Description

OnTAD: Topologically Associating Domains
This composite track displays topologically associating domains (TADs) and TAD boundaries identified using the OnTAD method (An et al. 2019) applied to Hi-C data from mouse hematopoietic cell types and cell lines. TADs are self-interacting genomic domains that play important roles in gene regulation by constraining enhancer-promoter interactions.

The track includes TAD calls and boundary annotations for two cell types:

G1E-ER4

An immortalized, GATA1-null cell line derived from mouse embryonic stem cells that undergoes terminal erythroid maturation when GATA1 function is restored. TAD calls are provided at 10kb resolution from pooled Hi-C data, with both standard and joint TAD calling approaches.

HPC7

An immortalized hematopoietic progenitor cell line. TAD calls are provided at 10kb resolution from pooled Hi-C data, with both standard and joint TAD calling approaches.

For each cell type, four tracks are provided: TADs from standard calling, TADs from joint calling (which identifies TADs shared across conditions), and boundaries for each approach.

Display Conventions and Configuration

TADs are displayed as colored rectangles spanning the genomic intervals of each domain. TAD boundaries are shown as shorter intervals at the edges of domains.

Methods

TADs and TAD boundaries were identified using OnTAD (An et al. 2019), which uses an adaptive algorithm to call hierarchical TADs from Hi-C contact matrices. The Hi-C data were processed at 10kb resolution. Joint TAD calling identifies TADs that are consistently found across replicates or conditions.

Credits

Lin An developed and ran the OnTAD method. Belinda Giardine generated the tracks displayed and developed the track hub.

References

An L, Yang T, Yang J, Nuebler J, Xiang G, Hardison RC, Li Q, Zhang Y. OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries. Genome Biol. 2019 Dec 23;20(1):282. doi: 10.1186/s13059-019-1893-y. PMID: 31868433; PMCID: PMC6927095.

Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Res. 2024 Aug 20;34(7):1089-1105. PMID: 38951027; PMCID: PMC11368181.

Data Release Policy

These data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu