Cohesin is required for long-range enhancer action at the Shh locus

Sanborn, A. L. et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc. Natl Acad. Sci. USA 112, E6456–E6465 (2015).

CAS  PubMed  PubMed Central  Google Scholar 

Fudenberg, G. et al. Formation of chromosomal domains by loop extrusion. Cell Rep. 15, 2038–2049 (2016).

CAS  Article  Google Scholar 

Rao, S. S. P. et al. Cohesin loss eliminates all loop domains. Cell 171, 305–320 (2017).

CAS  Article  Google Scholar 

Guo, Y. et al. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell 162, 900–910 (2015).

CAS  Article  Google Scholar 

de Wit, E. et al. CTCF binding polarity determines chromatin looping. Mol. Cell 60, 676–684 (2015).

Article  Google Scholar 

Nora, E. P. et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169, 930–933.e22 (2017).

CAS  Article  Google Scholar 

Wutz, G. et al. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 36, 3573–3599 (2017).

CAS  Article  Google Scholar 

Lupiáñez, D. G., Spielmann, M. & Mundlos, S. Breaking TADs: how alterations of chromatin domains result in disease. Trends Genet. 32, 225–237 (2016).

Article  Google Scholar 

Symmons, O. et al. The Shh topological domain facilitates the action of remote enhancers by reducing the effects of genomic distances. Dev. Cell 39, 529–543 (2016).

CAS  Article  Google Scholar 

Haarhuis, J. H. I. et al. The cohesin release factor WAPL restricts chromatin loop extension. Cell 169, 693–707.e14 (2017).

CAS  Article  Google Scholar 

Moore, J. M. et al. Loss of maternal CTCF Is associated with peri-implantation lethality of Ctcf null embryos. PLoS ONE 7, e34915 (2012).

CAS  Article  Google Scholar 

Soshnikova, N., Montavon, T., Leleu, M., Galjart, N. & Duboule, D. Functional analysis of CTCF during mammalian limb development. Dev. Cell 19, 819–830 (2010).

CAS  Article  Google Scholar 

Merkenschlager, M., Ege, A. & Nora, P. CTCF and cohesin in genome folding and transcriptional gene regulation. Annu. Rev. Genom. Hum. Genet 17, 17–43 (2016).

CAS  Article  Google Scholar 

Cuartero, S. et al. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat. Immunol. 19, 932–941 (2018).

CAS  Article  Google Scholar 

Calderon, L. et al. Cohesin-dependence of neuronal gene expression relates to chromatin loop length. eLife 11, e76539 (2022).

CAS  Article  Google Scholar 

Schwarzer, W. et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature 551, 51–56 (2017).

Article  Google Scholar 

Anderson, E., Devenney, P. S., Hill, R. E. & Lettice, L. A. Mapping the Shh long-range regulatory domain. Development 141, 3934–3943 (2014).

CAS  Article  Google Scholar 

Williamson, I. et al. Developmentally regulated Shh expression is robust to TAD perturbations. Development. 146, dev179523 (2019).

Lettice, L. A. et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12, 1725–1735 (2003).

CAS  Article  Google Scholar 

Sagai, T. et al. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development 132, 797–803 (2005).

CAS  Article  Google Scholar 

Williamson, I., Lettice, L. A., Hill, R. E. & Bickmore, W. A. Shh and ZRS enhancer colocalisation is specific to the zone of polarising activity. Development 143, 2994–3001 (2016).

CAS  PubMed  PubMed Central  Google Scholar 

Benabdallah, N. S. et al. Decreased enhancer–promoter proximity accompanying enhancer activation. Mol. Cell 76, 473–484.e7 (2019).

CAS  Article  Google Scholar 

Paliou, C. et al. Preformed chromatin topology assists transcriptional robustness of Shh during limb development. Proc. Natl Acad. Sci. USA 116, 12390–12399 (2019).

CAS  Article  Google Scholar 

Luan, J. et al. Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Cell Rep. 34, 108783 (2021).

CAS  Article  Google Scholar 

Rhodes, J. D. P. et al. Cohesin disrupts polycomb-dependent chromosome interactions in embryonic stem cells. Cell Rep. 30, 820–835 (2020).

CAS  Article  Google Scholar 

Benabdallah, N. S. et al. SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells. Open Biol. 6, 160197 (2016).

Article  Google Scholar 

Despang, A. et al. Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture. Nat. Genet. 51, 1263–1271 (2019).

CAS  Article  Google Scholar 

Kim, Y., Shi, Z., Zhang, H., Finkelstein, I. J. & Yu, H. Human cohesin compacts DNA by loop extrusion. Science 366, 1345–1349 (2019).

CAS  Article  Google Scholar 

Zuin, J. et al. Nonlinear control of transcription through enhancer-promoter interactions. Nature 604, 572–577 (2022).

Article  Google Scholar 

Boyle, S. et al. A central role for canonical PRC1 in shaping the 3D nuclear landscape. Genes Dev. 34, 931–949 (2020).

CAS  Article  Google Scholar 

Lim, B. & Levine, M. S. Enhancer–promoter communication: hubs or loops? Curr. Opin. Genet Dev. 67, 5–9 (2021).

CAS  Article  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).

CAS  Article  Google Scholar 

Bonev, B. et al. Multiscale 3D genome rewiring during mouse neural development. Cell 171, 557–572 (2017).

CAS  Article  Google Scholar 

Therizols, P. et al. Chromatin decondensation is sufficient to alter nuclear re-organization in embryonic stem cells. Science 346, 1238–1242 (2014).

CAS  Article  Google Scholar 

留言 (0)

沒有登入
gif