Knowledge about Chromatin Immunoprecipitation Sequencing (ChIP-Seq)

ChIP-Seq is a classical antibody-based method for studying protein-DNA interactions, which can selectively enrich DNA-binding proteins and their DNA targets, truly and completely reflecting the regulatory protein bound to the DNA sequence. CHIP-seq, a combination of CHIP and next-generation sequencing (NGS) technology, is a genome-wide analysis technique for DNA-binding proteins, histone modifications, or nucleosomes. Formaldehyde is used to cross-link and fix the target protein with chromatin, ultrasound is used to break chromatin into small fragments (generally 200-600 bp), the antibody that specifically bound to the target protein is added to precipitate the DNA fragments, and these DNA fragments are purified for sequencing after DNA-protein decrosslinking.

Fig.1 Overview of CHIP-seq workflow. (Park, 2009)

With its high resolution, high signal-to-noise ratio (SNR), wide coverage, and low cost, CHIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms.

ChIP-Seq-based Glycogene Expression Profiling at CD BioGlyco

CHIP-seq has demonstrated a powerful ability to uncover the epigenetic regulation of gene expression in human tumors, providing an important biological basis for tumor mechanism research and treatment. CD BioGlyco provides clients with standardized services and accurate analysis of CHIP-seq data.

Glycosylation modification plays an important role in epigenetic biological processes. O-GlcNAc modifications regulate chromatin remodeling factors and participate in the regulation of post-translational modifications of histones. Similarly, CHIP-seq is powerful for revealing the regulatory mechanisms of glycosylation in epigenetics and the role of glycogenes in signal transduction.

Fig.2 Our service workflow. (CD BioGlyco)

To meet your higher needs, CD BioGlyco provides you with cutting-edge new technologies to support your experiments:

• Native CHIP-seq: CHIP-seq is limited by the need for many cell samples to produce high-quality data sets. CD BioGlyco provides native CHIP-seq based on micrococcal nuclease, which uses micrococcal nuclease instead of ultrasonic interruption and does not require formaldehyde crosslinking and decrosslinking steps. Clients only need to provide a small number of cell samples to obtain high-resolution histone labeling profiles of whole-genome.
• Cleavage under targets and release using nuclease: This method omits the process of immunoprecipitation, and uses a fusion protein composed of protein A and micrococcal nuclease (pA-MN). The specific binding of protein A to the antibody causes micrococcal (MNase) nuclease to target and cut the DNA around the target protein. Clients only need to provide about 100 cells to get high SNR data at low sequencing depth.
• Cleavage under targets and tagmentation: This method uses Tn5 transposase instead of MNase to cut DNA, and does not require DNA purification subsequently, avoiding further DNA loss. Clients only need to provide a very small number of cells to obtain high SNR data. It supports single-cell detection.

Applications

• Investigate the epigenetic mechanism of gene expression in diseases, especially tumors
• Study histone modifications at specific locations in DNA
• Study the precise localization of RNA polymerase II and other trans-factors on the genome
• Explore the relationship between histone covalent modification and gene expression

Highlights

• CHIP-seq technology with high resolution, high SNR, wide coverage, and low cost
• Innovative CHIP-seq technology
• Professional experts and rigorous data analysis
• Reliable service quality

CD BioGlyco supports your research with its perfect Glycogenomics Platform in the field of glycobiology. Please feel free to contact us to learn more about how we can help you.