This track set displays topologically associating domains (TADs) and TAD boundaries in the human 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. +self-interacting regions of the genome, typically hundreds of kilobases to about a megabase. Their boundaries (frequently bound by CTCF and cohesin) insulate neighboring regions and -constrain enhancer-promoter contacts. Disruption of a TAD boundary can rewire gene regulation -and cause disease, and TADs are widely used to nominate candidate target genes for non-coding -variants. +constrain enhancer-promoter contacts.
The set contains three complementary sources:
The table below summarizes how each of these tracks' domains or boundaries were called and at what resolution:
Track Feature Calling method Resolution Dixon 2012 Domains Directionality-index HMM (lifted from hg18) 40 kb Schmitt 2016 Boundaries Insulation score (native hg19) 40 kb McArthur & Capra 2021 Boundaries (stability) Boundary sharing across 37 reprocessed cell-type maps (native hg19) 100 kb windows
Two further domain sources are available on the hg38 assembly:
-The domain track (Dixon) answers "are my variant and a candidate gene in the -same TAD?" and helps prioritize target genes at non-coding GWAS loci. The -boundary tracks (Schmitt, stability) answer "does my structural variant disrupt -an insulating boundary?" and help interpret the regulatory impact of deletions, -duplications, and inversions. -
-Each source is shown as a separate track because TAD calls are not directly comparable across studies: different algorithms (directionality index/HMM, insulation score) and resolutions (40–100 kb) produce different calls of the same underlying biology. -Domains are drawn as boxes spanning each self-interacting region; boundaries -are drawn as the short bins that divide adjacent domains. Because calls are made on binned -data, domain edges are uncertain to roughly the caller's bin size, and the bin width of a -boundary feature reflects this localization precision, not a measured physical width. Domains -do not tile the genome end to end; the gaps between domain boxes are inter-domain or -unorganized regions, not display artifacts. +Because TADs are called from Hi-C data analyzed in fixed-size bins, domain edges are +uncertain to roughly the bin size, and the width of a boundary reflects this precision, not +a measured physical width. Domains do not cover the whole genome, and the gaps between +domains are inter-domain or unorganized regions, not display artifacts.
Each source was called independently by its original study; the calling method and resolution for each are summarized in the table in the Description above. See the individual subtrack description pages for full methods, source publications, and assembly/liftOver details for each dataset.
The UCSC source for this track set is available on GitHub: doc/hg19.txt (makedoc), makeDb/scripts/tad (build scripts), and trackDb/human/hg19/tad.ra (trackDb).
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.
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 + +Topological domains in mammalian genomes identified by analysis of chromatin interactions. +Nature. 2012 Apr 11;485(7398):376-80. +DOI: 10.1038/nature11082; PMID: 22495300; PMC: PMC3356448
-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;108(2):269-283. -doi:10.1016/j.ajhg.2021.01.001 +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
-Schmitt AD, Hu M, Jung I, Xu Z, et al. -A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human -Genome. Cell Rep. 2016;17(8):2042-2059. -doi:10.1016/j.celrep.2016.10.061 +Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL et al. + +A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. +Cell Rep. 2016 Nov 15;17(8):2042-2059. +DOI: 10.1016/j.celrep.2016.10.061; PMID: 27851967; PMC: PMC5478386