Mitotic chromosome organization: General rules meet species-specific variability
Status PubMed-not-MEDLINE Jazyk angličtina Země Nizozemsko Médium electronic-ecollection
Typ dokumentu časopisecké články, přehledy
PubMed
32612754
PubMed Central
PMC7305364
DOI
10.1016/j.csbj.2020.01.006
PII: S2001-0370(19)30456-8
Knihovny.cz E-zdroje
- Klíčová slova
- Chromatin fiber folding, Chromosome cavities, Chromosome condensation, Chromosome conformation capture, Chromosome scaffold, Structural maintenance of chromosomes proteins,
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Research on the formation of mitotic chromosomes from interphase chromatin domains, ongoing for several decades, made significant progress in recent years. It was stimulated by the development of advanced microscopic techniques and implementation of chromatin conformation capture methods that provide new insights into chromosome ultrastructure. This review aims to summarize and compare several models of chromatin fiber folding to form mitotic chromosomes and discusses them in the light of the novel findings. Functional genomics studies in several organisms confirmed condensins and cohesins as the major players in chromosome condensation. Here we compare available data on the role of these proteins across lower and higher eukaryotes and point to differences indicating evolutionary different pathways to shape mitotic chromosomes. Moreover, we discuss a controversial phenomenon of the mitotic chromosome ultrastructure - chromosome cavities - and using our super-resolution microscopy data, we contribute to its elucidation.
Zobrazit více v PubMed
Schubert V. Super-resolution microscopy - applications in plant cell research. Front Plant Sci. 2017;8:531. PubMed PMC
Walther N., Ellenberg J. Chapter 4 - Quantitative live and super-resolution microscopy of mitotic chromosomes. In: Maiato H., Schuh M., editors. Methods in cell biology. Academic Press; 2018. pp. 65–90. PubMed
Baroux C., Schubert V. Technical review: microscopy and image processing tools to analyze plant chromatin: practical considerations. In: Bemer M., Baroux C., editors. Plant chromatin dynamics: methods and protocols. Springer; New York: 2018. pp. 537–589. PubMed
Danev R., Yanagisawa H., Kikkawa M. Cryo-electron microscopy methodology: current aspects and future directions. Trends Biochem Sci. 2019;44:837–848. PubMed
Sati S., Cavalli G. Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma. 2017;126:33–44. PubMed
Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–293. PubMed PMC
Wanner G., Schroeder-Reiter E., Ma W., Houben A., Schubert V. The ultrastructure of mono- and holocentric plant centromeres: an immunological investigation by structured illumination microscopy and scanning electron microscopy. Chromosoma. 2015;124:503–517. PubMed
Schroeder-Reiter E., Perez-Willard F., Zeile U., Wanner G. Focused ion beam (FIB) combined with high resolution scanning electron microscopy: a promising tool for 3D analysis of chromosome architecture. J Struct Biol. 2009;165:97–106. PubMed
Ou H.D., Phan S., Deerinck T.J., Thor A., Ellisman M.H., O'Shea C.C. ChromEMT: visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science. 2017;357:eaag0025. PubMed PMC
Chen B., Yusuf M., Hashimoto T., Estandarte A.K., Thompson G., Robinson I. Three-dimensional positioning and structure of chromosomes in a human prophase nucleus. Sci Adv. 2017;3:e1602231. PubMed PMC
Cremer T., Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol. 2010;2:a003889. PubMed PMC
