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<jats:title>ABSTRACT</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>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.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>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.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>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.</jats:p></jats:sec>

Original publication

DOI

10.1101/2020.09.28.316786

Type

Journal article

Publisher

Cold Spring Harbor Laboratory

Publication Date

01/10/2020