REVERSIBILITY OF STRUCTURAL REARRANGEMENTS IN MONONUCLEOSOMES INDUCED BY IONIC STRENGTH
Abstract
Using fluorescence microscopy of single particles with Förster resonance energy transfer recording, the structural rearrangements were studied that occurred in nucleosomes formed on the 603 DNA template at a high ionic strength. It is found that within the range of 0.7–1.3 M KCl, large-scale changes occur in the nucleosome structure that are accompanied by the formation of at least two states differing in the degree of DNA unwrapping from the histone octamer and affecting from 13 to 35 and more pairs of nucleotides. A fraction of nucleosomes with modified structure varies from 60% at 0.7 M KCl to 100% at 1.3 M KCl. Preservation of the association between core histones and DNA in the new conformational states ensures reversibility of structural changes when KCl concentration is reduced to a physiological level. Reversibility is ~100% after the transition from 0.7 M to 0.15 KCl and decreases to ~50% after the transition from 1.3 M to 0.15 KCl.
About the Authors
A. V. Feofanov
Lomonosov Moscow State University;
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
Russian Federation
Russian Federation
Bioengineering Department, Biological Faculty, Leninskiye Gory 1–12, Moscow, 119234;
ul. Miklukho-Maklaya 16/10, 117997, Moscow
T. V. Andreeva
Lomonosov Moscow State University
Russian Federation
Russian Federation
Bioengineering Department, Biological Faculty,
Leninskiye Gory 1–12, Moscow, 119234
V. M. Studitsky
Lomonosov Moscow State University;
Fox Chase Cancer Center
United States
United States
Bioengineering Department, Biological Faculty, Leninskiye Gory 1–12, Moscow, 119234;
Cottman Avenue 333, Philadelphia, 19111 Pennsylvania, USA
M. P. Kirpichnikov
Lomonosov Moscow State University;
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
Russian Federation
Russian Federation
Bioengineering Department, Biological Faculty, Leninskiye Gory 1–12, Moscow, 119234;
ul. Miklukho-Maklaya 16/10, 117997, Moscow
References
1. Thastrom A., Lowary P.T., Widlund H.R., Cao H., Kubista M., Widom J. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences // J. Mol. Biol. 1999. Vol. 288. N 2. P. 213–229.
2. Bondarenko V.A., Steele L.M., Ujvari A., Gaykalova D.A., Kulaeva O.I., Polikanov Y.S., Luse D.S., Studitsky V.M. Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II // Mol. Cell. 2006. Vol. 24. N 3. P. 469–479.
3. Gaykalova D.A., Kulaeva O.I., Bondarenko V.A., Studitsky V.M. Preparation and analysis of uniquely positioned mononucleosomes // Chromatin Protocols. Methods Mol. Biol. Vol. 523 / Ed. S.P. Chellappan. Humana Press, 2009. P. 109–123.
4. Böhm V., Hieb A.R., Andrews A.J., Gansen A., Rocker A., Tóth K., Luger K., Langowski J. Nucleosome accessibility governed by the dimer/tetramer interface // Nucleic Acids Res. 2011. Vol. 39. N 1. P. 3093–3102.
5. Hazan N.P., Tomov T.E., Tsukanov R., Liber M., Berger Y., Masoud R., Toth K., Langowski J., Nir E. Nucleosome core particle disassembly and assembly kinetics studied using single-molecule fluorescence // Biophys. J. 2015. Vol. 109. N 8. P. 1676–1685.
6. Kudryashova K.S., Chertkov O.V., Nikitin D.V., Pestov N.A., Kulaeva O.I., Efremenko A.V., Solonin A.S., Kirpichnikov M.P., Studitsky V.M., Feofanov A.V. Preparation of mononucleosomal templates for analysis of transcription with RNA polymerase using spFRET // Methods in Molecular Biology. Vol. 1288. Chromatin Protocols / Ed. S.P. Chellappan. Humana Press, 2015. P. 395–412.
7. Gansen A., Hieb A.R., Böhm V., Tóth K., Langowski J. Closing the gap between single molecule and bulk FRET analysis of nucleosomes // PLoS One. 2013. Vol. 8. N 4. e57018.
8. Valieva M.E., Armeev G.A., Kudryashova K.S., Gerasimova N.S., Shaytan A.K., Kulaeva O.I., McCullough L.L., Formosa T., Georgiev P.G., Kirpichnikov M.P., Studitsky V.M., Feofanov A.V. Large-scale ATP-independent nucleosome unfolding by a histone chaperone // Nat. Struct. Mol. Biol. 2016. Vol. 23. N 12. P. 1111–1116.
9. Kudryashova K.S., Nikitin D.V., Chertkov O.V., Gerasimova N.S., Valieva M.E. Studitsky V.M., Feofanov A.V. Development of fluorescently labeled mononucleosomes for the investigation of transcription mechanisms by single complex microscopy // Moscow Univ. Biol. Sci. Bull. 2015. Vol. 70. N 4. P. 189–193.
10. Chen Y., Tokuda J.M., Topping T., Meisburger S.P., Pabit S.A., Gloss L.M., Pollack L. Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core // Proc. Natl. Acad. Sci. U.S.A. 2017. Vol. 114. N 2. P. 334–339.
11. Ngo T.T.M., Ha T. Nucleosomes undergo slow spontaneous gaping // Nucleic Acids Res. 2015. Vol. 43. N 8. P. 3964–3971.
12. Chang H.W., Kulaeva O.I., Shaytan A.K., Kibanov M., Kuznedelov K., Severinov K.V., Kirpichnikov M.P., Clark D.J., Studitsky V.M. Analysis of the mechanism of nucleosome survival during transcription // Nucleic Acids Res. 2014. Vol. 42. N 3. P. 1619–1627.
13. Gaykalova D.A., Kulaeva O.I., Pestov N.A., Hsieh F.K., Studitsky V.M. Experimental analysis of the mechanism of chromatin remodeling by RNA polymerase II // Methods Enzymol. 2012. Vol. 512. P. 293–314.
14. Lyubitelev A.V., Studitsky V.M., Feofanov A.V., Kirpichnikov M.P. Effect of sodium and potassium ions on conformation of linker parts of nucleosomes // Moscow Univ. Biol. Sci. Bull. 2017. Vol. 72. N 3. P. 146–150.
15. Chertkov O.V., Valieva M.E., Malyuchenko N.V., Feofanov A.V. Analysis of nucleosome structure in polyacrylamide gel by the Förster resonance energy transfer method // Moscow Univ. Biol. Sci. Bull. 2017. Vol. 72. N 4. P. 196–200.
Review
For citations:
Feofanov A.V., Andreeva T.V., Studitsky V.M., Kirpichnikov M.P. REVERSIBILITY OF STRUCTURAL REARRANGEMENTS IN MONONUCLEOSOMES INDUCED BY IONIC STRENGTH. Vestnik Moskovskogo universiteta. Seriya 16. Biologiya. 2018;73(3):191-196. (In Russ.)
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