Making sense of the linear genome, gene function and TADs

Abstract

Background: Topologically associating domains (TADs) are thought to act as functional units in the genome. TADs co-localise genes and their regulatory elements as well as forming the unit of genome switching between active and inactive compartments. This has led to the speculation that genes which are required for similar processes may fall within the same TADs, allowing them to share regulatory programs and efficiently switch between chromatin compartments. Results: We investigated the relationship between TADs and gene function. To do this we developed a TAD randomisation algorithm to generate sets of "random TADs" to act as null distributions. We found that while pairs of paralogous genes are enriched in TADs overall, they are depleted in TADs with CTCF bound at both boundaries. By assessing gene constraint as a proxy for functional importance we found that genes which singly occupy a TAD have greater functional importance than genes which share a TAD, and these genes are enriched for developmental processes. We found little evidence that pairs of genes in CTCF bound TADs are more likely to be co-expressed or share functional annotations than can be explained by their linear proximity alone. Conclusions: These results suggest that algorithmically defined TADs consist of two functionally different groups, those which are bound by CTCF and those which are not. We detected no association between genes sharing the same CTCF TADs and increased co-expression or functional similarly, other than that explained by linear genome proximity. We do however find that functional important genes are more likely to fall within a TAD on their own suggesting that TADs play an important role in the insulation of these genes.

Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis

“…Because of the size distribution of TADs (Rao et al, 2014 ; Muro et al, 2019 ; Long et al, 2022 ), pair members in the larger distance categories, namely the SC_100–499 and SC_500+ groups, are likely too far apart from each other to be present in the same TAD in most if not all cases. Consistently, we found no significant differences for these categories.…”

Deciphering the species-level structure of topologically associating domains

“…We note that a systematic approach that can cover a large corpus of RNA-seq data is crucial for the statistical power to discern subtle links between chromatin structure and transcription. Such patterns may not be evident otherwise: e.g., in an analysis limited to only two cell types, Long et al [26] report not observing correlations of genes inside TADs beyond what gene proximity would suggest.…”

“…Recently, Mateo et al [24] described a multimodal single-cell technique to assay both DNA structure and gene expression but the study was limited to the Hox gene cluster in Drosophila. Also, though many prior studies broadly concur on the importance and role of TADs, some do not [25,26]. Unfortunately, studies that could help separate general principles from one-off phenomena have been limited by experimentally-determined TAD architecture's availability for only some cell types and differentiation conditions, far fewer than for which RNA-seq data is available.…”

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

“…Taken together, these results indicate that TAD boundaries are conserved but breakable, facilitating genome rearrangements during evolution while preserving intra-TAD functional and regulatory interactions. Indeed, certain classes of paralog protein-coding genes have been shown to co-localise within TADs and partially share regulatory elements in mammals (Ibn-Salem et al, 2017; Long et al, 2022) and clusters of conserved noncoding elements of key developmental genes coincide with TADs in human and flies (Harmston et al, 2017).…”