Transcription Factor ChIP-seq Service

Transcription factor ChIP-seq is a gold-standard method for identifying genome-wide DNA binding sites of transcription factors (TFs), cofactors, and chromatin-associated regulators. CD BioSciences offers an optimized ChIP-seq service specifically tailored to transcription factors, incorporating enhanced fixation and library strategies to overcome the unique challenges of profiling dynamic, transient TF–DNA interactions.

Introduction to Transcription Factor ChIP-seq

Transcription Factor ChIP-seq (Chromatin Immunoprecipitation followed by Sequencing) is a key technique for genome-wide identification of transcription factor (TF) binding sites on DNA. This method involves first crosslinking protein-DNA interactions with a fixative, then fragmenting the chromatin into small pieces. DNA sequences bound by the target transcription factor are enriched using a specific antibody, and finally, high-throughput sequencing is employed to precisely map their binding regions.

Unlike stable epigenetic marks such as histone modifications, interactions between transcription factors and chromatin are typically transient and dynamic, making them more difficult to fix and capture. To improve signal quality and enrichment efficiency, many studies employ a dual crosslinking strategy: first stabilizing protein complexes with a long-arm protein-protein crosslinker like DSG (disuccinimidyl glutarate), followed by traditional protein-DNA crosslinking with formaldehyde. This approach significantly enhances the ChIP enrichment efficiency and peak intensity for transiently bound transcription factors.

Fig.1 ChIP-seq overview of ERα, FOXA1, and H3K27ac binding profiles. (Singh, A. A., et al., 2018)

Furthermore, signals obtained from TF ChIP-seq typically appear as narrow peaks, which are closely associated with gene regulatory elements such as promoters and enhancers. The results are commonly used to reveal transcriptional regulatory networks, identify key regulatory factors, analyze regulatory mechanisms in diseases, and achieve functional annotation and target prediction through integration with data such as expression profiles.

Our Services

To accommodate diverse research needs—from basic mechanism studies to translational and clinical applications—CD BioSciences offers multiple TF ChIP-seq service formats. Each is tailored to different sample types, experimental goals, and technical requirements, ensuring reliable results even for difficult targets or limited input materials.

Standard TF ChIP-seq

For transcription factors in cultured cells or bulk tissue using validated antibodies.

Low-input TF ChIP-seq

Optimized protocols for rare samples, small biopsies, or low-abundance targets (e.g., hormone receptors in needle biopsies).

Clinical sample TF ChIP-seq

Compatible with fresh-frozen or lightly fixed human tumor tissues; incorporates dual crosslinking (DSG+FA) for maximum recovery of dynamic TF binding.

Co-factor & pioneer factor ChIP-seq

Targeting dynamic chromatin remodelers and TF partners (e.g., FOXA1, GATA3, RUNX1) with optimized fixation and enrichment strategies.

Comparative TF ChIP-seq

Multi-condition studies to identify differential binding events (e.g., drug-treated vs. control, different cell types).

Integrated multi-omic ChIP-seq

Designed to complement RNA-seq, ATAC-seq, or Hi-C for systems-level regulatory network reconstruction.

Supported Sample Types

1. Cultured Cells (e.g., mammalian)
2. Fresh-Frozen Tissue
3. Low-Input and Rare Subsets

1. FFPE Tissue Sections
2. Clinical Biopsy and Needle Core Samples
3. Other Types (Please Inquire)

Our Advantages

1. Dual-Crosslinking Enhancement: DSG + FA improves recovery of transient TF–DNA interactions.
2. Low-Abundance Target Compatibility: Effective for weakly expressed and pioneer transcription factors.
3. Validated for Clinical Samples: Proven success with core needle biopsies and primary tissues.
4. Comprehensive Motif and Co-binding Analysis: Reveals direct and collaborative TF regulation.
5. Antibody Selection Support: Includes consultation for antibody choice and control design.
6. Optional Multi-Target Integration: Combine with histone or Pol II ChIP for context-rich insights.

Start your transcription factor cistrome project today. Whether studying hormone signaling, enhancer logic, or TF target genes, CD BioSciences's TF ChIP-seq Service delivers high-resolution maps to advance your research. Contact us for consultation and project design.

Reference

1. Singh, A. A., et al. (2018). Optimized ChIP-seq method facilitates transcription factor profiling in human tumors. Life science alliance, 2(1), e201800115.