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. 2020 Dec 31;22(1):347. doi: 10.3390/ijms22010347

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© 2020 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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Downregulated TADs express stage specific genes and are reorganized during ESC to NCC differentiation. At interacting (q < 0.001) upregulated and downregulated anchor-anchor midpoints: (A) Differential gene expression. (B) TAD overlap. (C) Directionality Index. (D) Gene Ontology Category Enrichment. Two-way ANOVA Tukey Method: ESC versus NCC for each location shown, p < 1⁻²; p < 1⁻⁴; p < 1⁻⁶; p < 1⁻⁸; p < 1⁻¹⁰. At TAD borders aligned left and right based on regulated gene directionality (adjusted p < 0.05): (E) TAD reorganization. (F) Differential gene expression. (G) Differential interaction anchor strength. (H) Differential nFGFR1 binding. (I) Differential gene coding and regulator feature enrichment. Z-Score statistics indicate bins which are outside the mean of all bins p < 0.05; p < 0.01; p < 0.005. (J) Differential chromatin looping. (K) Differential nFGFR1 looping. (L) Differential CTCF looping. Paired T-Test Bonferroni adjusted p < 10⁻⁵; p < 10⁻¹⁵; p < 10⁻²⁵.

Inline graphic — Downregulated TADs express stage specific genes and are reorganized during ESC to NCC differentiation. At interacting (q < 0.001) upregulated and downregulated anchor-anchor midpoints: (A) Differential gene expression. (B) TAD overlap. (C) Directionality Index. (D) Gene Ontology Category Enrichment. Two-way ANOVA Tukey Method: ESC versus NCC for each location shown, p < 1⁻²; p < 1⁻⁴; p < 1⁻⁶; p < 1⁻⁸; p < 1⁻¹⁰. At TAD borders aligned left and right based on regulated gene directionality (adjusted p < 0.05): (E) TAD reorganization. (F) Differential gene expression. (G) Differential interaction anchor strength. (H) Differential nFGFR1 binding. (I) Differential gene coding and regulator feature enrichment. Z-Score statistics indicate bins which are outside the mean of all bins p < 0.05; p < 0.01; p < 0.005. (J) Differential chromatin looping. (K) Differential nFGFR1 looping. (L) Differential CTCF looping. Paired T-Test Bonferroni adjusted p < 10⁻⁵; p < 10⁻¹⁵; p < 10⁻²⁵.