On the existence and functionality of topologically associating domains

Abstract

Genomes across a wide range of eukaryotic organisms fold into higher-order chromatin domains. Topologically associating domains (TADs) were originally discovered empirically in low-resolution Hi-C heat maps representing ensemble average interaction frequencies from millions of cells. Here, we discuss recent advances in high-resolution Hi-C, single-cell imaging experiments, and functional genetic studies, which provide an increasingly complex view of the genome's hierarchical structure-function relationship. On the basis of these new findings, we update the definitions of distinct classes of chromatin domains according to emerging knowledge of their structural, mechanistic and functional properties.

Fig. 1 |. The structural features of topologically associating domains.

a–d, Heat-map representations (top) and schematized globular interactions (bottom) of TADs (a,b) and nested subTADs (c,d). e, Cartoon representation of different classes of contact domains parsed by their structural features and degree of nesting. f, Identification of contact-domain classes from e in cortical neuron Hi-C data from ref. , binned at 10-kb resolution. g, Cohesin translocation extrudes DNA in an ATP-dependent manner into long-range looping interactions that form the topological basis for TAD and subTAD loop domains. h–k, Contact frequency heat maps of high-resolution Hi-C data from ref. , performed on embryonic stem cells (ESC, h,j) and neural progenitor cells (nPC; i,k). h,i, Green arrows denote the corners of a subset of the nested chromatin domains evident in this genomic region. j,k, Green arrows annotate a high-insulation-strength, cell-type-invariant TAD boundary. Blue arrows point to a lower-insulation-strength, cell-type-dynamic subTAD boundary.

Fig. 2 |. Chromatin domains and their boundaries are present in single cells.

a,b, Cartoon representations of contact domains identified in single cells via high-resolution imaging. a, Wild-type cells display a biased preference for boundary locations. b, After knockout (KO) of cohesin, globular domains still exist but do not display the same boundary preference. c, Representative heat maps of the effects of cohesin and Nipbl removal on loop and compartment domains, as portrayed in refs. ^,.

Fig. 3 |. Evidence for and against TADs as a critical functional intermediary in the regulation of genes by developmentally active enhancers.

a–c, Schematics of three emerging mechanisms through which loop domains can influence transcription: direct, strong contact of enhancers and promoters via persistent loops (red arcs) at the corners of domains (a), transient, weak contact of enhancers and promoters via transient loop extrusion (blue arcs) across the loop domain (b), and developmental miswiring of enhancers to non-target promoters outside of the TAD or subTAD after genetic destruction of loop domain boundaries (c). d, Representation of the activity readout of a reporter assay after random integration in genomic loci, from refs. ^,. e, Three published examples of boundary disruption or inversion leading to developmental issues. f, Depiction of a model of long-range transcriptional regulation in which an enhancer’s regulatory contribution trends with its activity signature and Hi-C contact frequency with the target gene. g, Schematized box plot of measured distances from the enhancer to the Sox2 promoter in actively expressing (left) and inactive (right) cells. NS, not significant. h, Representation of the relatively modest transcriptional changes observed after cohesin and Nipbl depletion observed in refs. ^,. RPKM, reads per kilobase per million mapped reads. i, Cartoon of unencumbered development observed after perturbation of a TAD boundary opposing the Shh gene.