CaptureC

CaptureC is a chromosome conformation capture–based technique designed to map chromatin interactions at high resolution around selected genomic regions, most commonly gene promoters. It enriches for DNA fragments that physically interact with chosen promoters in a 3C-derived library by using sequence capture with biotinylated probes, enabling many promoters to be studied in parallel at reduced sequencing cost.

In practice, CaptureC begins with crosslinking of cells, followed by digestion of chromatin with a restriction enzyme and ligation to create a 3C library that links interacting DNA fragments. A pool of biotinylated oligonucleotide probes complementary to promoter regions is then hybridized to the library. Promoter-associated fragments are captured with streptavidin beads, amplified, and sequenced. Sequencing reads are mapped to identify fragments that contact each promoter, and interaction frequencies are quantified and normalized for comparison across samples.

Applications include delineating promoter–enhancer networks, identifying regulatory targets of genetic variants, and characterizing tissue-specific regulatory architectures. CaptureC is useful for studying regulatory landscapes in model organisms and humans, and it supports investigating thousands of promoters in parallel with targeted sequencing.

History and variants: CaptureC emerged as a targeted alternative to broader chromatin conformation methods, and is often referred to as Capture-C or promoter capture-C. It exists alongside related techniques such as Capture Hi-C and promoter-focused capture methods, with variations in probe design, capture chemistry, and sequencing strategies. The choice of restriction enzyme and probe set influences resolution and coverage.

Limitations include capture biases, dependence on restriction fragment distribution, and the need for careful normalization and bioinformatic processing. It provides targeted, high-resolution insight but does not capture genome-wide interactions without expanding the probe set.