Chromatin structure

Previous and Current Research

The group leader Prof. Sivolob has long-standing interests in structure and dynamics of chromatin at different levels of its organization. Previous studies were focused on conformational flexibility of the basic chromatin structural unit, the nucleosome. The molecular mechanisms of nucleosome conformational dynamics were described investigating the topology of single particles reconstituted on DNA minicircles.

Recently, the focus was shifted to higher levels of chromatin organization, the chromatin loops that play an important role in transcription regulation. An original approach has been developed based on the kinetic measurements of electrophoretic track (the so called comet tail) formation in the comet assay (single-cell gel electrophoresis). It has been confirmed that in the neutral comet assay (at neutral pH) and at low levels of DNA damages (and also in the case of undamaged cells) the comet tail is formed by extended DNA loops. More importantly, we have found that these loops are about the same as chromatin loops in the cell nuclei. Thus, the kinetic measurements in the comet assay give an opportunity to investigate the topology of the loops and large-scale features of the loop domain organization (and re-organization) in cells of different types.

Ongoing research aims to find out peculiarities of the chromatin loop organization in cells of different types and in different functional states.

Figure 1. A schematics of the approach (A) and an example of the kinetic plots obtained for the relative amount (f) of DNA in the comet tails and the contour length (S_m, in kilobase pairs) of the largest loops in the tails (B). An analysis of the plots helps to discriminate contributions of surface and inner loops in the tail formation, and also to estimate the supercoiling level in the loops and the loop size distribution.  

Methodological and Technical Expertise

• fluorescence spectroscopy;
• all variants of electrophoresis;
• thermodynamic and kinetic analysis;
• theoretical modeling, programming

Selected Publications

Afanasieva K., Sivolob A.

Physical principles and new applications of comet assay.

Biophysical Chemistry, 2018, 238, 1–7 (IF 1.745)

Afanasieva K., Chopei M., Lozovik A., Semenova A., Lukash L., Sivolob A.

DNA loop domain organization in nucleoids from cells of different types.

Biochemical and Biophysical Research Communications, 2017, 483, 142–146 (IF 2.559)

Afanasieva K., Chopei M., Sivolob A.

Single nucleus versus single cell gel electrophoresis: kinetics of DNA track formation.

Electrophoresis, 2015, 36, 973-977 (IF 3.028)

Afanasieva K., Chopei M., Zazhytska M., Vikhreva M., Sivolob A.

DNA loop domain organization as revealed by single-cell gel electrophoresis.

Biochimica et Biophysica Acta, 2013, 1833, 3237-3244 (IF 4.739)

Afanasieva K., Chopei M., Zazhytska M., Vikhreva M., Sivolob A.

DNA loop domain organization as revealed by single-cell gel electrophoresis.

Biochimica et Biophysica Acta, 2013, 1833, 3237-3244 (IF 4.739)

Afanasieva K., Zazhytska M., Sivolob A.

Kinetics of comet formation in single-cell gel electrophoresis: Loops and fragments.

Electrophoresis, 2010, 31, 512-519 (IF 3.028)

Sivolob A., Lavelle C., Prunell A.

Flexibility of nucleosomes on topologically constrained DNA.

In "The IMA Volumes in Mathematics and its Applications", Eds. C.J.Benham, S.Harvey, W.Olson, D.W.Sumners, D.Swigon, 2009, 150, 251-291.

Bancaud A., Wagner G., Conde e Silva N., Lavelle C., Wong H., Mozziconacci J., Barbi M., Sivolob A., Le Cam E., Mouawad L., Viovy J.-L., Victor J.-M., Prunell A.

Nucleosome chiral transition under positive torsional stress in single chromatin fibers.

Molecular Cell, 2007, 27, 135-147 (IF 14.548)

Conde e Silva N., Black B.E., Sivolob A., Filipski J., Cleveland D.W., Prunell A.

CENP-A-containing nucleosomes: easier disassembly versus exclusive centromeric localization.

Journal of Molecular Biology, 2007, 370, 555-573 (IF 4.894)

Sivolob A., Prunell A.

Nucleosome conformational flexibility and implications for chromatin dynamics.

Philosophical Transactions of the Royal Society of London A, 2004, 362, 1519-1547 (IF 3.093)  

Contacts

sivolob@univ.kiev.ua

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