DNA Methylation Profiling Simplified – Your Top Choice for Diverse Sequencing Solutions
DNA methylation analysis is essential for understanding gene regulation and disease. At CD Genomics, we provide high-throughput sequencing (e.g., WGBS, MeDIP), microarray, and long-read sequencing (e.g.,Oxford Nanopore) to map methylation patterns with precision, supporting research in cancer, neurology, and more.
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Achieve single-base resolution for accurate detection of methylation sites across the genome.
Tailor your analysis to specific regions of interest or perform whole-genome assessments based on your research needs.
Rigorous QC steps at each stage of the process, ensuring reliable and high-quality results.
What is DNA Methylation Analysis
DNA methylation analysis refers to the study of chemical modifications in the DNA, where a methyl group is added to the cytosine base, primarily at CpG sites. This process plays a crucial role in regulating gene expression without altering the DNA sequence itself, and is integral to epigenetic mechanisms in both normal biological functions and disease states.
Researchers are particularly interested in understanding methylation patterns as they can impact processes such as cell differentiation, cancer development, and gene silencing. Modern techniques allow for genome-wide investigation of methylation patterns, revealing key epigenetic changes associated with various conditions.
How to Analyze DNA Methylation
DNA methylation analysis involves various methods, each offering unique strengths for detecting and profiling methylation patterns.
Bisulfite Sequencing (BS-seq)
Bisulfite treatment converts unmethylated cytosines (C) to uracil (U), while methylated cytosines remain unchanged. During sequencing, uracil is read as thymine (T), enabling the distinction between methylated and unmethylated cytosines at a single-base resolution.
Methylation-Specific PCR (MSP)
MSP uses primers designed to distinguish between methylated and unmethylated DNA following bisulfite treatment. The amplification results indicate the methylation status of specific DNA regions.
Pyrosequencing
Pyrosequencing involves real-time DNA synthesis, detecting methylation changes at specific cytosines following bisulfite treatment. It provides quantitative data on the degree of methylation within targeted regions.
MeDIP utilizes antibodies that specifically bind to methylated cytosines, allowing the enrichment of methylated DNA fragments. These fragments can be further analyzed by high-throughput sequencing (MeDIP-seq) or microarray.
Methylation-Sensitive Restriction Enzyme Analysis
This method employs restriction enzymes that cut unmethylated DNA while leaving methylated sequences intact. By comparing the digested products, the methylation status can be inferred.
Methylation Arrays
DNA methylation arrays use probes targeting specific CpG sites to assess methylation levels. One commonly used platform is the Illumina Infinium Human Methylation BeadChip, which can assay hundreds of thousands of CpG sites simultaneously.
Nanopore sequencing directly reads long DNA molecules, detecting methylated cytosines without the need for bisulfite conversion or PCR amplification. Changes in electrical current as DNA passes through the nanopore indicate methylation status.
Discover advanced next-generation sequencing methods for DNA methylation analysis to enhance your research.
DNA Methylation Analysis: Choosing the Right Service
At CD Genomics, we understand that every research project is unique. Our tailored DNA methylation analysis services help you identify the most suitable methods based on your specific objectives, whether you're studying model organisms or non-model species.
1. High-throughput Sequencing Based
WGBS:
Provides the highest resolution; capable of detecting all types of methylation.
RRBS:
Cost-effective for large-scale sample analysis.
MethylRAD-Seq:
Suitable for methylation analysis of specific genomic regions in large-scale samples.
MeDIP Sequencing:
Enriches methylated regions for whole-genome scanning.
DNA 6mA Sequencing:
Focuses on non-CG site methylation.
MRE-Seq Service:
Suitable for RNA-guided DNA methylation analysis.
2. Microarray Technology Based
Human DNA Methylation Microarray Service:
Designed for comprehensive analysis of human methylation patterns, enabling efficient processing of multiple samples with high sensitivity.
Mouse DNA Methylation Microarray Service:
Tailored for detailed methylation profiling in mouse models, facilitating large-scale studies with reliable and reproducible results.
3. Long Read Sequencing Based
Long Read Sequencing DNA Methylation Service:
Provides in-depth methylation analysis across long DNA fragments, enabling comprehensive insights into complex genomic regions.
4. Classification Based on Sample Type
Human Samples:
Mouse Samples:
How Does DNA Methylation Analysis Work
Our DNA Methylation Analysis Workflow begins with collecting biological samples, followed by extracting high-quality genomic DNA using standardized protocols. We ensure every sample meets strict quality standards through spectrophotometry and gel electrophoresis. In the methylation treatment phase, DNA is treated with bisulfite to specifically mark methylation patterns. Next, sequencing libraries are prepared and amplified, ready for detailed sequencing on platforms like Illumina. The data is then meticulously analyzed to uncover methylation patterns and generate thorough reports.
Precision DNA Methylation Analysis with Leading-Edge Platforms
We utilize state-of-the-art platforms for our DNA methylation analysis services, ensuring high precision and reliability. Our platforms can be classified into the following categories:
- Next-Generation Sequencing (NGS) Platforms:
- Illumina Sequencing: Offers high-throughput sequencing capabilities for comprehensive methylation profiling.
- PacBio Sequel II: Enables long-read sequencing, allowing for detailed analysis of methylation patterns across larger genomic regions.
- Microarray Platforms:
- Agilent Microarrays: Provides robust solutions for targeted methylation analysis in human and mouse samples.
