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. 2019 Jul 2;9:9526. doi: 10.1038/s41598-019-45457-9

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Genome folding within topologically associating domains (TADs) can exhibit mesoscale core-periphery network structure. (A) Relative interaction frequency (Observed) and background-corrected interaction frequency (Observed/Expected) Hi-C heatmaps for a given TAD in mouse embryonic stem (ES) cells, neural progenitor cells (NPCs), and cortical neurons (CNs). Green lines, borders of TADs. Green arrowheads, genome structure signal indicative of a persistent looping interaction in ensemble Hi-C maps. (B) 3-D genome folding can be represented as a network where nodes correspond to bins of DNA and edges correspond to bin-bin interaction frequencies. Interaction frequency heatmaps of genome folding can be represented as adjacency matrices, allowing tools from graph theory and network science to be readily applied. Blue lines represent TAD boundaries. (C,D) To test for the possible presence of core-periphery structure created by looping interactions within TADs, we computed the core-periphery quality index Q for all true TADs compared to pseudo-TADs generated by choosing size-matched genomic regions at random. A Kolmogorov–Smirnov test was used to compare Q values for TADs vs. randomly placed, size-matched genomic regions in ES cells, NPCs, and CNs.