Mechanisms of long-range enhancer function

Vertebrate complexity is not explained by the relatively modest number of protein coding genes in the genome, but by the precise control of when and where genes are expressed. This control is encoded by hundreds of thousands of enhancers in the non-coding genome. Some enhancers activate their target genes across vast distances (up to one megabase or so). How they achieve this, and without activating inappropriate genes, remains unanswered. However, alignment of the regulatory domains of developmental genes with topologically associating domains (TADs) implicates 3D genome organisation and cohesin-mediated loop extrusion in both facilitating and restraining enhancer action¹.

By combining controlled protein degradation with synthetic transcription factors, we have shown that enhancers located far (several hundreds of kb) from their target genes in the mammalian genome require the cohesin complex to function, whereas enhancers located close to the target gene do not². We also recently revealed that some enhancers can unexpectedly act across TAD boundaries³.

Each rotation project will follow up these exciting discoveries, combining genome engineering, fluorescence in situ hybridisation, chromosome conformation capture and a CRISPR activation screen to address the following questions;

1. Does the same distance dependence on cohesion occur at different types of enhancers?
2. Is the ability of enhancers to activate genes beyond TAD boundaries affected by regulators of cohesin-mediated loop extrusion?

¹ Andrey G, Mundlos S. (2017) The three-dimensional genome: regulating gene expression during pluripotency and development. Development. 144:3646-3658. doi: 10.1242/dev.148304.

² Kane L, et al. (2022) Cohesin is required for long-range enhancer action at the Shh locus. Nat Struct Mol Biol. 29, 891-897. doi: 10.1038/s41594-022-00821-8.

³ Williamson I, et al. (2025) Bystander activation across a TAD boundary supports a cohesin-dependent transcription cluster model for enhancer function. Genes Dev. 39:1012-1024. doi: 10.1101/gad.352648.125.