ISSN 0564-3783  

Main page
Information to authors
Editorial board
Mobile version

In Ukrainian

Export citations

Inner and outer DNA loops in cell nuclei: evidence from pulsed-field comet assay

Chopei M., Olefirenko V., Afanasieva K., Sivolob A.


SUMMARY. At higher order levels chromatin is organized into loops, and this looping plays an important role in transcription regulation. In our previous works we investigated the kinetics of DNA loop migration during single cell gel electrophoresis (the comet assay) of nucleoids obtained from lysed cells. It was shown that there are three parts of DNA in nucleoids: DNA in rather small loops which migrate rapidly; DNA in the loops up to ~150 kb, the migration of which is retarded; and larger loops that cannot migrate. Here we applied, for the first time, the pulse-field electrophoresis in the comet assay. Our results show that the first rapid step during the usual comet assay can be attributed to loops on the nucleoid surface while the second slow component represents loops inside the nucleoid.

Tsitologiya i Genetika 2022, vol. 56, no. 4, pp. 3-9

  • Taras Shevchenko National University of Kyiv

E-mail: mariana.chopei, aphon

Chopei M., Olefirenko V., Afanasieva K., Sivolob A. Inner and outer DNA loops in cell nuclei: evidence from pulsed-field comet assay, Tsitol Genet., 2022, vol. 56, no. 4, pp. 3-9.

In "Cytology and Genetics":
M. Chopei, V. Olefirenko, K. Afanasieva & A. Sivolob Inner and Outer DNA Loops in Cell Nuclei: Evidence from Pulsed-Field Comet Assay, Cytol Genet., 2022, vol. 56, no. 4, pp. 313318
DOI: 10.3103/S0095452722040028


Afanasieva, K., Zazhytska, M., and Sivolob, A., Kinetics of comet formation in singlecell gel electrophoresis: Loops and fragments, Electrophoresis, 2010, vol. 31, no. 3, pp. 512519.

Afanasieva, K., Chopei, M., Zazhytska, M., et al., DNA loop domain organization as revealed by single-cell gel electrophoresis, Biochim. Biophys. Acta, Mol. Cell Res., 2013, vol. 1833, no. 12, pp. 32373244.

Afanasieva, K., Chopei, M., Lozovik, A., et al., Redistribution of DNA loop domains in human lymphocytes under blast transformation with interleukin 2, Ukr. Biochem. J., 2016, vol. 88, no. 6, pp. 4551.

Afanasieva, K., Chopei, M., Lozovik, A., et al., DNA loop domain organization in nucleoids from cells of different types, Biochem. Biophys. Res. Commun., 2017, vol. 483, no. 1, pp. 142146.

Afanasieva, K. and Sivolob, A., Physical principles and new applications of comet assay, Biophys. Chem., 2018, vol. 238, pp. 17.

Aughey, G. and Southall, T., Dam its good! DamID profiling of protein-DNA interactions, Wiley Interdiscip. Rev.: Dev. Biol., 2015, vol. 5, no. 1, pp. 2537.

Chopei, M., Afanasieva, K., and Sivolob, A., Protein intercalation in DNA as one of main modes of fixation of the most stable chromatin loop domains, Ukr. Biochem. J., 2014, vol. 86, no. 4, pp. 110118.

Cook, P. and Brazell, I., Super coils in human DNA, J. Cell Sci., 1975, vol. 19, no. 2, pp. 261279.

Cook, P., A model for all genomes: the role of transcription factories., J. Mol. Biol., 2010, vol. 395, no. 1, pp. 110.

Défontaines, A.D. and Viovy, J.L., Gel electrophoresis of an end-labeled DNA I. Dynamics and trapping in constant fields, Electrophoresis, 1993, vol. 14, no. 1, pp. 8‒17.

Dekker, J., Marti-Renom, M., and Mirny, L., Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data, Nat. Rev. Genet., 2013, vol. 14, no. 6, pp. 390403.

Dekker, J. and Misteli, T., Long-range chromatin interactions, Cold Spring Harbor Perspect. Biol., 2015, vol. 7, no. 10, art. ID a019356.

Kadauke, S. and Blobel, G., Chromatin loops in gene regulation, Biochim. Biophys. Acta, Gene Regul. Mech., 2009, vol. 1789, no. 1, pp. 1725.

Kieffer-Kwon, K., Nimura, K., Rao, S., et al., Myc regulates chromatin decompaction and nuclear architecture during B cell activation, Mol. Cell, 2017, vol. 67, no. 4, pp. 566578.

Kind, J., Pagie, L., de Vries, S., et al., Genome wide maps of nuclear lamina interactions in single human cells, Cell, 2015, vol. 163, no. 1, pp. 134147.

Krietenstein, N., Abraham, S., Venev, S., et al., Ultrastructural details of mammalian chromosome architecture, Mol. Cell, 2020, vol. 78, pp. 554565.

Liao, W., McNutt, M., and Zhu, W., The comet assay: A sensitive method for detecting DNA damage in individual cells, Methods, 2009, vol. 48, no. 1, pp. 4653.

Lieberman-Aiden, E., van Berkum, N., Williams, L., et al., Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, 2009, vol. 326, no. 5950, pp. 289293.

Maston, G., Evans, S., and Green, M., Transcriptional regulatory elements in the human genome, Ann. Rev. Genomics Hum. Genet., 2006, vol. 7, pp. 2959.

Meuleman, W., Peric-Hupkes, D., Kind, J., et al., Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence, Genome Res., 2012, vol. 23, no. 2, pp. 270280.

Nagano, T., Lubling, Y., Stevens, T., et al., Single-cell Hi-C reveals cell-to-cell variability in chromosome structure, Nature, 2013, vol. 502, no. 7469, pp. 5964.

Ong, C. and Corces, V., CTCF: An architectural protein bridging genome topology and function, Nat. Rev. Genet., 2014, vol. 15, no. 4, pp. 234246.

Olive, P., The comet assay: an overview of techniques, Methods Mol. Biol., 2002, vol. 203, pp. 179194.

Rao, S., Huntley, M., Durand, N., et al., A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, 2014, vol. 159, no. 7, pp. 16651680.

Rodríguez-Ubreva, J. and Ballestar, E., Chromatin Immunoprecipitation, Methods Mol. Biol., 2014, vol. 1094, pp. 309318.

Sanborn, A., Rao, S., Huang, S., et al., Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes, Proc. Natl. Acad. Sci. U. S. A., 2015, vol. 112, no. 47, pp. E6456E6465.

Shaposhnikov, S., Salenko, V., Brunborg, G., et al., Single-cell gel electrophoresis (the comet assay): Loops or fragments?, Electrophoresis, 2008, vol. 29, no. 14, pp. 30053012.

Van Bortle, K. and Corces, V., Nuclear organization and genome function, Ann. Rev. Cell Dev. Biol., 2012, vol. 28, pp. 163187.

Wagner, L. and Lai, E., Separation of large DNA molecules with high voltage pulsed field gel electrophoresis, Electrophoresis, 1994, vol. 15, no. 1, pp. 10781083.

Yáñez-Cuna, J., and van Steensel, B., Genomenuclear lamina interactions: from cell populations to single cells, Curr. Opin. Genet. Dev., 2017, vol. 43, pp. 6772.

Copyright© ICBGE 2002-2023 Coded & Designed by Volodymyr Duplij Modified 05.12.23