I have a basic question regarding enhancer screening using modified BACs.
Basically, as far as I know, endogenous spatiotemporal gene expression mediated by a specific enhancer requires the physical contact between said enhancer and its target gene promoter. The 3D topology is thus an important gene regulatory layer.
However, when using reporter-modified BACs to screen for enhancer activity within the region encompassed by the BAC, the tested region is then tested outside its genomic, conformational context. Still, many studies show reporter gene expression recapitulating endogenous gene expression, indicating the enhancers located within the BAC region are able to drive reporter gene expression, even though they are not in their endogenous 3D context.
Is the 3D conformation/physical contact therefore less important then described? Or am I missing something in my thinking here?
Thanks a lot for some insight!