What is the 5C technique?

What is the 5C technique?

We refer to this method as 3C-Carbon Copy, or “5C.” 5C uses highly multiplexed ligation-mediated amplification (LMA) to first “copy” and then amplify parts of the 3C library followed by detection on microarrays or by quantitative DNA sequencing.

What is the 5C technique designed to detect?

5C (many-vs-many) Chromosome conformation capture carbon copy (5C) detects interactions between all restriction fragments within a given region, with this region’s size typically no greater than a megabase. This is done by ligating universal primers to all fragments. However, 5C has relatively low coverage.

What is hi c sequencing?

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 3C Method?

Chromatin Conformation Capture (3C) is an important technique used to study chromatin structure, as well as the basis for several other derivative techniques. The protocol involves formaldehyde cross-linking of cells followed by chromatin isolation and digestion with a restriction enzyme.

What is Hi-C assay?

Hi-C: The Next-Gen Chromosome Conformation Capture Method Because Hi-C assays enable the investigation of genome-wide chromatin interactions, it is central to the ongoing efforts to understand the 3-dimensional organization of the genome and the physiological role it plays.

What does Bionano genomics do?

Bionano Genomics, Inc. provides a platform to analyze the long segments of genomic DNA and other biomolecules structural variations. The Company offers proprietary nanochannel chips, automated imaging instrument, integrated primary and secondary software, and application specific reagents.

What happened Hi-C?

McDonald’s discontinued Hi-C Orange Lavaburst –also referred to as the “orange drink” in 2017, saying it would replace it with the Sprite TropicBerry.

What is 3C manufacturing?

The 3C ´s stand for Concern, Cause and Countermeasure and encourage employees to think about the definitions of each of these steps.

What is in situ Hi-C?

In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method.

When did chromosome conformation capture carbon copy start?

Thus, chromosome conformation capture carbon copy (5C) entered the scene in 2006. In 5C, a region of interest (typically around one megabase) is queried for all interacting loci within it. 5C also follows the same initial steps as 3C and 4C, with crosslinking, digestion, ligation, and reversal of the crosslinking performed in the same fashion.

How are chromosome conformation capture assays used in bacteria?

Chromosome conformation capture assays in bacteria. Methods 58, 212-220. The organization of bacterial chromosomes has been assumed to be random. Recent 5C data are challenging this assumption. In this review, the results of 5C experiments in bacteria are presented and show that the chromosome is actually highly organized.

How is 5C used in the human genome?

This paper applies 5C to understand large-scale looping interactions in the human genome. The authors also integrate data from the ENCODE project to show how epigenetic marks influence chromosome looping. Umbarger, M.A. (2012).

Where does the 5C capture carbon copy take place?

We validated 5C by detection of several previously identified looping interactions in the beta-globin locus. We also identified a new looping interaction in K562 cells between the beta-globin Locus Control Region and the gamma-beta-globin intergenic region.