3C queries interactions on a one-by-one basis; 4C identifies interactions between a single region and the rest of the genome; 5C generates a high-resolution interaction matrix of a large genomic region; Capture Hi-C, ChIA-PET and other ChIP-based methods characterize chromatin-looping interactions over several different loci; and finally Hi-C queries genome-wide chromatin interactions at low or high resolution.Three-dimensional organization of the chromatin has important roles in transcription, replication, DNA repair, and pathologic events such as translocations. There are two fundamental ways to study higher-order chromatin organization: microscopic and molecular approaches. Chromosome Conformation Capture (3C) Chromosome conformation capture is used to identify the interaction frequency of two selected fragments in the genome. If 4C and 5C are sequels to 3C, then Hi-C is a total franchise reboot (and as The Dark Knight showed us, that can be a great thing). We further discuss the different types of data generated by the 3C-based methods and how they can be used to answer distinct biological questions.Contract Grant Sponsor: National Institutes of Health; Contract Grant Numbers: P01 CA082834 and R01 CA139322An overview of the 3C-based techniques for intra- and interchromosaomal interactions. At the end of the 3C procedure, a pool of genome-wide intra-and inter-chromosomal interactions is generated (Naumova et al., 2012). Chromosome conformation capture (3C) technology is a powerful and increasingly popular tool for analyzing the spatial organization of genomes. The cell cycle is a process and function of a cell with different phases essential for cell growth, proliferation, and replication. Methodology. Recently, we have shown, using a high-throughput approach (Capture-C), the interrogation of cis -interactions, at hundreds of loci at high-resolution in a single experiment 12 . This is illustrated by the demonstration that genes positioned near the nuclear periphery are often silenced, whereas genes in the interior of the nucleus are frequently active. The development of chromosome conformation capture (3C) 4 assays and, in particular, their recent high-throughput variants (e.g. High-resolution Chromosome Conformation Capture: Hi-C Schematic representation of Hi-C workflow adapted from Davies et al. Hi-C is the first of the 3C derivative technologies to be truly genome-wide. … It depends on the structure and … (2009). Advances in chromosome conformation capture techniques together with newly developed complementary methods have fueled an exciting era of discovery in chromosome structure and nuclear organization. It has been long recognized that nuclear and chromatin organization is strongly associated with gene activity and chromatin state. For both panels, contact frequencies were normalized, binned to 50-kb resolution. Nat Genet, 37, 31-40. Crosslinked chromatin is digested and the overhangs of the restriction enzymes are filled-inusing biotin-labelled nucleotides following blunt … By using 3C (chromosome conformation capture) and FISH (fluorescence in situ hybridization) to map the regions of chromosome intermingling, it was revealed that these regions contain a higher density of active genes and are enriched with markers of transcriptional activation and repression, such as activated RNAPII. Conventional chromosome conformation capture (3C), allows for the detailed analysis of the interactions between regulatory elements and promoters at individual loci 6-11. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. The ChIA-PET method combines ChIP-based methods (Kuo & Allis, 1999), and Chromosome conformation capture (3C), to extend the capabilities of both approaches.