- Illumina Infinium: Includes advanced arrays like the MSA270K and EPIC v2.0-935k, supporting large-scale methylation studies with enhanced coverage of CpG sites and high-throughput capabilities.
- PCR and Enrichment Platforms:
- Thermal Cyclers: Used for PCR amplification in various methylation analysis methods.
- Methylated DNA Enrichment Kits: These kits enrich for methylated regions, optimizing downstream analysis.
Unlock the potential of your DNA methylation research with our specialized microarray services, including the Methylation Screening Array 270K and the Illumina 935K Assay, tailored to meet your specific needs.
Publication-Ready Methylation Profiling Analysis Made Easy
Our reports provide clear and actionable insights for your methylation analysis.
- Methylation Preference Assessment
- Raw Data Overview
- Quality Assessment of Data
- Data Quality Control and Filtering
- Alignment Quality Control and Reporting
- Methylated Gene Alignment
- Methylation Level Distribution
- PCA/Correlation Analysis
- Differentially Methylated Site Analysis
- Differentially Methylated Region (DMR) Analysis
- Functional Annotation and Enrichment Analysis of DMRs
- Enrichment of Functional Regions of DMRs
- GO and KEGG Enrichment Analysis of Corresponding Genes of DMRs
- ...and more
Specific report details vary by service. Please contact us for more information tailored to your project.
Why Choose Our DNA Methylation Profiling Services
Our DNA methylation profiling services offer advanced techniques and customizable analysis options tailored to your research needs. With strict quality control measures, we ensure accurate and reliable results for your projects.
A seamless, one-stop service for library construction, sequencing, and bioinformatics, ensuring efficient workflows and reduced errors.
Advanced methylation conversion technologies enable precise analysis of methylation states at the single cytosine level, backed by strict quality control.
Supports genome-wide or targeted methylation profiling with enhanced methodologies like double RRBS for superior CpG coverage and high sequencing depth.
Offers customizable chip designs and the ability to analyze multiple samples simultaneously, ideal for large-scale studies with limited DNA input.
What Our Clients Say
"The DNA methylation analysis services from CD Genomics have been essential to our cancer epigenetics research. Their team delivered precise genome-wide methylation data, and the bioinformatics analysis was smooth. Thanks to their support, we've been able to advance our research with newfound confidence."
"CD Genomics' methylation services have truly enhanced our understanding of environmental epigenetics. The Whole Genome Bisulfite Sequencing they provided was high-resolution and has played a key role in our recent publications. I can't recommend their services enough for anyone in need of dependable and detailed methylation analysis."
"We've partnered with CD Genomics for DNA methylation profiling in our neuroscience projects, and their platform has been outstanding. The quality of the data and the customer support we received were fantastic. From sample prep to interpreting the results, they made everything straightforward."
"As a pharmaceutical researcher, accurate and timely methylation analysis is crucial for my work. CD Genomics has been a game-changer, providing top-quality data that has really sped up our drug discovery efforts for age-related diseases."
How is Methylation Profiling Used in Research
Our DNA methylation profiling services offer advanced techniques and customizable analysis options tailored to your research needs. With strict quality control measures, we ensure accurate and reliable results for your projects.
- Biomarkers: Detects epigenetic changes in tumor suppressor genes and oncogenes, aiding in early cancer detection and treatment decisions.
- Therapies: Supports the development of therapies that target abnormal methylation in cancer cells.
- Gene Regulation: Examines how methylation influences gene expression during cell differentiation and organism development.
- Imprinting Disorders: Helps diagnose conditions like Prader-Willi syndrome by identifying abnormal methylation patterns.
- Disease Associations: Links altered methylation patterns to disorders such as autism, schizophrenia, and Alzheimer’s disease.
- Epigenetic Memory: Investigates how environmental factors can lead to lasting epigenetic changes affecting mental health.
- Epigenetic Clocks: Tracks biological aging by measuring age-related methylation changes.
- Age-Related Diseases: Identifies methylation patterns linked to conditions like cardiovascular disease and neurodegeneration.
- Environmental Effects: Studies how factors like pollution and diet influence methylation and impact disease risk.
- Inheritance: Looks at how methylation changes from environmental exposures can be passed on to future generations.
- Immune Regulation: Explores the role of methylation in immune system function and autoimmune diseases.
- Cancer Immunotherapy: Investigates how reversing cancer-specific methylation changes may boost immunotherapy effectiveness.
- Drug Response: Uses methylation profiles to personalize treatments based on individual genetic responses to medications.
Publications
Here are selected publications demonstrating the impact of our DNA methylation services:
- Genomic imprinting-like monoallelic paternal expression determines sex of channel catfish. Sci. Adv, 2022. DOI:10.1126/sciadv.adc8786
- Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch. Sci. Adv, 2024. DOI:10.1126/sciadv.adp0975
- Methylation in the CHH context allows to predict recombination in rice. International Journal of Molecular Sciences, 2022. https://doi.org/10.3390/ijms232012505
- Natural Recombination among Type I Restriction-Modification Systems Creates Diverse Genomic Methylation Patterns among Xylella fastidiosa Strains. Appl Environ Microbiol, 2023. https://doi.org/10.1128/aem.01873-22
- Exploiting DNA methylation in cassava under water deficit for crop improvement. PLOS ONE, 2024. https://doi.org/10.1371/journal.pone.0296254