Dixon J.R., Selvaraj S., Yue F., Kim A., Li Y., Shen Y. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376–380. PubMed PMC
Ramirez F., Bhardwaj V., Arrigoni L., Lam K.C., Gruning B.A., Villaveces J. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat Commun. 2018;9:189. PubMed PMC
Szabo Q., Bantignies F., Cavalli G. Principles of genome folding into topologically associating domains. Sci Adv. 2019;5:eaaw1668. PubMed PMC
Nora E.P., Lajoie B.R., Schulz E.G., Giorgetti L., Okamoto I., Servant N. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485:381–385. PubMed PMC
Dixon Jesse R., Gorkin David U., Ren B. Chromatin domains: the unit of chromosome organization. Mol Cell. 2016;62:668–680. PubMed PMC
Dong P., Tu X., Li H., Zhang J., Grierson D., Li P. Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains. J Integr Plant Biol. 2019;44 PubMed
Stam M., Tark-Dame M., Fransz P. 3D genome organization: a role for phase separation and loop extrusion? Curr Opin Plant Biol. 2019;48:36–46. PubMed
Sedat J., Manuelidis L. A direct approach to the structure of eukaryotic chromosomes. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 1):331–350. PubMed
Finch J.T., Klug A. Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA. 1976;73:1897–1901. PubMed PMC
Woodcock C.L., Frado L.L., Rattner J.B. The higher-order structure of chromatin: evidence for a helical ribbon arrangement. J Cell Biol. 1984;99:42–52. PubMed PMC
Ohnuki Y. Structure of chromosomes. I. Morphological studies of the spiral structure of human somatic chromosomes. Chromosoma. 1968;25:402–428. PubMed
Manton I. The spiral structure of chromosomes. Biol Rev Camb Philos Soc. 1950;25:486–508. PubMed
Rattner J.B., Lin C.C. Radial loops and helical coils coexist in metaphase chromosomes. Cell. 1985;42:291–296. PubMed
Maeshima K., Ide S., Babokhov M. Dynamic chromatin organization without the 30-nm fiber. Curr Opin Cell Biol. 2019;58:95–104. PubMed
Hansen J.C., Connolly M., McDonald C.J., Pan A., Pryamkova A., Ray K. The 10-nm chromatin fiber and its relationship to interphase chromosome organization. Biochem Soc Trans. 2018;46:67–76. PubMed PMC
Grigoryev S.A., Bascom G., Buckwalter J.M., Schubert M.B., Woodcock C.L., Schlick T. Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes. Proc Natl Acad Sci USA. 2016;113:1238–1243. PubMed PMC
Dekker J., Rippe K., Dekker M., Kleckner N. Capturing chromosome conformation. Science. 2002;295:1306–1311. PubMed
Davies J.O., Oudelaar A.M., Higgs D.R., Hughes J.R. How best to identify chromosomal interactions: a comparison of approaches. Nat Methods. 2017;14:125–134. PubMed
Naumova N., Imakaev M., Fudenberg G., Zhan Y., Lajoie B.R., Mirny L.A. Organization of the mitotic chromosome. Science. 2013;342:948–953. PubMed PMC
Wanner G., Formanek H. A new chromosome model. J Struct Biol. 2000;132:147–161. PubMed
Wanner G., Schroeder-Reiter E., Formanek H. 3D Analysis of chromosome architecture: advantages and limitations with SEM. Cytogenet Genome Res. 2005;109:70–78. PubMed
Paulson J.R., Laemmli U.K. The structure of histone-depleted metaphase chromosomes. Cell. 1977;12:817–828. PubMed
Laemmli U.K., Cheng S.M., Adolph K.W., Paulson J.R., Brown J.A., Baumbach W.R. Metaphase chromosome structure: the role of nonhistone proteins. Cold Spring Harb Symp Quant Biol. 1978;42:351–360. PubMed
Poonperm R., Takata H., Hamano T., Matsuda A., Uchiyama S., Hiraoka Y. Chromosome scaffold is a double-stranded assembly of scaffold proteins. Sci Rep. 2015;5 Article 11916. PubMed PMC
Sun M.X., Biggs R., Hornick J., Marko J.F. Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold. Chromosome Res. 2018;26:277–295. PubMed PMC
