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. 2020 Mar 31;2(2):lqaa020. doi: 10.1093/nargab/lqaa020

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© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://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 7. — Demonstrations of PHi-C for Hi-C data of DT-40 cells. (A) PHi-C analysis for chromosome 7 of DT-40 cells at G2 (0 min), 5, 15, 30 and 60 min. Contact matrices of the Hi-C experiment with 100-kb bins (upper) and optimized contact matrices with the correlation value (lower). (B) Snapshots of polymer conformations in a 4D polymer dynamics simulation. (C) Time series of the shape lengths of the major (yellow) and minor (purple) axes for polymer conformations in 100 polymer dynamics simulations starting from the same initial conformation. Thick curves represent the averages. (D) Curves of optimized interaction parameters, , averaged at each genomic distance (separation, |i − j| × 100 kb). A triangle indicates a position of a local peak inducing compaction within 2 Mb. Arrows indicate positions of a local peak generating periodicity of attractive interactions around 4, 6 and 10 Mb at 15, 30 and 60 min, respectively.

Inline graphic — Demonstrations of PHi-C for Hi-C data of DT-40 cells. (A) PHi-C analysis for chromosome 7 of DT-40 cells at G2 (0 min), 5, 15, 30 and 60 min. Contact matrices of the Hi-C experiment with 100-kb bins (upper) and optimized contact matrices with the correlation value (lower). (B) Snapshots of polymer conformations in a 4D polymer dynamics simulation. (C) Time series of the shape lengths of the major (yellow) and minor (purple) axes for polymer conformations in 100 polymer dynamics simulations starting from the same initial conformation. Thick curves represent the averages. (D) Curves of optimized interaction parameters, , averaged at each genomic distance (separation, |i − j| × 100 kb). A triangle indicates a position of a local peak inducing compaction within 2 Mb. Arrows indicate positions of a local peak generating periodicity of attractive interactions around 4, 6 and 10 Mb at 15, 30 and 60 min, respectively.