amount of C and T incorporation during the sequence extension. The main limitation of this method is the cost of the technology. However, Pyrosequencing does well allow for extension to high-throughput screening methods.
A variant of this technique, described by Wong et al., uses allele-specific primers that incorporate single-nucleotide polymorphisms into the sequence of the sequencing primer, thus allowing for separate analysis of maternal and paternal alleles.[9] This technique is of particular usefulness for genomic imprinting analysis.
Methylation-sensitive single-strand conformation analysis (MS-SSCA)
This method is based on the single-strand conformation polymorphism analysis (SSCA) method developed for single-nucleotide polymorphism (SNP) analysis.[10] SSCA differentiates between single-stranded DNA fragments of identical size but distinct sequence based on differential migration in non-denaturating electrophoresis. In MS-SSCA, this is used to distinguish between bisulfite-treated, PCR-amplified regions containing the CpG sites of interest. Although SSCA lacks sensitivity when only a single nucleotide difference is present, bisulfite treatment frequently makes a number of C-to-T conversions in most regions of interest, and the resulting sensitivity approaches 100%. MS-SSCA also provides semi-quantitative analysis of the degree of DNA methylation based on the ratio of band intensities. However, this method is designed to assess all CpG sites as a whole in the region of interest rather than individual methylation sites.
High resolution melting analysis (HRM)
A further method to differentiate converted from unconverted bisulfite-treated DNA is using high-resolution melting analysis (HRM), a
Methylation-sensitive single-nucleotide primer extension (MS-SnuPE)
MS-SnuPE employs the primer extension method initially designed for analyzing
A number of methods can be used to determine this C:T ratio. At the beginning, MS-SnuPE relied on radioactive
Base-specific cleavage/MALDI-TOF
A recently described method by Ehrich et al. further takes advantage of bisulfite-conversions by adding a base-specific cleavage step to enhance the information gained from the nucleotide changes.
Methylation-specific PCR (MSP)
This alternative method of methylation analysis also uses bisulfite-treated DNA but avoids the need to sequence the area of interest.
The MethyLight method is based on MSP, but provides a quantitative analysis using
Further methodology using MSP-amplified DNA analyzes the products using
Microarray-based methods
Limitations
5-Hydroxymethylcytosine
Bisulfite sequencing is used widely across mammalian genomes, however complications have arisen with the discovery of a new mammalian DNA modification
Incomplete conversion
Bisulfite sequencing relies on the conversion of every single unmethylated cytosine residue to uracil. If conversion is incomplete, the subsequent analysis will incorrectly interpret the unconverted unmethylated cytosines as methylated cytosines, resulting in
Degradation of DNA during bisulfite treatment
A major challenge in bisulfite sequencing is the degradation of DNA that takes place concurrently with the conversion. The conditions necessary for complete conversion, such as long incubation times, elevated temperature, and high bisulfite concentration, can lead to the degradation of about 90% of the incubated DNA.[28] Given that the starting amount of DNA is often limited, such extensive degradation can be problematic. The degradation occurs as depurinations resulting in random strand breaks.[29] Therefore, the longer the desired PCR amplicon, the more limited the number of intact template molecules will likely be. This could lead to the failure of the PCR amplification, or the loss of quantitatively accurate information on methylation levels resulting from the limited sampling of template molecules. Thus, it is important to assess the amount of DNA degradation resulting from the reaction conditions employed, and consider how this will affect the desired amplicon. Techniques can also be used to minimize DNA degradation, such as cycling the incubation temperature.[29]
In 2020, New England Biolabs developed NEBNext Enzymatic Methyl-seq an alternative enzymatic approach to minimize DNA damage.[30]
Other concerns
A potentially significant problem following bisulfite treatment is incomplete
A final concern is that bisulfite treatment greatly reduces the level of complexity in the sample, which can be problematic if multiple PCR reactions are to be performed (2006).[5] Primer design is more difficult, and inappropriate cross-hybridization is more frequent.
Applications: genome-wide methylation analysis
The advances in bisulfite sequencing have led to the possibility of applying them at a
Epigenomic mapping is inherently more complex than
Direct benefits of epigenomic mapping include probable advances in
Large-scale epigenome mapping efforts are under way around the world and have been organized under the Human Epigenome Project.[33] This is based on a multi-tiered strategy, whereby bisulfite sequencing is used to obtain high-resolution methylation profiles for a limited number of reference epigenomes, while less thorough analysis is performed on a wider spectrum of samples. This approach is intended to maximize the insight gained from a given amount of resources, as high-resolution genome-wide mapping remains a costly undertaking.
Gene-set analysis (for example using tools like DAVID and GoSeq) has been shown to be severely biased when applied to high-throughput methylation data (e.g. genome-wide bisulfite sequencing); it has been suggested that this can be corrected using sample label permutations or using a statistical model to control for differences in the numberes of CpG probes / CpG sites that target each gene.[34]
Oxidative bisulfite sequencing
5-Methylcytosine and 5-hydroxymethylcytosine both read as a C in bisulfite sequencing.[24] Oxidative bisulfite sequencing is a method to discriminate between 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution. The method employs a specific (Tet-assisted) chemical oxidation of 5-hydroxymethylcytosine to 5-formylcytosine, which subsequently converts to uracil during bisulfite treatment.[35] The only base that then reads as a C is 5‑methylcytosine, giving a map of the true methylation status in the DNA sample. Levels of 5‑hydroxymethylcytosine can also be quantified by measuring the difference between bisulfite and oxidative bisulfite sequencing.
See also
References
- ^ Chatterjee A, Stockwell PA, Rodger EJ and Morison IM 2012. Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Research 40(10): e79.
- ^ PMID 12238773.
- PMID 14713229.
- S2CID 19574628.
- ^ PMID 16651376.
- ^ PMID 1542678.
- PMID 12866414.
- PMID 12866415.
- PMID 17191619.
- S2CID 22814772.
- PMID 17289753.
- PMID 9171109.
- S2CID 43737807.
- S2CID 3178841.
- PMID 16243968.
- PMID 8790415.
- PMID 10734209.
- PMID 12095268.
- PMID 12376091.
- PMID 18344521.
- PMID 11861926.
- ^ Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, BrudnoY, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine inmammalian DNA by MLL partner TET1. Science. 2009;324(5929):930-5.
- ^ Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science.2009;324(5929):929-30.
- ^ a b Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A. The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing. PLOS ONE.2010;5(1):e8888.
- ^ Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Jin, P., Ren, B., He, C. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat. Protocols 2012, 7, 2159.
- PMID 9016686.
- PMC 5037628.
- PMID 11433041.
- ^ PMID 17259213.
- . Retrieved 2021-05-19.
- PMID 16699174.
- ^ PMID 14691553.
- ^ PMID 16357125.
- PMID 23732277.
- ^ Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, et al. quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science. 2012;336(6083):934-7.
External links
- Bisulfite conversion protocol
- Human Epigenome Project (HEP) - Data — by the Sanger Institute
- The Epigenome Network of Excellence