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. 2021 Dec 20;50(1):207–226. doi: 10.1093/nar/gkab1242

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© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 1. — Acute depletion of endogenous CTCF protein maintains compartment organization, but compromises global TAD insulation. (A) The mAID-mClover3 cassette for auxin-inducible degron is tagged to the C-terminus of CTCF on both alleles in a HCT116 cell line wherein OsTIR1 is integrated at the AAVS1 locus. (B) Immunoblotting shows complete degradation of endogenous mAID-mClover3-tagged CTCF (CTCF-mAC) upon auxin treatment. (C and D) Heatmaps (C) and scatterplots (D) of ChIP-Seq signals called for CTCF (left) and SMC1 (right) show marked reductions in the global occupancies of both proteins upon auxin treatment. (E) Hi-C contact maps generated by HiCExplorer at 100- and 10-kb resolution (version 3.4.3) (113). ChIP-seq signal tracks for CTCF and SMC1 were aligned below the contact maps at 10-kb resolution. (F) Distributions of cis Eigenvector 1 values across the entirety of chromosome 8 with and without auxin treatment. (G) Scatterplot shows that CTCF depletion does not affect genome-wide cis Eigenvector 1 values. (H) Saddle plots of compartmentalization strength with and without auxin treatment. (I) Number of TAD boundaries obtained with Hi-C data. (J) Genome-wide averaged insulation scores plotted against distance around insulation center at WT TAD boundaries. (K) Heatmaps show the average observed/expected Hi-C interactions in the TAD regions. (L) Boxplot shows TAD strength with and without auxin treatment.