Li, S., Vemuri, C. & Chen, C. DNA topology: a central dynamic coordinator in chromatin regulation. Curr. Opin. Struct. Biol. 87, 102868 (2024).
Article CAS PubMed Google Scholar
Jha, R. K., Levens, D. & Kouzine, F. Mechanical determinants of chromatin topology and gene expression. Nucleus 13, 94–115 (2022).
Article CAS PubMed PubMed Central Google Scholar
Kim, E., Gonzalez, A. M., Pradhan, B., van der Torre, J. & Dekker, C. Condensin-driven loop extrusion on supercoiled DNA. Nat. Struct. Mol. Biol. 29, 719–727 (2022).
Article CAS PubMed Google Scholar
Teves, S. S. & Henikoff, S. Transcription-generated torsional stress destabilizes nucleosomes. Nat. Struct. Mol. Biol. 21, 88–94 (2014).
Article CAS PubMed Google Scholar
Sheinin, M. Y., Li, M., Soltani, M., Luger, K. & Wang, M. D. Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss. Nat. Commun. 4, 2579 (2013).
Finzi, L. & Dunlap, D. Supercoiling biases the formation of loops involved in gene regulation. Biophys. Rev. 8, 65–74 (2016).
Article CAS PubMed PubMed Central Google Scholar
Chedin, F. & Benham, C. J. Emerging roles for R-loop structures in the management of topological stress. J. Biol. Chem. 295, 4684–4695 (2020).
Article CAS PubMed PubMed Central Google Scholar
Liu, Y., Bondarenko, V., Ninfa, A. & Studitsky, V. M. DNA supercoiling allows enhancer action over a large distance. Proc. Natl Acad. Sci. USA 98, 14883–14888 (2001).
Article CAS PubMed PubMed Central Google Scholar
Ma, J., Bai, L. & Wang, M. D. Transcription under torsion. Science 340, 1580–1583 (2013).
Article CAS PubMed PubMed Central Google Scholar
Chong, S., Chen, C., Ge, H. & Xie, X. S. Mechanism of transcriptional bursting in bacteria. Cell 158, 314–326 (2014).
Article CAS PubMed PubMed Central Google Scholar
Patel, H. P. et al. DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes. Mol. Cell 83, 1573–1587 (2023).
Article CAS PubMed PubMed Central Google Scholar
Kim, S., Beltran, B., Irnov, I. & Jacobs-Wagner, C. Long-distance cooperative and antagonistic RNA polymerase dynamics via DNA supercoiling. Cell 179, 106–119 (2019).
Article CAS PubMed Google Scholar
Kouzine, F., Sanford, S., Elisha-Feil, Z. & Levens, D. The functional response of upstream DNA to dynamic supercoiling in vivo. Nat. Struct. Mol. Biol. 15, 146–154 (2008).
Article CAS PubMed Google Scholar
Zhi, X. et al. Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli. J. Biol. Chem. 292, 14566–14575 (2017).
Article CAS PubMed PubMed Central Google Scholar
Joshi, R. S., Nikolaou, C. & Roca, J. Structure and chromosomal organization of yeast genes regulated by topoisomerase II. Int. J. Mol. Sci. 19, 134 (2018).
Article PubMed PubMed Central Google Scholar
Peter, B. J. et al. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 5, R87 (2004).
Article PubMed PubMed Central Google Scholar
Bordes, P. et al. DNA supercoiling contributes to disconnect σS accumulation from σS-dependent transcription in Escherichia coli. Mol. Microbiol. 48, 561–571 (2003).
Article CAS PubMed Google Scholar
Picker, M. A. et al. Localized modulation of DNA supercoiling, triggered by the Shigella anti-silencer VirB, is sufficient to relieve H-NS-mediated silencing. Nucleic Acids Res. 51, 3679–3695 (2023).
Article CAS PubMed PubMed Central Google Scholar
Vijayan, V., Zuzow, R. & O’Shea, E. K. Oscillations in supercoiling drive circadian gene expression in cyanobacteria. Proc. Natl Acad. Sci. USA 106, 22564–22568 (2009).
Article CAS PubMed PubMed Central Google Scholar
Pommier, Y., Nussenzweig, A., Takeda, S. & Austin, C. Human topoisomerases and their roles in genome stability and organization. Nat. Rev. Mol. Cell Biol. 23, 407–427 (2022).
Article CAS PubMed PubMed Central Google Scholar
Durand-Dubief, M., Persson, J., Norman, U., Hartsuiker, E. & Ekwall, K. Topoisomerase I regulates open chromatin and controls gene expression in vivo. EMBO J. 29, 2126–2134 (2010).
Article CAS PubMed PubMed Central Google Scholar
Miller, E. L. et al. TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nat. Struct. Mol. Biol. 24, 344–352 (2017).
Article CAS PubMed PubMed Central Google Scholar
Rialdi, A. et al. Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science 352, aad7993 (2016).
Article PubMed PubMed Central Google Scholar
Amatullah, H. et al. Epigenetic reader SP140 loss of function drives Crohn’s disease due to uncontrolled macrophage topoisomerases. Cell 185, 3232–3247 (2022).
Article CAS PubMed PubMed Central Google Scholar
Austin, C. A., Cowell, I. G., Khazeem, M. M., Lok, D. & Ng, H. T. TOP2B’s contributions to transcription. Biochem. Soc. Trans. 49, 2483–2493 (2021).
Article CAS PubMed Google Scholar
Pedersen, J. M. et al. DNA topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae. PLoS Genet. 8, e1003128 (2012).
Article PubMed PubMed Central Google Scholar
Roedgaard, M., Fredsoe, J., Pedersen, J. M., Bjergbaek, L. & Andersen, A. H. DNA topoisomerases are required for preinitiation complex assembly during GAL gene activation. PLoS ONE 10, e0132739 (2015).
Article PubMed PubMed Central Google Scholar
Morao, A. K., Kim, J., Obaji, D., Sun, S. & Ercan, S. Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans. Mol. Cell 82, 4202–4217 (2022).
Article CAS PubMed PubMed Central Google Scholar
Papapietro, O. & Nejentsev, S. Topoisomerase 2β and DNA topology during B cell development. Front. Immunol. 13, 982870 (2022).
留言 (0)