TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function

Abstract

Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find that only 14% of all human TAD boundaries are shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons, compared to species-specific boundaries. CRISPR-Cas9 knockouts of two ultraconserved boundaries in mouse models leads to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations, and showcase the functional importance of TAD evolution.

Evolutionary analysis of gene ages across TADs associates chromatin topology with whole genome duplications

“…Future availability of TADs in a wider diversity of species will allow to investigate the conservation of these TADs and their chromatin interactions. [50][51][52] Interestingly, we noticed that gene age co-localisation patterns vary depending on TAD insulation and the co-localisation is actually not observed in lowly insulated TADs. In contrast, very high insulated TADs are more enriched in recently born genes and genes there tend to co-localise more with genes with genes born immediately before or after them.…”

Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees

“…To explore this conservation in a deeper phylogenetic context with experimental data, we analyzed conserved topologically associated domains (TADs) identified from Hi-C data generated from four murine and four primate species (Okhovat et al, 2023). We quantified patterns of 3D divergence among Pan individuals in these deeply conserved regions.…”

“…We compared the distribution of Pan 3D divergence overlapping experimentally validated conserved TAD boundaries to the genome-wide distribution. We used two sets of 10 kb conserved boundaries among autosomes and the X chromosome from Okhovat et al, 2023: 1) “primateconserved” boundaries (N = 491), defined as conserved among Homo sapiens , Hylobates moloch , Nomascus leucogenys , and Macaca mulatta , and 2) “ultraconserved” boundaries (N = 1,023), defined as conserved among all four primate species as well as four murines— Mus caroli , M. musculus , M. pahari , and Rattus norvegicus . We used liftOver (Hinrichs et al, 2006) with all default settings to convert boundaries from hg38 to panTro6 coordinates, resulting in 415 primate-conserved and 915 ultraconserved boundaries.…”

“… (A) The distribution of maximum 3D divergence for all windows (N = 4,420) and the most central window intersecting primate-conserved TAD boundaries from Okhovat et al, 2023 (N = 415). Distributions are shown in 0.01 divergence bins and the dashed line indicates the distribution means.…”

“…The genome-wide distribution and mean are shown in purple and the primate-conserved distribution and mean shown in yellow. (B) The distribution of maximum 3D divergence for all windows (N = 4,420) and the most central window intersecting ultra-conserved TAD boundaries from Okhovat et al, 2023 (N = 915). Distributions are shown in 0.01 divergence bins and the dashed line indicates the distribution means.…”