Epigenetic Services

Bisulfite sequencing

DNA Methylation can’t be analyzed using standard sequencing methods because the methyl group is covalently bound to the cytosine (5-methylcytosine, 5-mC). So bisulfite sequencing has become the gold standard to make epigenetic biomarker validation simple. Bisulfite reagents convert unmethylated cytosine residues to uracils, leaving the methylated ones as is, so during PCR, the DNA polymerization recognizes the uracils as thymosine and the unmethylated cytosines as is. The final output is then compared to reference materials. In NGS methods, the bisulfite-converted DNA samples are constructed into libraries that contain adaptors for NGS sequencing. The most popular NGS methods include Reduced Representation Busilfute Sequencing (RRBS), Targeted Bisulfite Sequencing (TBS), and Whole Genome Bisulfite Sequencing (WGBS).

The main difference is the percentage of the total genome that is sequenced. If the customer is at discovery phase and has a limited budget, we usually recommend starting with RRBS or TBS since these 2 platforms enrich CpG dense regions. If you prefer to look at the entire genome or CHG and CHH context, WGBS would be a better option.

Genome coverage: RRBS < TBS < WGBS

• Reduced Representation Bisulfite Sequencing (RRBS) enriches for CpG-rich regions across the DNA genome using restriction enzyme digestion before proceeding with bisulfite sequencing library preparation. This is the most cost-effective solution to screen for genome-wide DNA methylation.
• Whole Genome Bisulfite Sequencing (WGBS) detects the methylation states of all the cytosines in the sample giving a comprehensive profile of DNA methylation across the genome. This is very thorough but comes at a large cost to obtain a significant level of sequencing depth.
• Targeted Bisulfite Sequencing (TBS) enables site-specific DNA methylation analysis at specific loci on the sample DNA. This is used to validate data from broader genome-wide methods and targeted sample screening.

Whether you need to validate methylation array data in a large sample cohort or investigate a specific gene region, our expert scientists can help design, validate and evaluate DNA methylation changes with targeted bisulfite sequencing.

Genome-wide DNA Methylation

Comprehensive and reliable DNA methylation sequencing analysis. Boster Bio’s DNA methylation services are genome-wide/whole-genome DNA methylation analysis at single nucleotide resolution, each designed to suit your specific coverage needs.

Methylated DNA Immunoprecipitation (MeDIP) is a bisulfite-free method for analyzing genome-wide methylation using antibodies targeting 5-mC to enrich for methylated DNA. This enriched fraction is then used in analysis or quantification via ELISA technique.

Services included in Basic analysis #1-5 and full analysis

• DNA samples QC assessment
• Bisulfite conversion, library preparation, and QC assessment
• Sequencing data generation
• Raw data alignment, methylation calling, and genome browser tracks
• Fast file delivery
• Statistical comparisons including results tables listing the most differentially methylated cytosines
• Violin plots
• DNA methylation overview plots
• Differentially methylation region analysis
• Clustering heatmap

Chip-Seq Services

Histone modifications to the core histone proteins can affect gene expression as well. This can be detected using Chromatin Immunoprecipitation (ChIP), where proteins are crosslinked to DNA and protein-specific antibodies are used to selectively precipitate bound DNA fragments to the protein. These enriched fragments can be sequenced via ChIP-seq NGS sequencing for a genome-wide profile of histone modification.

Boster Bio’s Chip-seq services cater for genome-wide mapping of histone modifications, protein DNA interactions, and identifying consensus protein binding sites in DNA for transcription factors or other enzymes.

The Assay for Transposase-Accessible Chromatin (ATAC-seq) is a derivative of ChIP-seq where the presence or absence of open chromatin is measured. This method uses transposase which can only insert adaptor sequences into open chromatin sites to distinguish unique binding sites or transcription factors bound within the native chromatin and to help us understand the role of chromatin structure changes.

Services Include

• Genome-wide analysis to detect nearly all CpG islands and gene promoters
• Biomarker discontainy to detect twice as many unique CpG sites compared to Classic RRBS
• DNA methylation information on entire methylome, including less common CHG and CHH contexts
• Customisable design plan and ChIP-seq workflow
• Custom Report

Epigenetic Aging Services

Accelerated biological aging can occur via the accumulation of epigenetic drift or mutations over time characterized by an increase in gene expression noise and can be associated with a number of diseases such as cancer and obesity-related illnesses. Biological age refers to epigenetic alternation and DNA methylation and can be determined by measuring DNA methylation at multiple sites.

Boster’s Epigenetic Aging Service utilizes the Simplified Whole-panel Amplification Reaction Method (SWARM®), which is a robust targeted bisulfite sequencing approach to deliver reproducible high-throughput methylation data. Applications include biomarker studies as well as arthritis, allergies, forensics, fertility, diabetes, alzheimers/parkinson’s and circadian rhythm research.

Services Include:

• DNA extraction and QC assessment
• Bisulfite conversion, library preparation
• Sequencing data generation
• DNA methylation value data analysis for biological age determination via multiple linear regression modeling.
• Epigenetic age data delivery