Although enhancers activate transcription from long distances, they stimulate transcription only through short-range interactions with the RNA polymerase II machinery. I posit that action at a distance is mediated by loops between distal and proximal enhancers that thereby bring proteins associated with distal enhancers near promoters.
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References
Cosma, M. P. et al. Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell 97, 299–311 (1999).
Core, L. J. et al. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat. Genet. 46, 1311–1320 (2014).
Richter, W. F. et al. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat. Rev. Mol. Cell Biol. 23, 732–749 (2022).
Chen, W. Y. et al. A TAF4 coactivator function for E proteins that involves enhanced TFIID binding. Genes Dev. 27, 1596–1609 (2013).
Nolis, I. K. et al. Transcription factors mediate long-range enhancer-promoter interactions. Proc. Natl Acad. Sci. USA 106, 20222–20227 (2009).
Deng, W. et al. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149, 1233–1244 (2012).
Struhl, K. Genetic properties and chromatin structure of the yeast gal regulatory element; an enhancer-like sequence. Proc. Natl Acad. Sci. USA 81, 7865–7869 (1984).
Jensen, C. L. et al. Long-range regulation of transcription scales with genomic distance in a gene-specific manner. Mol. Cell 85, 347–361 (2025).
Thomas, H. F. et al. Enhancer cooperativity can compensate for loss of activity over large genomic distances. Mol. Cell 85, 362–375 (2025).
Li, X. et al. GAGA-associated factor fosters loop formation in the Drosophila genome. Mol. Cell 83, 1519–1526.e1514 (2023).
Petrascheck, M. et al. DNA looping induced by a transcriptional enhancer in vivo. Nucl. Acids Res. 33, 3743–3750 (2005).
Sun, F. et al. The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter-enhancer looping. Genes Dev. 35, 1175–1189 (2021).
Ramasamy, S. et al. The Mediator complex regulates enhancer-promoter interactions. Nat. Struct. Mol. Biol. 30, 991–1000 (2023).
Aboreden, N. G. et al. LDB1 establishes multi-enhancer networks to regulate gene expression. Mol. Cell 85, 376–393 (2025).
Zhang, W. et al. FOXP3 recognizes microsatellites and bridges DNA through multimerization. Nature 624, 433–441 (2023).
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Struhl, K. Distal enhancers loop to proximal enhancers, not to promoters. Nat Rev Mol Cell Biol 26, 730–731 (2025). https://doi.org/10.1038/s41580-025-00889-2
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DOI: https://doi.org/10.1038/s41580-025-00889-2