Walther N., Hossain M.J., Politi A.Z., Koch B., Kueblbeck M., Odegard-Fougner O. A quantitative map of human condensins provides new insights into mitotic chromosome architecture. J Cell Biol. 2018;217:2309–2328. PubMed PMC
Poirier M.G., Marko J.F. Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold. Proc Natl Acad Sci USA. 2002;99:15393–15397. PubMed PMC
Biggs R., Liu P.Z., Stephens A.D., Marko J.F. Effects of altering histone posttranslational modifications on mitotic chromosome structure and mechanics. Mol Biol Cell. 2019;30:820–827. PubMed PMC
Kimura K., Rybenkov V.V., Crisona N.J., Hirano T., Cozzarelli N.R. 13S Condensin actively reconfigures DNA by introducing global positive writhe: implications for chromosome condensation. Cell. 1999;98:239–248. PubMed
Ono T., Losada A., Hirano M., Myers M.P., Neuwald A.F., Hirano T. Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells. Cell. 2003;115:109–121. PubMed
Hirano T. Condensin-based chromosome organization from bacteria to vertebrates. Cell. 2016;164:847–857. PubMed
Piskadlo E., Oliveira R.A. A Topology-centric view on mitotic chromosome architecture. Int J Mol Sci. 2017;18:E2751. PubMed PMC
Maeshima K., Laemmli U.K. A two-step scaffolding model for mitotic chromosome assembly. Dev Cell. 2003;4:467–480. PubMed
Poonperm R., Takata H., Uchiyama S., Fukui K. Interdependency and phosphorylation of KIF4 and condensin I are essential for organization of chromosome scaffold. PLoS One. 2017;12:e0183298. PubMed PMC
Ohta S., Taniguchi T., Sato N., Hamada M., Taniguchi H., Rappsilber J. Quantitative proteomics of the mitotic chromosome scaffold reveals the association of BAZ1B with chromosomal axes. Mol Cell Proteomics. 2019;18:169–181. PubMed PMC
Uhlmann F. SMC complexes: from DNA to chromosomes. Nat Rev Mol Cell Biol. 2016;17:399–412. PubMed
Nasmyth K. Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis. Annu Rev Genet. 2001;35:673–745. PubMed
Alipour E., Marko J.F. Self-organization of domain structures by DNA-loop-extruding enzymes. Nucleic Acids Res. 2012;40:11202–11212. PubMed PMC
Goloborodko A., Marko J.F., Mirny L.A. Chromosome compaction by active loop extrusion. Biophys J. 2016;110:2162–2168. PubMed PMC
Ganji M., Shaltiel I.A., Bisht S., Kim E., Kalichava A., Haering C.H. Real-time imaging of DNA loop extrusion by condensin. Science. 2018;360:102–105. PubMed PMC
Ono T., Fang Y., Spector D.L., Hirano T. Spatial and temporal regulation of condensins I and II in mitotic chromosome assembly in human cells. Mol Biol Cell. 2004;15:3296–3308. PubMed PMC
Green L.C., Kalitsis P., Chang T.M., Cipetic M., Kim J.H., Marshall O. Contrasting roles of condensin I and condensin II in mitotic chromosome formation. J Cell Sci. 2012;125:1591–1604. PubMed PMC
Kakui Y., Uhlmann F. SMC complexes orchestrate the mitotic chromatin interaction landscape. Curr Genet. 2018;4:335–339. PubMed PMC
Takahashi M., Hirota T. Folding the genome into mitotic chromosomes. Curr Opin Cell Biol. 2019;60:19–26. PubMed
Gibcus J.H., Samejima K., Goloborodko A., Samejima I., Naumova N., Nuebler J. A pathway for mitotic chromosome formation. Science. 2018;359:eaao6135. PubMed PMC
Östergen G. Colchicine mitosis, chromosome contraction, narcosis and protein chain folding. Hereditas. 1944;30:429–467.
Moser S.C., Swedlow J.R. How to be a mitotic chromosome. Chromosome Res. 2011;19:307–319. PubMed PMC
Koyani P.R., Saiyad S.S. Study of effect of colchicine exposure on length of chromosome during mitosis. J. Anat. Soc. India. 2011;60:177–180.
