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Fig 2.
TADs and their genomic features (A) Browser screenshot of the genomic region surrounding wdr16, a MCC expressed gene. Top track is correlation coefficient between 3D chromosome conformation data between wild-type ectoderm and ectoderm injected with Multicilin, middle tracks show ChIPseq results as labeled, bottom track is called topological domains. (B) Interaction matrix of tethered conformation capture of the same genomic region. High-throughput methods of determining 3-dimensional chromatin structure such as TCC or HiC involve isolating DNA-protein complexes either via dilution (classical HiC), by fixing the proteins to avidin beads (TCC) or in situ nuclear fixation (in situ HiC), cutting DNA in this folded state with a restriction enzyme at many positions, religating, and sequencing. Restriction sites near loops of DNA will ligate across the loops at some frequency, which can then be used to reconstruct the frequency of contact between two close or distant regions of the genome. Here, regions interacting across the genome more often than a linear model of DNA would predict are shown, with darker red indicating a higher frequency of interactions.[6–9] (C-F) Metagene plots showing the distribution of various features relative to all TADs. All domains are normalized to the same size, the domain region is in the center of each plot, and the two vertical lines denote the domain boundaries. Areas in outer edges of the plot denote flanking genomic regions of some 200 kb. Each quartile of the plot (one quartile upstream, two quartiles inside the domain region itself, and one quartile downstream) is broken into 175 bins, and each dot denotes the measured values of one bin. Image published in: Quigley IK and Kintner C (2017) © 2017 Quigley, Kintner. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View |