Skip to main content
SpringerLink
Log in

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

  • MOLECULAR CELL BIOLOGY
  • Published:
Molecular Biology Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.
Fig. 7.

Similar content being viewed by others

REFERENCES

  1. Cremer T., Cremer M., Cremer C. 2018. The 4D nucleome: Genome compartmentalization in an evolutionary context. Biochemistry (Moscow). 83 (4), 313–325.

    CAS  PubMed  Google Scholar 

  2. Postberg J., Lipps H.J., Cremer T. 2010. Evolutionary origin of the cell nucleus and its functional architecture. Essays Biochem. 48, 1–24.

    Article  CAS  PubMed  Google Scholar 

  3. Razin S.V., Ulianov S.V., Gavrilov A.A. 2019. 3D Genomics. Mol. Biol. (Moscow). 53 (6), 911–923.

    Article  CAS  Google Scholar 

  4. Razin S.V. 1996. Functional architecture of chromosomal DNA domains. Crit. Rev. Eukaryot. Gene Expr. 6, 247–269.

    Article  CAS  PubMed  Google Scholar 

  5. Cockerill P.N., Garrard W.T. 1986. Chromosomal loop anchorage sites appear to be evolutionarily conserved. FEBS Lett. 204, 5–7.

    Article  CAS  PubMed  Google Scholar 

  6. Gasser S.M., Laemmli U.K. 1986. The organization of chromatin loops: characterization of a scaffold attachment site. EMBO J. 5, 511–518.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Iarovaia O., Hancock R., Lagarkova M., Miassod R., Razin S.V. 1996. Mapping of genomic DNA loop organization in a 500-kilobase region of the Drosophila X chromosome by the topoisomerase II-mediated DNA loop excision protocol. Mol. Cell. Biol. 16, 302–308.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Marsden M.P.F., Laemmli U.K. 1979. Metaphase chromosome structure: Evidence for a radial loop model. Cell. 17, 849–858.

    Article  CAS  PubMed  Google Scholar 

  9. Belmont A.S., Sedat J.W., Agard D.A. 1987. A three-dimensional approach to mitotic chromosome structure: Evidence for a complex hierarchical organization. J. Cell Biol. 105, 77–92.

    Article  CAS  PubMed  Google Scholar 

  10. Zatsepina O.V., Polyakov V.Yu., Chentsov Yu.S. 1983. Chromonema and chromomere. Chromosoma. 88(2) 91–97.

    Article  Google Scholar 

  11. Cook P.R. 1995. A chromomeric model for nuclear and chromosome structure. J. Cell Sci. 108, 2927–2935.

    Article  CAS  PubMed  Google Scholar 

  12. Razin S.V., Iarovaia O.V., Vassetzky Y.S. 2014. A requiem to the nuclear matrix: From a controversial concept to 3D organization of the nucleus. Chromosoma. 123, 217–224.

    Article  CAS  PubMed  Google Scholar 

  13. Nishino Y., Eltsov M., Joti Y., Ito K., Takata H., Takahashi Y., Hihara S., Frangakis A.S., Imamoto N., Ishikawa T., Maeshima K. 2012. Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure. EMBO J. 31, 1644–1653.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Ou H.D., Phan S., Deerinck T.J., Thor A., Ellisman M.H., O’Shea C.C. 2017. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science. 357 (6349), eaag0025.

  15. Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., Sandstrom R., Bernstein B., Bender M.A., Groudine M., Gnirke A., et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 326, 289–293.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kalhor R., Tjong H., Jayathilaka N., Alber F., Chen L. 2012. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat. Biotechnol. 30, 90–98.

    Article  CAS  Google Scholar 

  17. Kantidze O.L., Razin S.V. 2020. Weak interactions in higher-order chromatin organization. Nucleic Acids Res. 48, 4614–4626.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Razin S.V., Gavrilov A.A. 2018. Structural–functional domains of the eukaryotic genome. Biochemistry (Moscow). 83 (4), 302–312.

    CAS  PubMed  Google Scholar 

  19. Jahn C.L., Klobutcher L.A. 2002. Genome remodeling in ciliated Protozoa. Ann. Rev. Microbiol. 56, 489–520.

    Article  CAS  Google Scholar 

  20. Raikov I.B. 1982. The protozoan nucleus. Morphology and evolution. Cell Biol. Monogr. 9, 1–474.

    Google Scholar 

  21. Nekrasova I.V., Potekhin A.A. 2018. RNA interference in the formation of somatic genome in the ciliates Paramecium and Tetrahymena. Ekol. Genet. 16, 5–22.

    Article  Google Scholar 

  22. Martinkina L.P., Vengerov Yu.Yu., Bespalova I.A., Tikhonenko A.S., Sergejeva G.I. 1983. The structure of inactive interphase macromolecular chromatin of the ciliate Bursaria truncatella. Radial loops in the structure of chromatin clumps. Eur. J. Cell Biol. 30, 47–53.

    CAS  PubMed  Google Scholar 

  23. Borkhsenius O.N., Belyaeva N.N., Osipov D.V. 1988. Chromatin structure in the somatic nucleus of the ciliate Spirostomum ambiguum. Tsitologiya. 30, 762–769.

    Google Scholar 

  24. Karajan B.P., Popenko V.I., Raikov I.B. 1995. Organization of transcriptionally inactive chromatin of interphase macronucleus of the ciliate Didinium nasutum. Acta Protozool. 34, 135–141.

    CAS  Google Scholar 

  25. Leonova O.G., Ivanova Yu.L., Karajan B.P., Popenko V.I. 2004. Dynamics of ultrastructural changes of chromatin and nucleoli in the macronucleus of ciliates Paramecium caudatum and Bursaria truncatella under hypotonic treatment. Tsitologiya. 46, 456–464.

