Batty, P. & Gerlich, D. W. Mitotic chromosome mechanics: how cells segregate their genome. Trends Cell Biol. 29, 717–726 (2019).
Oldenkamp, R. & Rowland, B. D. A walk through the SMC cycle: from catching DNAs to shaping the genome. Mol. Cell 82, 1616–1630 (2022).
Yatskevich, S., Rhodes, J. & Nasmyth, K. Organization of chromosomal DNA by SMC complexes. Annu. Rev. Genet. 53, 445–482 (2019).
Hoencamp, C. & Rowland, B. D. Genome control by SMC complexes. Nat. Rev. Mol. Cell Biol. 24, 633–650 (2023).
Kim, E., Barth, R. & Dekker, C. Looping the genome with SMC complexes. Annu. Rev. Biochem. 92, 15–41 (2023).
Davidson, I. F. & Peters, J. M. Genome folding through loop extrusion by SMC complexes. Nat. Rev. Mol. Cell Biol. 22, 445–464 (2021).
Fudenberg, G. et al. Formation of chromosomal domains by loop extrusion. Cell Rep. 15, 2038–2049 (2016).
Nora, E. P. et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169, 930–944 (2017).
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).
Rao, S. S. P. et al. Cohesin loss eliminates all loop domains. Cell 171, 305–320 (2017).
Schwarzer, W. et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature 551, 51–56 (2017).
Haarhuis, J. H. I. et al. The cohesin release factor WAPL restricts chromatin loop extension. Cell 169, 693–707 (2017).
Zhang, H. et al. CTCF and transcription influence chromatin structure re-configuration after mitosis. Nat. Commun. 12, 5157 (2021).
Haering, C. H., Lowe, J., Hochwagen, A. & Nasmyth, K. Molecular architecture of SMC proteins and the yeast cohesin complex. Mol. Cell 9, 773–788 (2002).
Nasmyth, K. Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis. Annu. Rev. Genet. 35, 673–745 (2001).
Haering, C. H., Farcas, A. M., Arumugam, P., Metson, J. & Nasmyth, K. The cohesin ring concatenates sister DNA molecules. Nature 454, 297–301 (2008).
Ochs, F. et al. Sister chromatid cohesion is mediated by individual cohesin complexes. Science 383, 1122–1130 (2024).
Srinivasan, M., Fumasoni, M., Petela, N. J., Murray, A. & Nasmyth, K. A. Cohesion is established during DNA replication utilising chromosome associated cohesin rings as well as those loaded de novo onto nascent DNAs. eLife 9, e56611 (2020).
Cameron, G. et al. Sister chromatid cohesion establishment during DNA replication termination. Science 384, 119–124 (2024).
Zheng, G., Kanchwala, M., Xing, C. & Yu, H. MCM2-7-dependent cohesin loading during S phase promotes sister-chromatid cohesion. eLife 7, e33920 (2018).
Bastie, N. et al. Sister chromatid cohesion halts DNA loop expansion. Mol. Cell 84, 1139–1148 (2024).
Chatzidaki, E. E. et al. Ovulation suppression protects against chromosomal abnormalities in mouse eggs at advanced maternal age. Curr. Biol. 31, 4038–4051 (2021).
Waizenegger, I. C., Hauf, S., Meinke, A. & Peters, J. M. Two distinct pathways remove mammalian cohesin from chromosome arms in prophase and from centromeres in anaphase. Cell 103, 399–410 (2000).
Zhang, H. et al. Chromatin structure dynamics during the mitosis-to-G1 phase transition. Nature 576, 158–162 (2019).
Abe, S. et al. The initial phase of chromosome condensation requires Cdk1-mediated phosphorylation of the CAP-D3 subunit of condensin II. Genes Dev. 25, 863–874 (2011).
Kagami, Y., Ono, M. & Yoshida, K. Plk1 phosphorylation of CAP-H2 triggers chromosome condensation by condensin II at the early phase of mitosis. Sci. Rep. 7, 5583 (2017).
Gibcus, J. H. et al. A pathway for mitotic chromosome formation. Science https://doi.org/10.1126/science.aao6135 (2018).
Tedeschi, A. et al. Wapl is an essential regulator of chromatin structure and chromosome segregation. Nature 501, 564–568 (2013).
