We generated Hi-C contact matrices in two formats, namely cool and hic. Both contact matrices were generated from the same BAM file by using read pairs where both ends were aligned with a mapping quality of 60.

TADs were identified using the Arrowhead program implemented in the Juicertools package. We call TADs at 3 different resolutions: 10 kbp, 25 kbp, and 50 kbp. The parameters used were -k KR -m 2000 -r 10000 , -k KR -m 2000 -r 25000, and -k KR -m 2000 -r 50000

A/B compartments were identified at 1 Mbp using the eigenvector program implemented in the Juicertools package. The parameters used were KR BP 1000000.

Isochores were predicted using the isofinder program. The parameters used were 0.90 p2 3000. The output was post-processed to convert it to a bedpe format.

CTCF sites were predicted using the cread program. The position weight matrix was downloaded from CTCFBSDB 2.0 website. The output was then post-processed to convert it to a bed file.

Multires files were generated using the clodius package. These files can be loaded in HiGlass: an open source visualization tool.

One of the fundamental units of chromatin topology. TADs are regions of chromatin wherein all of the chromatin is in closer physical proximity. It is thought that regulatory signals can be conveyed more easily within a TAD than between TADs. TAD boundaries often occur at CTCF binding sites and are thought to be established and maintained by Cohesin/CTCF complex.

The whole genome could be divided into two spatial compartments, namely A and B. A compartments are associated with active/euchromatin and B compartments are associated with inactive/heterochromatin.

Extended genomic regions (typically 300kb to multimegabase) of uniform, characteristic GC content.

CCCTC-binding factor (CTCF) is a DNA binding protein, established as the main player in physical establishment of TAD boundaries.