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Fig. 5 | Molecular Cytogenetics

Fig. 5

From: Differentially accessible, single copy sequences form contiguous domains along metaphase chromosomes that are conserved among multiple tissues

Fig. 5

Localization of DA domains in metaphase homologs relative to topologically associated domains (TADs) in interphase. The heat map (generated by 3D Genome Browser [38]) shows interaction frequencies between chromatin within each domain (yellow-turquoise areas) and surrounding chromatin in UCSC Genome Browser image (GRCh37/hg19). Each heatmap spans the chromosome coordinates indicated above. Alternating dark grey and light grey bars represent separate TADs assigned by the 3D Genome Browser. The scale in top left measures the intensity of contact frequency as the normalized number of contacts between 2 points. The frequency of intra-TAD interactions within and around each domain can be assessed by areas of frequent contact shown as bright red triangular signals occurring above the domain. Red intensity increases with higher frequency of interactions. The long-range interactions (white, pale red) > million bp in panels A-F have been covered to accommodate the insets magnifying intra-TAD interactions within each domain. A XDH domain localizes within a single TAD (dark grey). The XDH domain is within a section of genome with multiple intra-TAD interactions observed by multiple areas of high contact frequency at varying distances. B FGF6 domain localizes within a single TAD (dark grey). C COX5A domain is at one end of a single TAD (light grey). D HMGB1P1 domain is in the middle of a single TAD (dark grey) with frequent interactions occurring with loci in proximity with the domain. E TPM1 domain localizes within a single TAD (dark grey) approaching the boundary with the adjacent TAD. There are some intra-TAD interactions with sequences close to the domain but compared to other DA domains, they are fewer and less frequent. F The HMGB1P5 domain is the only domain not within a TAD. The proximity of the domain to the boundary of the TAD (dark grey) can be clearly seen

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