BISULFITE PROFILING

BISULFITE PROFILING (BS-SEQ)

Overview - What is whole-genome bisulfite sequencing (WGBS)?

One of the most commonly methylated sites in human DNA is 5-methylcytosine (5mC). In plants, 5mC is concentrated at CpG, CHG and CHH sequences (where H is either A, C or T). In vertebrates, 5mC is predominantly found at CpG islands, where the methylation functions in various processes such as gene expression regulation, embryonic development and carcinogenesis. Recent noninvasive diagnostic techniques are using the epigenetic state of cell-free DNA as a diagnostic biomarker for cancer.    

Whole-genome bisulfite sequencing (WGBS) or bisulfite sequencing (Bisulfite-Seq or BS-Seq) combines bisulfite treatment with next-generation sequencing (NGS) for epigenetic analysis of the methylome of nearly any organism with single-base resolution. For vertebrates, this is the only technique that offers complete genome-wide coverage of CpGs. The method is considered the gold standard for epigenome profiling by the International Human Epigenome Consortium.   

Applications - What are the advantages of BS-Seq?

Whole-genome bisulfite sequencing is considered the ultimate method for methylcytosine analysis, as the technique allows researchers to:

  • Simultaneously observe the methylation patterns of all CpG, CHG and CHH sites present in the sample of interest
  • Compare differentially methylated loci from different samples (ex.: healthy controls versus patients with cancer)
  • Derive correlations between cytosine methylation and transcriptional regulation
  • Investigate inherited methylations in nearly any organism
  • Profile DNA methylations in the entire methylome for studies on development, cell differentiation, cell cycle, DNA repair, genomic imprinting 
  • Analyse the collective effect of methylation levels on cancer, autoimmunity, etc.

Workflow - Methods & technologies for WGBS

BS-Seq is the method of choice for obtaining a comprehensive analysis of the methylation patterns in the genome. The multi-step process employs bisulfite conversion, PCR amplification and next-generation sequencing to determine the methylation sites across the methylome.

Chemical treatment of DNA with sodium bisulfite converts unmethylated cytosines into uracils. Methylated cytosines are protected from bisulfite conversion by their methyl group, hence they remain unchanged during the conversion process. The DNA is then subjected to a PCR assay, where all uracils are converted to thymidines. The resulting DNA amplicons are sequenced with high sequencing coverage. The obtained sequencing reads are mapped against a reference genome to enable the identification of the methylated loci in the sample. 

Figure 1: Detection of methylated cytosines with chemical bisulfite conversion

Methylation array vs. whole-genome bisulfite sequencing

Methylation arrays are a traditional technique for assessing the methylation status of cytosines. This method is used to target hundreds of thousands of methylation sites, rather than to probe the entire epigenome.

Focusing only on known methylated regions decreases the computational analysis of the assay; methylation arrays also suffer from significant setbacks compared to WGBS. Some of these disadvantages include:

  • Limited possibilities for exploring organisms other than humans
  • Inability to simultaneously detect both genetic mutations and epigenetic modifications 
  • Analysis of pre-determined genomic regions only
  • Danger of cross-reactivity with non-targeted genomic regions or loci containing single nucleotide polymorphisms (SNPs)
  • Extra computational analysis required for control of batch effects

Scientific expertise: BS-seq

GATC Biotech takes advantage of industry-leading platforms to offer extensive methylation analysis across the entire genome. Combined with thorough BioIT analysis, GATC Biotech can provide unmatched flexibility in delivering reliable data for achieving various research aims ranging from cancer research to understanding basic cellular processes.  
GATC Biotech is involved in exploring epigenetic mechanisms for clinical purposes. For example, GATC Biotech aims to take advantage of differences in the DNA methylation signatures of healthy versus cancer cells for improved diagnostics and therapeutics of breast and ovarian cancer (see also the publicly funded EpiFemCare project). 

Publications

Find here, a list of selected research articles supported by GATC Biotech’s sequencing products, including articles on epigenetics.

Related products to BS-seq

Would you like to try BS-seq for yourself? Benefit from hassle-free, reliable results for your methylome analysis with our all-in-one service package INVIEW EPIGENOME BS-SEQ. We offer DNA isolation from various starting materials, expert library preparation, sequencing on the industry-leading Illumina platform, BioIT analysis and a GATC Data Analysis report with a detailed results summary.

Further reading on whole-genome bisulfite sequencing

Hsieh, T.F. Whole-genome DNA methylation profiling with nucleotide resolution. Methods Mol. Biol. 1284, 27 – 40 (2015).

Johnson, M.D., Mueller, M., Game, L., Aitman, T.J. Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing. Curr. Protoc. Mol. Biol. Chapter 21:Unit21.23  (2012).