4C-seq Service

4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing) is a versatile, cost-effective solution for profiling all chromatin interactions associated with a specific genomic region of interest (a "viewpoint"), making it particularly well-suited for chromatin looping studies. CD BioSciences' 4C-seq service provides end-to-end support—from viewpoint design and library construction to data processing and interpretation—so you can validate enhancer–promoter communication, map viewpoint-centered contact domains, and compare locus-specific interaction rewiring across conditions.

Introduction to 4C-seq

Chromosome conformation capture (3C) and its sequencing-based derivatives enable chromatin topology to be interrogated with far higher throughput—and often finer, more quantitative resolution. 4C-seq is a targeted 3C variant that measures interaction frequencies between one selected genomic site and all other genomic regions, generating high-resolution contact profiles for your loci of interest without the need for deep sequencing. After generating a standard 3C template, the 3C product is trimmed with a secondary restriction enzyme and circularized by a second ligation step. An inverse PCR is then performed using primers designed on the viewpoint fragment to amplify its ligation partners ("captures") for sequencing-based quantification.

In this manner, 4C-seq can produce high-resolution contact profiles from less than one million sequencing reads in many designs.

Fig.1 Outline of the 4C-seq procedure. (Krijger, P. H. L., et al., 2020)

Features of 4C-seq

1. One-vs-all interaction mapping centered on a defined viewpoint (promoter/enhancer/variant/edited locus)
2. High-resolution contact profiles without deep sequencing, enabling cost-effective locus-centric studies
3. Efficient identification of regulatory and architectural chromatin loops (e.g., enhancer–promoter loops, CTCF-site loops)
4. Supports discovery of neo-TAD formation and 3D mechanisms such as enhancer hijacking in disease contexts
5. Reveals viewpoint-centered large-scale co-localization patterns by analyzing capture frequencies across broader genomic intervals

Our Services

CD BioSciences delivers a standardized, reproducible 4C-seq service for hypothesis-driven 3D genome interrogation. We help you define optimal viewpoint strategy, generate sequencing-ready 4C libraries, and deliver analysis-ready outputs that are easy to visualize and interpret.

Viewpoint Strategy & Primer Design

1. Viewpoint placement near your region of interest and restriction-fragment selection
2. Primer design for inverse PCR and indexing-ready workflow (multiplex-friendly strategy)

3C Template Generation

1. Crosslinking, restriction digestion, and proximity ligation to build a 3C template
2. QC checkpoints to confirm digestion/ligation performance before 4C conversion

Data Processing, Visualization & Interpretation

1. Capture identification/quantification and viewpoint-centered contact profiling
2. Outputs formatted for standard genome-browser visualization and downstream analysis
3. Optional peak-style/enriched-contact calling (e.g., peakC-ready results)
4. Interpretation guidance: near-cis vs far-cis patterns, loop-centric windows, condition comparisons

4C Template Preparation & Inverse PCR Library Construction

1. Secondary restriction digest and second ligation to circularize fragments
2. Inverse PCR to amplify viewpoint ligation partners ("captures") for sequencing
3. Library purification/QC and sequencing planning (depth per viewpoint)

Supported Sample Types

1. Cultured Cells
2. Primary Cells
3. Fresh-Frozen Tissues and Solid Tumors

1. Time-Course or Drug-Treated Samples
2. Genome-Edited or Variant-Centered Models
3. Other Types (Please Inquire)

Our Advantages

1. Cost-Effective, Viewpoint-Driven Loop Interrogation: Targeted 3C variants such as 4C-seq generate high-resolution contact profiles for selected loci without deep sequencing.
2. Proven Utility for Regulatory and Architectural Mechanisms: 4C-seq has been widely used to identify regulatory/architectural loops, neo-TADs, and enhancer hijacking principles.
3. Visualization-Ready Data Delivery: Processing pipelines can output formats compatible with standard genome browsers and common downstream tools.

Interrogate chromatin looping from your locus of interest with a targeted, cost-effective 3D genome approach. CD BioSciences' 4C-seq service delivers reproducible viewpoint-centered contact profiles and interpretation-ready outputs to support regulatory mechanism studies, loop validation, and condition-driven chromatin architecture analysis—contact us to discuss your viewpoint design, sample type, and study goals.

Reference

1. Krijger, P. H. L., et al. (2020). 4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis. Methods (San Diego, Calif.), 170, 17–32. https://doi.org/10.1016/j.ymeth.2019.07.014