This track collection shows the original mouse topologically associating domain (TAD) calls from Dixon et al. 2012, the study that defined TADs. Two cell types are shown: mouse embryonic stem cells (mESC) and mouse cortex. TADs are self-interacting genomic regions whose boundaries (frequently bound by CTCF and cohesin) insulate neighboring regions and constrain enhancer-promoter contacts.
The calls were made on mm9 and are displayed here lifted to this assembly (see Methods).
The two cell types are separate subtracks. Domains were called from Hi-C data analyzed in fixed-size 40 kb bins, so domain edges are uncertain to roughly ±20 kb, and domains do not cover the whole genome.
TAD domains were called by Dixon et al. 2012 with the directionality-index hidden Markov model at 40 kb resolution (the published "Combined" replicate call set: 2,200 mESC and 1,518 cortex domains, mm9). UCSC lifted the mm9 coordinates to this assembly with liftOver (a small percentage of domains that did not map cleanly were dropped) and reformatted them to bigBed; no re-calling was performed. Lifted domains that came out more than twice their original size were also removed, because this happens when a domain spans a gap or a rearranged region between the two assemblies.
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 Apr 11;485(7398):376-80. DOI: 10.1038/nature11082; PMID: 22495300; PMC: PMC3356448