Grigory A. Armeev

Lomonosov Moscow State University

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AК

Alexey К. Shaytan

Lomonosov Moscow State University

МП

М. П. Кирпичников

Institute of Bioorganic Chemistry

Vasily M. Studitsky

Fox Chase Cancer Center

Alexey V. Feofanov

Lomonosov Moscow State University

Anna R. Panchenko

Queen's University

Victor B. Zhurkin

National Cancer Institute

Olesya Volokh

Lomonosov Moscow State University

David Landsman

National Center for Biotechnology Information

Olga S. Sokolova

Lomonosov Moscow State University

КВ

К. В. Шайтан

Lomonosov Moscow State University

Cooperative Institutions

Lomonosov Moscow State University

Moscow State University

Rutgers, The State University of New Jersey

Russian Academy of Sciences

Fox Chase Cancer Center

National Institutes of Health

Institute of Bioorganic Chemistry

Institute of Gene Biology

National Center for Biotechnology Information

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Structure and Dynamics of Compact Dinucleosomes: Analysis by Electron Microscopy and spFRET

International Journal of Molecular Sciences (2023)

Maria E. Stefanova Olesya Volokh О. В. Чертков Grigory A. Armeev Alexey К. Shaytan

Formation of compact dinucleosomes (CODIs) occurs after collision between adjacent nucleosomes at active regulatory DNA regions. Although CODIs are likely dynamic structures, their structural heterogeneity and dynamics were not systematically addressed. Here, single-particle Förster resonance energy transfer (spFRET) and electron microscopy were employed to study the structure and dynamics of CODIs. spFRET microscopy in solution and in gel revealed considerable uncoiling of nucleosomal DNA from the histone octamer in a fraction of CODIs, suggesting that at least one of the nucleosomes is destabilized in the presence of the adjacent closely positioned nucleosome. Accordingly, electron microscopy analysis suggests that up to 30 bp of nucleosomal DNA are involved in transient uncoiling/recoiling on the octamer. The more open and dynamic nucleosome structure in CODIs cannot be stabilized by histone chaperone Spt6. The data suggest that proper internucleosomal spacing is an important determinant of chromatin stability and support the possibility that CODIs could be intermediates of chromatin disruption.

Histone octamer

10.3390/ijms241512127

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N-Terminal Tails of Histones H2A and H2B Differentially Affect Transcription by RNA Polymerase II In Vitro

Cells (2022)

Han-Wen Chang Alexey V. Feofanov A. V. Lyubitelev Grigory A. Armeev E. Yu. Kotova

Histone N-terminal tails and their post-translational modifications affect various biological processes, often in a context-specific manner; the underlying mechanisms are poorly studied. Here, the role of individual N-terminal tails of histones H2A/H2B during transcription through chromatin was analyzed in vitro. spFRET data suggest that the tail of histone H2B (but not of histone H2A) affects nucleosome stability. Accordingly, deletion of the H2B tail (amino acids 1-31, but not 1-26) causes a partial relief of the nucleosomal barrier to transcribing RNA polymerase II (Pol II), likely facilitating uncoiling of DNA from the histone octamer during transcription. Taken together, the data suggest that residues 27-31 of histone H2B stabilize DNA-histone interactions at the DNA region localized ~25 bp in the nucleosome and thus interfere with Pol II progression through the region localized 11-15 bp in the nucleosome. This function of histone H2B requires the presence of the histone H2A N-tail that mediates formation of nucleosome-nucleosome dimers; however, nucleosome dimerization per se plays only a minimal role during transcription. Histone chaperone FACT facilitates transcription through all analyzed nucleosome variants, suggesting that H2A/H2B tails minimally interact with FACT during transcription; therefore, an alternative FACT-interacting domain(s) is likely involved in this process.

Histone octamer

Histone Methylation

Linker DNA

RNA polymerase II

Histone code

Histone H2B

Transcription

10.3390/cells11162475

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Citations (3)

Polymorphism of Histone Tail Interactions in Nucleosome

Biophysical Journal (2015)

Alexey К. Shaytan Grigory A. Armeev Victor B. Zhurkin David Landsman Anna R. Panchenko

Linker DNA

Chromatosome

Histone octamer

Histone code

10.1016/j.bpj.2014.11.431

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Abstract P-43: Approximating Protein Alpha-Helices with Cylinders for Free Electron Lasers Diffraction Experiments

International Journal of Biomedicine (2019)

Grigory A. Armeev Mikhail Lozhnikov Valery Novoseletsky Aleksandr V. Kudriavtsev Alexey К. Shaytan

Free electron model

Alpha (finance)

10.21103/ijbm.9.suppl_1.p43

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Nucleosome Dynamics at Microsecond Timescale: DNA-Protein Interactions, Water-Mediated Interactions and Nucleosome Formation

Biophysical Journal (2016)

Alexey К. Shaytan Grigory A. Armeev Alexander Goncearenco Victor B. Zhurkin David Landsman

Histone octamer

Linker DNA

Chromatosome

Histone Methylation

Histone code

10.1016/j.bpj.2015.11.2189

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Citations (3)

Structure of an Intranucleosomal DNA Loop That Senses DNA Damage during Transcription

Cells (2022)

Н. С. Герасимова Olesya Volokh Nikolay A. Pestov Grigory A. Armeev М. П. Кирпичников

Transcription through chromatin by RNA polymerase II (Pol II) is accompanied by the formation of small intranucleosomal DNA loops containing the enzyme (i-loops) that are involved in survival of core histones on the DNA and arrest of Pol II during the transcription of damaged DNA. However, the structures of i-loops have not been determined. Here, the structures of the intermediates formed during transcription through a nucleosome containing intact or damaged DNA were studied using biochemical approaches and electron microscopy. After RNA polymerase reaches position +24 from the nucleosomal boundary, the enzyme can backtrack to position +20, where DNA behind the enzyme recoils on the surface of the histone octamer, forming an i-loop that locks Pol II in the arrested state. Since the i-loop is formed more efficiently in the presence of SSBs positioned behind the transcribing enzyme, the loop could play a role in the transcription-coupled repair of DNA damage hidden in the chromatin structure.

Transcription bubble

RNA polymerase II

Transcription

Histone octamer

Processivity

Histone Methylation

10.3390/cells11172678

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Citations (6)