Description

This track set displays topologically associating domains (TADs) in the mouse genome, assembled from published Hi-C studies. TADs are self-interacting regions of the genome, typically hundreds of kilobases to about a megabase, and themselves nested, with smaller contact domains contained within larger top-level TADs. Their boundaries (frequently bound by CTCF and cohesin) insulate neighboring regions and constrain enhancer-promoter contacts.

The set contains three complementary sources, all domain calls:

• Dixon 2012 TADs – the original TAD domains in mESC and cortex (lifted from mm9).
• ENCODE contact domains – uniformly called TAD domains across mouse biosamples (Arrowhead/Hi-C), browsable by a faceted selector. Native mm10; lifted to mm39.
• 3D Genome Browser domains – TAD domains across mouse Hi-C/Micro-C datasets, exactly as called and published by the 3D Genome Browser, browsable by a faceted selector. Native mm10; lifted to mm39.

The human counterpart of this track set (on hg38) additionally includes TAD boundary tracks (Schmitt 2016, and a boundary-stability track); those datasets are human-only and have no mouse equivalent, so the mouse set is domains only.

How to Use These Tracks

The domain tracks (Dixon, ENCODE, 3D Genome Browser) answer "are my variant and a candidate gene in the same TAD?" and help prioritize target genes at non-coding regulatory loci. Because the domain tracks are nested (ENCODE calls smaller sub-TAD contact domains; Dixon and the 3D Genome Browser call larger top-level TADs), "which TAD?" is answered at different scales by different tracks. This mouse set is domains only; to ask whether a structural variant disrupts an insulating boundary, see the human (hg38) counterpart, which adds dedicated TAD boundary tracks.

Display Conventions and Configuration

Each source is shown as a separate track because TAD calls are not directly comparable across studies: different algorithms and resolutions produce different calls of the same underlying biology. Domains are drawn as boxes spanning each self-interacting region. Calls native to an earlier mouse assembly are lifted to the assembly being viewed (Dixon from mm9; ENCODE and the 3D Genome Browser from mm10 when viewed on mm39); the lift is noted in each track's long label. The ENCODE and 3D Genome Browser tracks contain many biosamples and are browsable with a faceted selector on their configuration pages.

Methods

See the individual subtrack description pages for full methods, source publications, and the liftOver details for each dataset. In brief: Dixon domains were called with the directionality-index HMM at 40 kb; ENCODE contact domains with Arrowhead (Juicer) on the ENCODE uniform Hi-C pipeline; and the 3D Genome Browser domains are that resource's own per-dataset TAD calls, shown verbatim (format normalization only).

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser's REST API. The underlying bigBed files can be downloaded from our download server.

References

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376-80. doi:10.1038/nature11082

Yu S, Fu Y, Wong JH, Wang J, Zhao H, Zhao J, Yue F. The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome architecture. Nucleic Acids Res. 2026;54(D1):D48-D54. doi:10.1093/nar/gkaf1109