This track shows TAD boundary stability: for each 100 kb genomic window, how many of 37 cell-type contact maps place a TAD boundary there (McArthur & Capra, 2021). Boundaries shared by many cell types are evolutionarily constrained and enriched for complex-trait heritability.
This is a derived, cross-study summary, not a primary set of TAD calls. The 37 maps were uniformly re-processed (via the 3D Genome Browser, using the Dixon directionality pipeline) from five earlier studies (Rao 2014, Dixon 2015, Leung 2015, Schmitt 2016, and ENCODE cancer cell lines); 9 of those contexts overlap the Schmitt boundaries track in this set, so the two are not independent. The input maps were called at heterogeneous resolution (25 kb for the Rao-lab set, 40 kb for the others).
Each boundary (about 100 kb) is shaded by the number of cell-type maps sharing it (1–37): darker indicates a boundary shared by more cell types. Use the filter to show only boundaries shared by at least a chosen number of maps.
Interpreting the score: the score counts how many independent cell-type maps agree on a boundary, which serves as a confidence measure. High values mark stable boundaries shared across cell types: the most reliable, and enriched for CTCF binding and evolutionary constraint. Boundaries seen in only one or a few maps are largely cell-type-specific. Raising the filter yields a smaller, higher-confidence set of boundaries.
Stability groups: McArthur & Capra divided boundaries into quartiles of stability by the number of maps sharing them: 1 map (cell-type unique), 2–4, 5–13, and 14 or more of the 37 maps. These groups can serve as a guide when setting the filter. By default all boundaries are shown.
TAD boundaries from 37 re-processed cell-type maps were each represented as the 100 kb windows at both ends of every TAD. The genome was divided into 100 kb windows and, for each window, the number of maps with a boundary in it was counted (McArthur & Capra, 2021). Data were obtained from the authors' repository on assembly hg19 and lifted to this assembly with the UCSC liftOver tool where needed. Lifted boundaries that came out more than twice their original size were also removed, because this happens when a boundary spans a gap or a rearranged region between the two assemblies. One boundary bin that runs past the end of chromosome 17 on hg19 was shortened to end at the chromosome end. Each item is named by its source position on hg19.
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.
McArthur E, Capra JA. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. Am J Hum Genet. 2021 Feb 4;108(2):269-283. DOI: 10.1016/j.ajhg.2021.01.001; PMID: 33545030; PMC: PMC7895846