Methodology (Denker & de Laat, 2017): Explain the difference between "one-to-all" (4C) and "all-to-all" (Hi-C) technologies. In what research scenario would you choose Capture-C over standard Hi-C?

What is the scope of genomic interactions measured by 4C?

A "one-to-all" approach that identifies all genomic regions contacting a specific sequence of interest (viewpoint or anchor).

What is the scope of genomic interactions measured by Hi-C?

An "all-to-all" technology that interrogates interactions between all pairs of fragments across the entire genome simultaneously.

What is 4C (Circularized 3C) useful for?

Studying the regulatory environment of a single gene, such as discovering which remote enhancers loop to a specific promoter, without requiring a priori hypotheses.

What does Hi-C render?

A whole-genome contact map represented as a matrix of pairwise interaction frequencies.

What structural features did Hi-C help confirm?

The existence of major genomic compartments (A and B) and Topologically Associated Domains (TADs).

Why would a researcher choose Capture-C over standard Hi-C?

Because Hi-C becomes prohibitively expensive for high-resolution data on specific regions, as most sequencing reads are superfluous when focus is limited to certain sequences.

In what research scenario would you choose Capture-C over standard Hi-C?

When the research question is directed at a large but defined series of sites (e.g., hundreds or thousands of specific gene promoters, enhancers, or CTCF-binding sites).

What advantage does Capture-C offer in terms of cost and resolution?

It uses oligonucleotide "baits" to enrich ligation junctions of interest, allowing detailed contact maps for specific sites at significantly lower sequencing cost than standard Hi-C.

What specific application is Capture-C useful for regarding SNPs?

Linking single-nucleotide polymorphisms (SNPs) within regulatory sequences to the specific genes they contr