Nabet, B. et al. The dTAG system for immediate and target-specific protein degradation. Nat. Chem. Biol. 14, 431–441 (2018).
Yesbolatova, A. et al. The auxin-inducible degron 2 technology provides sharp degradation control in yeast, mammalian cells, and mice. Nat. Commun. 11, 5701 (2020).
Xie, L. et al. BRD2 compartmentalizes the accessible genome. Nat. Genet. 54, 481–491 (2022).
Busslinger, G. A. et al. Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl. Nature 544, 503–507 (2017).
Ladurner, R. et al. Sororin actively maintains sister chromatid cohesion. EMBO J. 35, 635–653 (2016).
Nishiyama, T. et al. Sororin mediates sister chromatid cohesion by antagonizing Wapl. Cell 143, 737–749 (2010).
Dreier, M. R., Bekier, M. E. 2nd & Taylor, W. R. Regulation of sororin by Cdk1-mediated phosphorylation. J. Cell Sci. 124, 2976–2987 (2011).
Nishiyama, T., Sykora, M. M., Huis in ‘t Veld, P. J., Mechtler, K. & Peters, J. M. Aurora B and Cdk1 mediate Wapl activation and release of acetylated cohesin from chromosomes by phosphorylating Sororin. Proc. Natl Acad. Sci. USA 110, 13404–13409 (2013).
Naumova, N. et al. Organization of the mitotic chromosome. Science 342, 948–953 (2013).
Zhao, H. et al. Genome folding principles uncovered in condensin-depleted mitotic chromosomes. Nat. Genet. 56, 1216–1224 (2024).
Mitter, M. et al. Conformation of sister chromatids in the replicated human genome. Nature 586, 139–144 (2020).
Nagasaka, K. et al. Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms. Mol. Cell 83, 3049–3063 (2023).
Kim, E., Kerssemakers, J., Shaltiel, I. A., Haering, C. H. & Dekker, C. DNA-loop extruding condensin complexes can traverse one another. Nature 579, 438–442 (2020).
Pradhan, B. et al. SMC complexes can traverse physical roadblocks bigger than their ring size. Cell Rep. 41, 111491 (2022).
Brandao, H. B., Ren, Z., Karaboja, X., Mirny, L. A. & Wang, X. DNA-loop-extruding SMC complexes can traverse one another in vivo. Nat. Struct. Mol. Biol. 28, 642–651 (2021).
Murayama, Y. et al. Coordination of cohesin and DNA replication observed with purified proteins. Nature 626, 653–660 (2024).
Srinivasan, M. et al. The cohesin ring uses its hinge to organize DNA using non-topological as well as topological mechanisms. Cell 173, 1508–1519 (2018).
Uhlmann, F. & Nasmyth, K. Cohesion between sister chromatids must be established during DNA replication. Curr. Biol. 8, 1095–1101 (1998).
Samejima, K. et al. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. Preprint at bioRxiv https://doi.org/10.1101/2024.04.18.590027 (2024).
Dequeker, B. J. H. et al. MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Nature 606, 197–203 (2022).
Emerson, D. J. et al. Cohesin-mediated loop anchors confine the locations of human replication origins. Nature 606, 812–819 (2022).
Weiss, M. J., Yu, C. & Orkin, S. H. Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a gene-targeted cell line. Mol. Cell. Biol. 17, 1642–1651 (1997).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Abdennur, N. & Mirny, L. A. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36, 311–316 (2020).
Flyamer, I. M., Illingworth, R. S. & Bickmore, W. A. Coolpup.py: versatile pile-up analysis of Hi-C data. Bioinformatics 36, 2980–2985 (2020).
Thompson, A. P. et al. LAMMPS—a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comput. Phys. Commun. https://doi.org/10.1016/j.cpc.2021.108171 (2022).
Dogan, N. et al. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin 8, 16 (2015).
Wu, W. et al. Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. Genome Res. 24, 1945–1962 (2014).
Luan, J. et al. Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Cell Rep. 34, 108783 (2021).
Liu, F. & Zhang, H. Hi-C and ChIP-seq analysis related code. Zenodo https://doi.org/10.5281/zenodo.10968270 (2024).
Qin, S. & Lyu, F. Extensive mutual influences of SMC complexes shape 3D genome folding. Zenodo https://doi.org/10.5281/zenodo.14545472 (2024).
