Deciphering the complex landscape of DNA modifications is essential for understanding gene regulation, development, and disease. DNA immunoprecipitation sequencing (DIP-seq) provides a direct and powerful method to map specific epigenetic marks genome-wide. At CD BioSciences, we eliminate the technical barriers of antibody optimization and complex workflows, offering a fully supported, end-to-end DIP-seq service.
The fundamental principle of DNA immunoprecipitation sequencing (DIP-seq) is the specific antibody-mediated enrichment of DNA fragments containing a target modification (e.g., 5mC, 5hmC, or 6mA), followed by high-throughput sequencing to map their genome-wide locations. Genomic DNA is first fragmented, and a highly specific antibody is used to immunoprecipitate only those fragments bearing the epigenetic mark of interest. The enriched DNA is then purified, converted into a sequencing library, and analyzed via NGS, allowing for the precise identification and quantification of modification-enriched regions across the entire genome without the need for chemical conversion.
Fig.1 A flow-chart for the DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) protocol. (Thomson J P, et al., 2015)
DNA immunoprecipitation sequencing (DIP-seq) offers a powerful and direct approach for profiling specific DNA modifications across the genome. Its core advantage lies in using highly specific antibodies to directly capture and enrich DNA fragments containing a target epigenetic mark, enabling the precise mapping of enriched regions without subjecting the DNA to harsh chemical conversion steps that can cause degradation and bias.
Direct and Specific Detection
DIP-seq uses highly specific antibodies to directly target and capture DNA fragments containing the modification of interest (e.g., 5hmC, 6mA). This provides a clear and direct signal for the presence of the mark, unlike indirect methods like bisulfite sequencing.
No Sequence Conversion Artifacts
Unlike bisulfite-based methods, it does not subject DNA to harsh chemical treatments that cause degradation and sequence context biases. This preserves DNA integrity and allows for more uniform genome coverage.
Broad Applicability
DIP-seq is a versatile platform that can theoretically be applied to any DNA modification for which high-quality specific antibodies are available, including 5mC and its oxidized derivatives (5hmC, 5fC, 5caC) and adenine methylation (6mA).
Suitable for Low-Input/Complex Samples
The protocol can be more tolerant of lower DNA input amounts and is often more robust for challenging samples like FFPE tissues or cell-free DNA (cfDNA), where bisulfite conversion efficiency can be poor.
Addressing the technical challenges of DIP-seq, particularly antibody specificity and finding a delicate balance between signal enrichment and background noise, requires specialized knowledge and rigorous validation. CD BioSciences, leveraging its advanced technology, provides end-to-end DIP-seq solutions that translate these challenges into reliable data. Our core strength lies in our rigorously validated antibody library and optimized, standardized experimental protocols, ensuring high specificity, maximum enrichment efficiency, and low background noise, thereby achieving precise localization of target DNA modifications.
Our comprehensive DIP-seq service is built on a rigorously validated antibody enrichment platform that enables precise and reliable whole-genome localization of a variety of DNA modifications, including 5mC, 5hmC, 5fC, and 5caC and 6mA .
| Service | Target Modification | Description |
|---|---|---|
| MeDIP-based Service | 5-Methylcytosine (5mC) | Utilizes a highly specific anti-5mC antibody to enrich for globally methylated genomic regions. An excellent alternative to bisulfite sequencing for efficient whole-genome methylation profiling, particularly effective for CpG-dense regions like promoters and CpG islands. |
| hMeDIP-based Service | 5-Hydroxymethylcytosine (5hmC) | Employs a validated anti-5hmC antibody to specifically map the genomic landscape of this stable oxidation product of 5mC. Crucial for studying active demethylation, neurobiology, stem cell regulation, and cancer epigenetics. |
| 6mA-DIP Service | N6-Methyladenine (6mA) | Leverages an anti-6mA antibody to profile this emerging epigenetic mark in eukaryotic and prokaryotic genomes. Supports pioneering research into the potential gene regulatory roles of DNA adenine methylation. |
| f/caC-DIP Service | 5-Formylcytosine (5fC) & 5-Carboxylcytosine (5caC) | Designed for mapping the rare, transient oxidation intermediates in the TET-mediated demethylation pathway. These ultra-sensitive protocols are key for investigating the complete cycle of active DNA demethylation. |
| Custom DIP Service | User-Specified Novel or Rare Modifications | A flexible service for exploratory research. We adapt our platform to work with a researcher-provided, high-quality antibody against a specific DNA adduct or novel modification, facilitating discovery of new epigenetic layers. |
As a dedicated provider of cutting-edge epigenetic research services, CD BioSciences empowers your discovery with expert, end-to-end solutions. Our DIP-seq service combines rigorously validated antibodies, an optimized standardized workflow, and deep bioinformatic expertise to deliver precise, reliable, and actionable maps of DNA modifications—turning complex epigenetic questions into clear biological insights. Contact us today to advance your research.
Reference 1. Thomson J P, Fawkes A, Ottaviano R, et al. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures[J]. Scientific Reports, 2015, 5(1): 9778.
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