![]() ![]() As a result, biotin-marked ligation junctions can be purified more efficiently by streptavidin-coated magnetic beads, and chromatin interaction data can be obtained by direct sequencing of the Hi-C library. While 3C focuses on the analysis of a set of predetermined genomic loci to offer “one-versus-some” investigations of the conformation of the chromosome regions of interest, Hi-C enables “all-versus-all” interaction profiling by labeling all fragmented chromatin with a biotinylated nucleotide before ligation. The relative abundance of these chimeras, or ligation products, is correlated to the probability that the respective chromatin fragments interact in 3D space across the cell population. Then, the chromatin is solubilized and fragmented, and interacting loci are re-ligated together to create a genomic library of chimeric DNA molecules. The general procedure of Hi-C involves first crosslinking chromatin material using formaldehyde. 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. Hi-C comprehensively detects genome-wide chromatin interactions in the cell nucleus by combining 3C and next-generation sequencing (NGS) approaches and has been considered as a qualitative leap in C-technology (chromosome conformation capture-based technologies) development and the beginning of 3D genomics. In general, Hi-C is considered as a derivative of a series of chromosome conformation capture technologies, including but not limited to 3C (chromosome conformation capture), 4C (chromosome conformation capture-on-chip/circular chromosome conformation capture), and 5C (chromosome conformation capture carbon copy). Hi-C (or standard Hi-C) is a high-throughput genomic and epigenomic technique first described in 2009 by Lieberman-Aiden et al. An overview of the Hi-C workflow and its applications in research. If the nucleotide differences of two different alleles occur within the restriction site of a particular restriction enzyme, digestion of segments of DNA from individuals with different alleles for that particular gene with that enzyme would produce different fragments and that will each yield different band patterns in gel electrophoresis.Figure 1. In agarose gel electrophoresis, the restriction fragments yield a band pattern characteristic of the original DNA molecule and restriction enzyme used, for example the relatively small DNA molecules of viruses and plasmids can be identified simply by their restriction fragment patterns. These short extensions, called sticky ends, can form hydrogen bonded base pairs with complementary sticky ends on any other DNA cut with the same enzyme (such as a bacterial plasmid). In recombinant DNA technology, specific restriction endonucleases are used that will isolate a particular gene and cleave the sugar phosphate backbones at different points (retaining symmetry), so that the double-stranded restriction fragments have single-stranded ends. Illustration of typical restriction enzyme cleavage. Restriction fragments can be analyzed using techniques such as gel electrophoresis or used in recombinant DNA technology. A particular DNA molecule will always yield the same set of restriction fragments when exposed to the same restriction enzyme. Many cuts are made by one restriction enzyme because of the chance repetition of these sequences in a long DNA molecule, yielding a set of restriction fragments. Most restriction sites are palindromic, (the sequence of nucleotides is the same on both strands when read in the 5' to 3' direction of each strand), and are four to eight nucleotides long. Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site. JSTOR ( January 2020) ( Learn how and when to remove this template message)Ī restriction fragment is a DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme (restriction endonucleases), a process called restriction.Unsourced material may be challenged and removed.įind sources: "Restriction fragment" – news Please help improve this article by adding citations to reliable sources. This article needs additional citations for verification. ![]()
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