Table of Contents
What does Hi-C measure?
Similar to the classic 3C technique, Hi-C measures the frequency (as an average over a cell population) at which two DNA fragments physically associate in 3D space, linking chromosomal structure directly to the genomic sequence.
How does Hi-C work?
The Hi-C approach extends 3C-Seq to map chromatin contacts genome-wide, and it has also been applied to studying in situ chromatin interactions. In this method, DNA-protein complexes are crosslinked with formaldehyde. The sample is fragmented, and the DNA is extracted, ligated, and digested with restriction enzymes.
What is a Hi-C matrix?
Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C’s resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces researchers to artificially reduce the resolution of Hi-C matrices at a loss of biological interpretability.
What is promoter capture Hi-C?
Promoter Capture Hi-C (PCHi-C) identifies significant interactions between promoters and distal regions, enabling the assignment of potential regulatory sequences to their target genes.
What is Hi-C seq?
Hi-C sequencing is high‐throughput chromosome conformation capture technique to analyze spatial genome organization and map higher‐order chromosome folding and topological associated domains.
Is Hi-C sold in stores?
Product lines. Hi-C is currently sold in drink boxes, soda fountains, and drink mix form. There are other flavors at Coca-Cola Freestyle. There were soft frozen versions of Flashin’ Fruit Punch and Orange Lavaburst made by J & J Snack Foods and could be found in stores like Dollar Tree.
What is capture C?
NG Capture-C is a refinement of 3C-Seq and Hi-C. It represents a family of methods used to analyze chromatin interactions. NG Capture-C adds multiple pull-down steps of the biotinylated fragments with magnetic beads to the 3C method.
Is Ctcf a dimer?
According to a current hypothetical model, cohesin extrudes chromatin loops until it encounters a CTCF dimer formed by two molecules of CTCF bound to the convergent binding sites (17, 39).
What are Ctcf loops?
CTCF binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures like the nuclear lamina. It also defines the boundaries between active and heterochromatic DNA. Since the 3D structure of DNA influences the regulation of genes, CTCF’s activity influences the expression of genes.
How does DNase seq work?
In this method, DNA-protein complexes are treated with DNase l, followed by DNA extraction and sequencing. Sequences bound by regulatory proteins are protected from DNase l digestion. Deep sequencing provides accurate representation of the location of regulatory proteins in the genome.
Why is it called Hi-C?
The name “Hi-C” referred to its high vitamin content. Hot-packed in enamel-lined 56-ounce (1.66 L) cans, the product needed no refrigeration before opening.