Fig. 2
From: 3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering
Representative output of 3C, 4C, 5C, ChIA-PET and Hi-C analysis. a A profile of 3C experiment for the murine β-globin locus showing looping and interaction between the Locus Control Region (LCR) and the expressing βmaj gene (reproduced from [47] with permission from Elsevier, ©2002). The murine β-globin locus contains hypersensitive sites (HS, red arrows and ellipses), an LCR being comprised of 5’HS1–6, globin genes including εy, βh1, βmaj and βmin (triangles), and olfactory receptor (OR) genes (white boxes). The x-axis represents position in the locus, and y-axis represents relative cross-linking frequency for the βmaj gene (black shading) with the rest of restriction fragments (gray shading). In erythroid cells, βmaj is active (red line), and the LCR come in close spatial proximity with the gene. However, the gene is silent in brain cells (blue line), and no such situation is observed. In 3C assay, primers are designed for restriction fragments of interest. Then, the spatial information between restriction fragments (one vs one) can be achieved by assessing the amplification efficiency. b 4C interactome of FIS2 gene on chromosome 2 in Arabidopsis (reproduced from [18] with permission from CC BY 2.0 license). FIS2 is defined as a viewpoint, and the genome is queried for positions that contact this site in space (one vs all). The results showed that chromosomal interactions have been centred around the viewpoint. c Interaction map of 5C assay for the 4.5-Mbp region containing Xist in undifferentiated mouse embryonic stem cells (reproduced from [75] with permission from Nature Publishing Group, ©2012). 5C analyses showed discrete self-associating chromosomal domains occurring at the sub-megabase scale (TADs A–I). 5C experiment requires a mix of 3C templates and thousands of primers (5C-Forward and 5C-Reverse) to allow concurrent determination of interactions between multiple fragments (many vs many). d Visualization of ChIA-PET associations mediated by Cut14-Pk (condensin) on chromosome II in fission yeast (reproduced from [139] with permission from Nature Publishing Group, ©2016). ChIA-PET offers the results of chromatin interactions exclusively to those fragments bound by protein of interest (all vs all mediated by specific protein). e Heat maps of Hi-C interactions among all chromosomes from human lymphoblast. Interaction matrix of the genome (all vs all) is built with bin size of 1Mbp (reproduced with permission from Nature Publishing Group, ©2011)