Daban J.R. Stacked thin layers of metaphase chromatin explain the geometry of chromosome rearrangements and banding. Sci Rep. 2015;5 Article 14891. PubMed PMC
Gállego I., Castro-Hartmann P., Caravaca J.M., Caño S., Daban J.-R. Dense chromatin plates in metaphase chromosomes. Eur Biophys J. 2009;38:503–522. PubMed
Chicano A., Crosas E., Oton J., Melero R., Engel B.D., Daban J.R. Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure. Embo J. 2019;38:e99769. PubMed PMC
Chicano A., Daban J.R. Chromatin plates in the interphase nucleus. FEBS Lett. 2019;593:810–819. PubMed
Piskadlo E., Tavares A., Oliveira R.A. Metaphase chromosome structure is dynamically maintained by condensin I-directed DNA (de)catenation. Elife. 2017;6 PubMed PMC
Chen C., Lim H.H., Shi J., Tamura S., Maeshima K., Surana U. Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo. Mol Biol Cell. 2016;27:3357–3368. PubMed PMC
Gan L., Ladinsky M.S., Jensen G.J. Chromatin in a marine picoeukaryote is a disordered assemblage of nucleosomes. Chromosoma. 2013;122:377–386. PubMed PMC
Cai S., Chen C., Tan Z.Y., Huang Y., Shi J., Gan L. Cryo-ET reveals the macromolecular reorganization of S. pombe mitotic chromosomes in vivo. Proc Natl Acad Sci USA. 2018;115:10977–10982. PubMed PMC
Fuchs J., Loidl J. Behaviour of nucleolus organizing regions (NORs) and nucleoli during mitotic and meiotic divisions in budding yeast. Chromosome Res. 2004;12:427–438. PubMed
Schalbetter S.A., Goloborodko A., Fudenberg G., Belton J.M., Miles C., Yu M. SMC complexes differentially compact mitotic chromosomes according to genomic context. Nat Cell Biol. 2017;19:1071–1080. PubMed PMC
Freeman L., Aragon-Alcaide L., Strunnikov A. The condensin complex governs chromosome condensation and mitotic transmission of rDNA. J Cell Biol. 2000;149:811–824. PubMed PMC
Hirano T. Condensins: universal organizers of chromosomes with diverse functions. Genes Dev. 2012;26:1659–1678. PubMed PMC
Fullwood M.J., Ruan Y. ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem. 2009;107:30–39. PubMed PMC
Tanizawa H., Kim K.-D., Iwasaki O., Noma K.-I. Architectural alterations of the fission yeast genome during the cell cycle. Nat Struct Mol Biol. 2017;24:965–976. PubMed PMC
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. 2000;103:399–410. PubMed
Bolaños-Villegas P., De K., Pradillo M., Liu D., Makaroff C.A. In favor of establishment: regulation of chromatid cohesion in plants. Front Plant Sci. 2017;8:846. PubMed PMC
Kakui Y., Rabinowitz A., Barry D.J., Uhlmann F. Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast. Nat Genet. 2017;49:1553–1557. PubMed PMC
Lazar-Stefanita L., Scolari V.F., Mercy G., Muller H., Guerin T.M., Thierry A. Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle. EMBO J. 2017;36:2684–2697. PubMed PMC
Lawrimore J., Doshi A., Friedman B., Yeh E., Bloom K. Geometric partitioning of cohesin and condensin is a consequence of chromatin loops. Mol Biol Cell. 2018;29:2737–2750. PubMed PMC
Nishide K., Hirano T. Overlapping and non-overlapping functions of condensins I and II in neural stem cell divisions. PLoS Genet. 2014;10 PubMed PMC
Oliveira R.A., Heidmann S., Sunkel C.E. Condensin I binds chromatin early in prophase and displays a highly dynamic association with Drosophila mitotic chromosomes. Chromosoma. 2007;116:259–274. PubMed
Herzog S., Nagarkar Jaiswal S., Urban E., Riemer A., Fischer S., Heidmann S.K. Functional dissection of the Drosophila melanogaster condensin subunit Cap-G reveals its exclusive association with condensin I. PLoS Genet. 2013;9:e1003463. PubMed PMC
Fujiwara T., Tanaka K., Kuroiwa T., Hirano T. Spatiotemporal dynamics of condensins I and II: evolutionary insights from the primitive red alga Cyanidioschyzon merolae. Mol Biol Cell. 2013;24:2515–2527. PubMed PMC
