Figure 2. Tethering improves the signal-to-noise ratio of conformation capture.
(a,b) TCC can reproduce the results obtained by Hi-C10. A genome-wide contact frequency map is compiled from the ligation frequency data generated by tethered (TCC) (a) and non-tethered (Hi-C) (b) conformation capture. The portion of each map that corresponds to the intra-chromosomal contacts of chromosome 2 is shown. The intensity of the red color in each position of the map represents the observed frequency of contact between corresponding segments of the chromosome which are shown on the top and to the left of the map. In these maps, chromosomes 2 is divided into segments that span 277 HindIII sites each, resulting in 258 segments of ∼1 Mb (Supplementary Methods). A pair of tick marks on the ideogram encompasses 4986 HindIII sites. In this and other figures, the white lines in the heatmaps mark the unalignable region of the centromeres. See Supplementary Figure 1a for the tethered contact frequency maps of all the other chromosomes.
(c) The observed fractions of intra (dark red) and inter-chromosomal (light blue) ligations in tethered (T) and non-tethered (NT) libraries produced using HindIII or MboI. The random ligation (RL) bar represents the expected fractions if all ligations occurred between non-crosslinked DNA fragments. For the non-tethered MboI library only, these fractions were determined by sequencing 160 individual DNA molecules from three replicates of the experiment. See Supplementary Table 1 for the sequencing output information of the other three libraries.
(d,e) The genome-wide enrichment map for chromosome 2, compiled from the tethered (d) and non-tethered (e) HindIII libraries. Enrichment is calculated as the ratio of the observed frequency in each position to its expected value; expected values were obtained assuming completely random ligations (Methods). Red and light blue respectively indicate enrichment and depletion of a contact in accordance with the color key between the panels. Chromosome 2 (left) extends along the Y-axis while all 23 chromosomes (top) extend along the X-axis. The zoomed panel to the right of each map magnifies the section that corresponds to contacts between the small arm of chromosome 2 and chromosomes 20, 21, 22, and X. For these maps, each chromosome is divided into segments that span 558 HindIII sites, leading to respectively 116 and 1384 segments of ∼1.5 Mb for chromosome 2 and all other chromosomes. A pair of tick marks on chromosome 2 spans 5022 HindIII sites.