Developmental enhancers are typically located in the same topologically associating domain (TAD) as their target genes, and the prevailing notion has been that the merger or rearrangement of TADs leads to ectopic gene expression, as shown at some loci. However, whether all genes are affected in a similar manner was unclear. Now, a study in Nature Genetics shows that genomic rearrangements that cause extensive changes to chromatin topology do not alter expression for the majority of genes, suggesting that properties other than chromatin topology determine enhancer–promoter interactions.
In vertebrates, CTCF binding is enriched at the boundaries of TADs. As CTCF has been shown to act as an insulator in both insulator assays in Drosophila melanogaster and at imprinted loci, it has been assumed that TAD boundaries act as insulators that block enhancers from interacting with genes on the other side of the boundaries. “That TAD boundaries restrict enhancer function, that is, that enhancers can only regulate genes in the same TAD and not ‘cross’ the boundary, has since almost become a dogma,” says senior author Eileen Furlong (EMBL Heidelberg, Germany).
To assess this question more systematically, Ghavi-Helm et al. chose the D. melanogaster balancer chromosomes as a source of genome rearrangements. These highly rearranged chromosomes, generated mainly by X-ray irradiation, can be used to genetically screen a model organism population and select for heterozygotes carrying a lethal recessive mutation. The team crossed a balancer strain to an isogenic wild-type strain and then performed allele-specific Hi-C and RNA sequencing (RNA-seq) to determine the impact on topology and gene expression of both the balancer and the wild-type chromosome.
Strikingly, the researchers found that while TAD boundaries mattered for some genes, as shown previously, these instances were rare. In the majority of cases, gene expression was not affected by genomic rearrangements even though many TADs were reshuffled, sometimes doubling in size. In other words, enhancers still regulated their correct genes despite other genes now being in their vicinity. “This finding is very surprising to many, but it actually fits with recent emerging data from others,” says Furlong. For example, previously “published imaging data show huge cell-to-cell heterogeneity in TAD size, so the location of the ‘boundary’ is different and therefore cannot be the key to restraining enhancer activity, otherwise gene expression would vary greatly from cell to cell.”
“you can massively disrupt genome organization without large-scale effects on gene expression”
The notion that you can massively disrupt genome organization without large-scale effects on gene expression is important, as it emphasizes that TADs are not essential for regulating the expression of all genes. How far these findings can be extrapolated considering that the original balancer inversions were viable needs to be determined. Regardless, it is evident that many lessons remain to be learned about the relationship between chromatin topology and gene expression.
Ghavi-Helm, Y. et al. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nat. Genet. https://doi.org/10.1038/s41588-019-0462-3 (2019)
Schoenfelder, S. & Fraser, P. Long-range enhancer–promoter contacts in gene expression control. Nat. Rev. Genet. 20, 437–455 (2019)