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Packaging of Subchromosomal-Size DNA Molecules in Chromatin Bodies in the Ciliate Macronucleus

  • MOLECULAR CELL BIOLOGY
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Abstract

A fundamental difference between somatic nuclei (macronuclei) of ciliates and cell nuclei of higher eukaryotes is that the macronuclear genome is a huge number (up to tens or hundreds of thousands) of gene-sized (0.5–25 kb) or subchromosomal (up to 2000 kb) minichromosomes. Electron microscopy shows that macronuclear chromatin usually looks like chromatin bodies or fibrils 200–300 nm thick in the interphase. However, the question of how many DNA molecules are contained in an individual chromatin body remains open. The organization of chromatin in macronuclei was studied in the ciliates Didinium nasutum and three Paramecium sp., which differ in pulsed-field gel electrophoresis (PFGE) karyotype, and compared with the model of topologically associated domains (TADs) of higher eukaryotic nuclei. PFGE showed that the sizes of macronuclear DNAs ranged from 50 to 1700 kb, while the majority of the molecules were less than 500 kb in length. A comparative quantitative analysis of the PFGE and electron microscopic data showed that each chromatin body contained one minichromosome in P. multimicronucleatum in the logarithmic growth phase, while bodies in the D. nasutum macronucleus contained two or more DNA molecules each. Chromatin bodies aggregated during starvation, when activity of the macronuclei decreased, leading to an increase of chromatin body size or the formation of 200- to 300-nm fibrils of several chromatin bodies. A model was proposed to explain the formation of such structures. In terms of topological characteristics, macronuclear chromatin bodies with subchromosomal DNA molecules were found to correspond to higher eukaryotic TADs.

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Funding

This work was supported by the Program of Basic Research at the State Academies of Sciences from 2013 to 2020 (project no. 01201363823).

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Authors and Affiliations

  1. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia

    O. G. Leonova, V. S. Prassolov & V. I. Popenko

  2. Faculty of Biology, St. Petersburg State University, 199034, St. Petersburg, Russia

    A. A. Potekhin & I. V. Nekrasova

  3. Zoological Institute, Russian Academy of Sciences, 199034, St. Petersburg, Russia

    A. A. Potekhin

  4. Institute of Cytology, Russian Academy of Sciences, 194064, St. Petersburg, Russia

    B. P. Karajan

  5. Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation, 119435, Moscow, Russia

    B. V. Syomin

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  1. O. G. Leonova
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Correspondence to V. I. Popenko.

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Conflict of interests. The authors declare that they have no conflicts of interest.

This work does not contain any studies involving animals or human subjects performed by any of the authors.

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Translated by T. Tkacheva

Abbreviations: TAD, topologically associated domain; PFGE, pulsed-field gel electrophoresis; TeBP, telomere-binding protein.

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Leonova, O.G., Potekhin, A.A., Nekrasova, I.V. et al. Packaging of Subchromosomal-Size DNA Molecules in Chromatin Bodies in the Ciliate Macronucleus. Mol Biol 55, 899–909 (2021). https://doi.org/10.1134/S0026893321050083

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