King T.D., Leonard C.J., Cooper J.C., Nguyen S., Joyce E.F., Phadnis N. Recurrent losses and rapid evolution of the condensin II complex in insects. Mol Biol Evol. 2019:2195–2204. PubMed PMC
Csankovszki G., Collette K., Spahl K., Carey J., Snyder M., Petty E. Three distinct condensin complexes control C. elegans chromosome dynamics. Curr Biol. 2009;19:9–19. PubMed PMC
Schubert V., Lermontova I., Schubert I. The Arabidopsis CAP-D proteins are required for correct chromatin organisation, growth and fertility. Chromosoma. 2013;122:517–533. PubMed
Liu C.-M., McElver J., Tzafrir I., Joosen R., Wittich P., Patton D. Condensin and cohesin knockouts in Arabidopsis exhibit a titan seed phenotype. Plant J. 2002;29:405–415. PubMed
Tzafrir I., McElver J.A., Liu C.-M., Yang L.J., Wu J.Q., Martinez A. Diversity of TITAN Functions in Arabidopsis seed development. Plant Physiol. 2002;128:38–51. PubMed PMC
Fujimoto S., Yonemura M., Matsunaga S., Nakagawa T., Uchiyama S., Fukui K. Characterization and dynamic analysis of Arabidopsis condensin subunits, AtCAP-H and AtCAP-H2. Planta. 2005;222:293–300. PubMed
Sakamoto T., Inui Y.T., Uraguchi S., Yoshizumi T., Matsunaga S., Mastui M. Condensin II alleviates DNA damage and is essential for tolerance of boron overload stress in Arabidopsis. Plant Cell. 2011;23:3533–3546. PubMed PMC
Sakamoto T., Sugiyama T., Yamashita T., Matsunaga S. Plant condensin II is required for the correct spatial relationship between centromeres and rDNA arrays. Nucleus. 2019;10:116–125. PubMed PMC
Shintomi K., Takahashi T.S., Hirano T. Reconstitution of mitotic chromatids with a minimum set of purified factors. Nat Cell Biol. 2015;17:1014–1023. PubMed
Orlandini E., Marenduzzo D., Michieletto D. Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology. Proc Natl Acad Sci USA. 2019;116:8149–8154. PubMed PMC
Hao S., Jiao M., Huang B. Chromosome organization revealed upon the decondensation of telophase chromosomes in Allium. Chromosoma. 1990;99:371–378.
Hao S., Xing M., Jiao M. Chromatin-free compartments and their contents in anaphase chromosomes of higher plants. Cell Biol Int Rep. 1988;12:627–635.
Kuznetsova M.A., Chaban I.A., Sheval E.V. Visualization of chromosome condensation in plants with large chromosomes. BMC Plant Biol. 2017;17 Article 153. PubMed PMC
Sparvoli E., Gay H., Kaufmann B.P. Number and pattern of association of chromonemata in chromosomes of Tradescantia. Chromosoma. 1965;16:415–435. PubMed
Hamano T., Dwiranti A., Kaneyoshi K., Fukuda S., Kometani R., Nakao M. Chromosome interior observation by Focused ion beam/Scanning electron microscopy (FIB/SEM) Using ionic liquid technique. Microsc Microanal. 2014;20:1340–1347. PubMed
Weisshart K., Fuchs J., Schubert V. Structured illumination microscopy (SIM) and photoactivated localization microscopy (PALM) to analyze the abundance and distribution of RNA polymerase II molecules on flow-sorted arabidopsis nuclei. Bio-protocol. 2016;6:e1725.
Palozola K.C., Liu H., Nicetto D., Zaret K.S. Low-level, global transcription during mitosis and dynamic gene reactivation during mitotic exit. Cold Spring Harb Symp Quant Biol. 2017;82:197–205. PubMed
Mumbach M.R., Rubin A.J., Flynn R.A., Dai C., Khavari P.A., Greenleaf W.J. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods. 2016;13:919–922. PubMed PMC
Cardozo Gizzi A.M., Cattoni D.I., Fiche J.-B., Espinola S.M., Gurgo J., Messina O. Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms. Mol Cell. 2019;74:212–222.e5. PubMed
Bintu B., Mateo L.J., Su J.-H., Sinnott-Armstrong N.A., Parker M., Kinrot S. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science. 2018;362:eaau1783. PubMed PMC
Helical coiling of metaphase chromatids
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
Prospects and limitations of expansion microscopy in chromatin ultrastructure determination