Histone ChIP-seq Service

Histone modifications are key to epigenetic regulation of gene expression. Their genomic distributions are most commonly measured using ChIP-seq, a next-generation sequencing method which results in pileups of sequencing reads near regions with modified histones. CD BioSciences offers a high-quality, full-service Histone ChIP-seq platform optimized for diverse biological samples and histone targets, enabling you to uncover chromatin states, regulatory element activity, and epigenetic mechanisms that shape gene expression.

Introduction to Histone ChIP-seq

Histone ChIP-seq combines chromatin immunoprecipitation (ChIP) with next-generation sequencing (NGS) to identify genomic regions enriched with specific histone post-translational modifications (e.g. H3K4me3, H3K27ac, H3K27me3). These marks act as epigenetic signals that indicate transcriptional activation, repression, enhancer priming, heterochromatin formation, and other regulatory events. In a typical assay, DNA-protein interactions are first cross-linked in cells or tissues using formaldehyde (for histone marks) or a combination of formaldehyde and long-chain crosslinkers (for histone modifiers). Chromatin is then fragmented (typically by sonication), and the target histone modification is pulled down using a modification-specific antibody. DNA fragments bound to the target are purified, converted into sequencing libraries, and subjected to high-throughput sequencing. The sequencing reads are aligned to the genome to identify enriched regions (peaks) corresponding to histone modification occupancy.

Key strengths of ChIP-seq for histones include:

1. Profiling both active and repressive histone marks
2. Mapping broad (e.g. H3K27me3) and narrow (e.g. H3K4me3) peaks
3. Analyzing histone modifier enzyme occupancy
4. High compatibility with tissue samples and frozen material

Fig.1 Workflow of chromatin immunoprecipitation (ChIP) assay for analyzing histone modifications and modifiers. (Kaya-Okur, H. S., et al., 2020)

Application of Histone ChIP-seq

1. Epigenetic landscape mapping (e.g. active/repressive chromatin states)
2. Gene regulation analysis through promoter and enhancer modifications
3. Transcriptional memory and cell identity profiling
4. Mechanism of action studies for chromatin-modifying drugs
5. Comparative chromatin analysis across cell types, treatments, or disease states
6. Histone writer/eraser binding profiling (e.g. LSD1, EZH2)

Our Services

CD BioSciences offers a complete ChIP-seq solution with optimized protocols for histone modifications and chromatin-associated proteins. We provide expert support from sample preparation through bioinformatics analysis.

Sample Preparation and Crosslinking

1. Accept a wide range of sample types: cells, tissues, cryopreserved material
2. Single formaldehyde fixation is used for most histone marks
3. Dual crosslinking (formaldehyde + DSG or DTBP) applied for histone-modifying enzymes
4. Chromatin is sonicated to produce DNA fragments (~200–500 bp) for optimal resolution

Immunoprecipitation

1. Incubation with validated, modification-specific antibodies
2. Use of appropriate Protein A/G magnetic beads
3. Parallel IgG negative controls included
4. Stringent washes to remove background and non-specific signal

DNA Recovery and Library Preparation

1. Crosslinks reversed and DNA purified by phenol-chloroform or column-based methods
2. Adapter ligation and library construction with optimized PCR cycles
3. QC by Bioanalyzer/Tapestation to ensure proper fragment size and complexity

Sequencing

1. Paired-end sequencing (Illumina platform)
2. Recommended depth: 20–50M reads/sample depending on histone mark
3. Low duplication and high mapping rates ensured via quality filtering

Bioinformatics and Reporting

1. Read alignment and duplicate removal
2. Peak calling via MACS2 with shape-adjusted parameters (broad/narrow)
3. Signal visualization (IGV tracks, heatmaps, metaplots)
4. Functional annotation using tools like GREAT and DAVID
5. Optional: motif analysis, GO enrichment, enhancer/promoter annotation

Supported Sample Types

1. Cultured Cells (e.g., mammalian)
2. Fresh-Frozen Tissue
3. FFPE Tissue Sections

1. Purified Genomic DNA or Nuclei
2. Other Types (Please Inquire)

Ready to profile your chromatin landscape with precision? CD BioSciences's expert team will help you design and execute a customized histone ChIP-seq project—from experimental setup to biological interpretation. Contact us to get started with your histone ChIP-seq project.

Reference

1. Hino, S., et al. (2023). Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers. Methods in molecular biology (Clifton, N.J.), 2577, 55–64.