    CAS  Google Scholar 

  26. Sonneborn T.M. 1970. Methods in Paramecium research. Methods Cell Physiol. 4, 241–339.

    Google Scholar 

  27. Rautian M.S., Potekhin A.A. 2002. Electrokaryotypes of macronuclei of several Paramecium species. J. Eukaryot. Microbiol. 49, 296–304.

    Article  PubMed  Google Scholar 

  28. Nekrasova I.V., Przybos E., Rautian M.S., Potekhin A.A. 2010. Electrophoretic karyotype polymorphism of sibling species of the Paramecium aurelia complex. J. Eukaryot. Microbiol. 57, 494–507.

    Article  CAS  PubMed  Google Scholar 

  29. Timofeeva A.S., Rautian M.S. 1997. Pulsed-field electrophoresis used to determining the genome size of intranuclear symbiotic bacterium Holospora undulata. Tsitologiya. 39, 634–639.

    Google Scholar 

  30. Kornberg R.D. 1977. Structure of chromatin. Annu. Rev. Biochem. 46, 931–954.

    Article  CAS  PubMed  Google Scholar 

  31. Olins A.L., Olins D.E. 1974. Spheroid chromatin units (ν bodies). Science. 183, 330–332.

    Article  CAS  PubMed  Google Scholar 

  32. Tikhonenko A.S., Bespalova I.A., Martinkina L.P., Popenko V.I., Sergejeva G.I. 1984. Structural organization of macronuclear chromatin of the ciliate Bursaria truncatella in resting cysts and at excysting. Eur. J. Cell. Biol. 33, 37–42.

    CAS  PubMed  Google Scholar 

  33. Sloane N.J.A. 1984. The packing of spheres. Sci. Am. 25, 116–124.

    Article  Google Scholar 

  34. Duret L., Cohen J., Jubin C., Dessen F., Goüt J.-F., Mousset S., Aury J.-M., Jaillon O., Noël B., Arnaiz O., Bétermier M., Wincker P., Meyer E., Sperling L. 2008. Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline. Genome Res. 18, 585–596.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Pritchard A.E., Seilhamer J.J., Mahalingam R., Sable C.L., Venuti S.E., Cummings D.J. 1990. Nucleotide sequence of the mitochondrial genome of Paramecium. Nucleic Acids Res. 18, 173–180.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Johri P., Marinov G.K., Doak T.G., Lynch M. 2019. Population genetics of Paramecium mitochondrial genomes: Recombination, mutation spectrum, and efficacy of selection. Genome Biol. Evol. 11, 1398–1416.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Arnaiz O., Meyer E., Sperling L. 2020. Paramecium DB 2019: Integrating genomic data across the genus for functional and evolutionary biology. Nucleic Acids Res. 48, D599–D605.

    CAS  PubMed  Google Scholar 

  38. Bernhard W. 1969. A new staining procedure for electron microscopical cytology. J. Ultrastruct. Res. 27, 250–265.

    Article  CAS  PubMed  Google Scholar 

  39. Richmond T.J., Davey C.A. 2003. The structure of DNA in the nucleosome core. Nature. 423, 145–150.

    Article  CAS  PubMed  Google Scholar 

  40. Murti K.G., Prescott D.M. 1999. Telomeres of polytene chromosomes in a ciliated protozoan terminate in duplex DNA loops. Proc. Natl. Acad. Sci. U. S. A. 96, 14436–14439.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Murti K.G., Prescott D.M. 2002. Topological organization of DNA molecules in the macronucleus of hypotrichous ciliated protozoa. Chromosome Res. 10, 165–173.

    Article  CAS  PubMed  Google Scholar 

  42. Jönsson F., Postberg J., Schaffitzel C., Lipps H.J. 2002. Organization of the macronuclear gene-sized pieces of stichotrichous ciliates into a higher order structure via telomere–matrix interactions. Chromosome Res. 10, 445–453.

    Article  PubMed  Google Scholar 

  43. Schaffitzel C., Postberg J., Paeschke K., Lipps H.J. 2010. Probing telomeric G-quadruplex DNA structures in cells with in vitro generated single-chain antibody fragments. Meth. Mol. Biol. 608, 159–181.

    Article  CAS  Google Scholar 

  44. Novikova E.G., Popenko V.I. 1998. Visualization of chromatin structural organization centers in the macronucleus of a ciliate Bursaria truncatella. Mol. Biol. (Moscow). 32 (3), 439–446.

    CAS  Google Scholar 

  45. Gavrilov A.A., Shevelyov Y.Y., Ulianov S.V., Khrameeve E.E., Kos P., Chertovich A., Razin S.V. 2016. Unraveling the mechanisms of chromatin fibril packaging. Nucleus. 7, 319–324.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Rao S.S., Huntley M.H., Durand N.C., Stamenova E.K., Bochkov I.D., Robinson J.T., Sanborn A.L., Machol I., Omer A.D., Lander E.S., Aiden E.L. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 159, 1665–1680.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Kolesnikova T.D. 2018. Banding pattern of polytene chromosomes as a representation of universal principles of chromatin organization into topological domains. Biochemistry (Moscow). 83 (4), 338–349.

    CAS  PubMed  Google Scholar 

Download references

Funding

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

Author information

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

Authors
  1. O. G. Leonova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. A. Potekhin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. I. V. Nekrasova
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. B. P. Karajan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. B. V. Syomin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. V. S. Prassolov
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. V. I. Popenko
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to V. I. Popenko.

Ethics declarations

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.

Additional information

Translated by T. Tkacheva

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

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026893321050083

Keywords:

Search

Navigation