Bentovim, L., Harden, T. T. & DePace, A. H. Transcriptional precision and accuracy in development: from measurements to models and mechanisms. Development 144, 3855–3866 (2017).
Article CAS PubMed PubMed Central Google Scholar
Ong, C.-T. & Corces, V. G. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat. Rev. Genet. 12, 283–293 (2011).
Article CAS PubMed PubMed Central Google Scholar
Field, A. & Adelman, K. Evaluating enhancer function and transcription. Annu. Rev. Biochem. 89, 213–234 (2020).
Article CAS PubMed Google Scholar
Zabidi, M. A. & Stark, A. Regulatory enhancer–core-promoter communication via transcription factors and cofactors. Trends Genet. 32, 801–814 (2016).
Article CAS PubMed PubMed Central Google Scholar
Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455–461 (2014).
Article ADS CAS PubMed PubMed Central Google Scholar
Spitz, F. & Furlong, E. E. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13, 613–626 (2012).
Article CAS PubMed Google Scholar
Banerji, J., Olson, L. & Schaffner, W. A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes. Cell 33, 729–740 (1983).
Article CAS PubMed Google Scholar
Gillies, S. D., Morrison, S. L., Oi, V. T. & Tonegawa, S. A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene. Cell 33, 717–728 (1983).
Article CAS PubMed Google Scholar
Mercola, M., Wang, X.-F., Olsen, J. & Calame, K. Transcriptional enhancer elements in the mouse immunoglobulin heavy chain locus. Science 221, 663–665 (1983).
Article ADS CAS PubMed Google Scholar
Banerji, J., Rusconi, S. & Schaffner, W. Expression of a β-globin gene is enhanced by remote SV40 DNA sequences. Cell 27, 299–308 (1981).
Article CAS PubMed Google Scholar
Halfon, M. S. Studying transcriptional enhancers: the founder fallacy, validation creep, and other biases. Trends Genet. 35, 93–103 (2019).
Article CAS PubMed Google Scholar
Galouzis, C. C. & Furlong, E. E. Regulating specificity in enhancer–promoter communication. Curr. Opin. Cell Biol. 75, 102065 (2022).
Article CAS PubMed Google Scholar
van Arensbergen, J., van Steensel, B. & Bussemaker, H. J. In search of the determinants of enhancer–promoter interaction specificity. Trends Cell Biol. 24, 695–702 (2014).
Article PubMed PubMed Central Google Scholar
Furlong, E. E. & Levine, M. Developmental enhancers and chromosome topology. Science 361, 1341–1345 (2018).
Article ADS CAS PubMed PubMed Central Google Scholar
Moreau, P. et al. The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. Nucleic Acids Res. 9, 6047–6068 (1981).
Article ADS CAS PubMed PubMed Central Google Scholar
Travers, A. Chromatin modification by DNA tracking. Proc. Natl Acad. Sci. USA 96, 13634–13637 (1999).
Article ADS CAS PubMed PubMed Central Google Scholar
Hatzis, P. & Talianidis, I. Dynamics of enhancer–promoter communication during differentiation-induced gene activation. Mol. Cell 10, 1467–1477 (2002).
Article CAS PubMed Google Scholar
Bulger, M. & Groudine, M. Looping versus linking: toward a model for long-distance gene activation. Genes Dev. 13, 2465–2477 (1999).
Article CAS PubMed Google Scholar
Chen, Z. et al. Widespread increase in enhancer–promoter interactions during developmental enhancer activation in mammals. Preprint at bioRxiv https://doi.org/10.1101/2022.11.18.516017 (2022).
Gasperini, M. et al. A genome-wide framework for mapping gene regulation via cellular genetic screens. Cell 176, 377–390 (2019).
Article CAS PubMed PubMed Central Google Scholar
Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012).
Article CAS PubMed PubMed Central Google Scholar
Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012).
Article ADS CAS PubMed PubMed Central Google Scholar
Goel, V. Y., Huseyin, M. K. & Hansen, A. S. Region capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments. Nat. Genet. 55, 1048–1056 (2023).
Article CAS PubMed PubMed Central Google Scholar
Zuin, J. et al. Nonlinear control of transcription through enhancer–promoter interactions. Nature 604, 571–577 (2022).
Article ADS CAS PubMed PubMed Central Google Scholar
Brückner, D. B., Chen, H., Barinov, L., Zoller, B. & Gregor, T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science 380, 1357–1362 (2023).
Article ADS PubMed Google Scholar
Mateo, L. J. et al. Visualizing DNA folding and RNA in embryos at single-cell resolution. Nature 568, 49–54 (2019).
Article ADS CAS PubMed PubMed Central Google Scholar
Chen, H. et al. Dynamic interplay between enhancer–promoter topology and gene activity. Nat. Genet. 50, 1296–1303 (2018).
Article CAS PubMed PubMed Central Google Scholar
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).
Article CAS PubMed PubMed Central Google Scholar
Deng, W. et al. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell 158, 849–860 (2014).
Article CAS PubMed PubMed Central Google Scholar
Hsieh, T.-H. S. et al. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Mol. Cell 78, 539–553 (2020).
Article CAS PubMed PubMed Central Google Scholar
Hsieh, T.-H. S. et al. Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1. Nat. Genet. 54, 1919–1932 (2022).
Article CAS PubMed PubMed Central Google Scholar
Aljahani, A. et al. Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nat. Commun. 13, 2139 (2022).
Article ADS CAS PubMed PubMed Central Google Scholar
Fulco, C. P. et al. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations. Nat. Genet. 51, 1664–1669 (2019).
Article CAS PubMed PubMed Central Google Scholar
Karr, J. P., Ferrie, J. J., Tjian, R. & Darzacq, X. The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication. Genes Dev. 36, 7–16 (2022).
Article CAS PubMed PubMed Central Google Scholar
Alexander, J. M. et al. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 8, e41769 (2019).
留言 (0)