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  • 1
    Keywords: SACCHAROMYCES-CEREVISIAE ; transcription ; BINDING ; ORGANIZATION ; LINKER HISTONE ; GENE-REGULATION ; CHROMATIN-STRUCTURE ; LARGE LIGANDS ; EUKARYOTIC GENOME ; PHASE-TRANSITION
    Abstract: The nucleosome repeat length (NRL) is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a systematic theoretical description of NRL as a function of DNA sequence and epigenetic determinants is currently lacking. To address this problem, we have performed an integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters. We show that in simple eukaryotes such as yeast, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action. For higher eukaryotes, also the upper limit exists since NRL is an increasing but saturating function of the linker histone concentration. Counterintuitively, smaller H1 variants or non-histone architectural proteins can initiate larger effects on the NRL due to entropic reasons. Furthermore, we demonstrate that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects or vice versa. We consider several classes of genomic regions with apparently different regimes of the NRL variation. As one extreme, our analysis reveals that the period of oscillations of the nucleosome density around bound RNA polymerase coincides with the period of oscillations of positioning sites of the corresponding DNA sequence. At another extreme, we show that although mouse major satellite repeats intrinsically encode well-defined nucleosome preferences, they have no unique nucleosome arrangement and can undergo a switch between two distinct types of nucleosome positioning.
    Type of Publication: Journal article published
    PubMed ID: 24992723
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  • 2
    Keywords: RESOLUTION ; COMPLEX ; DNA ; CHROMATIN FIBER STRUCTURE ; LINKER HISTONE ; H1 ; STOICHIOMETRY ; STATE ; POLYELECTROLYTE ADSORPTION ; CHARGE-DISTRIBUTION
    Abstract: Within a simple biophysical model we describe the effect of electrostatic binding of H1 histone proteins on the nucleosome repeat length in chromatin. The length of wrapped DNA optimizes its binding energy to the histone core and the elastic energy penalty of DNA wrapping. The magnitude of the effect predicted from our model is in agreement with the systematic experimental data on the linear variation of nucleosome repeat lengths with H1/nucleosome ratio (Woodcock C L et al 2006 Chromos. Res. 14 17-25). We compare our model to the data for different cell types and organisms, with a widely varying ratio of bound H1 histones per nucleosome. We underline the importance of this non-specific histone-DNA charge-balance mechanism in regulating the positioning of nucleosomes and the degree of compaction of chromatin fibers in eukaryotic cells.
    Type of Publication: Journal article published
    PubMed ID: 25078656
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  • 3
    Keywords: NUCLEOSOME CORE PARTICLES ; Repeat length ; DNA DOUBLE HELICES ; SYNAPTONEMAL COMPLEX
    Abstract: Chromatin domains formed in vivo are characterized by different types of 3D organization of interconnected nucleosomes and architectural proteins. Here, we quantitatively test a hypothesis that the similarities in the structure of chromatin fibers (which we call "structural homology") can affect their mutual electrostatic and protein-mediated bridging interactions. For example, highly repetitive DNA sequences in heterochromatic regions can position nucleosomes so that preferred inter-nucleosomal distances are preserved on the surfaces of neighboring fibers. On the contrary, the segments of chromatin fiber formed on unrelated DNA sequences have different geometrical parameters and lack structural complementarity pivotal for stable association and cohesion. Furthermore, specific functional elements such as insulator regions, transcription start and termination sites, and replication origins are characterized by strong nucleosome ordering that might induce structure-driven iterations of chromatin fibers. We propose that shape-specific protein-bridging interactions facilitate long-range pairing of chromatin fragments, while for closely-juxtaposed fibers electrostatic forces can in addition yield fine-tuned structure-specific recognition and pairing. These pairing effects can account for some features observed for mitotic and inter-phase chromatins.
    Type of Publication: Journal article published
    PubMed ID: 23860914
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  • 4
    ISSN: 1572-817X
    Keywords: Dense resonant medium ; hysteresis ; self-diffraction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Notes: Abstract On the basis of the modified Bloch equations a theory is developed of the light self-diffraction in a thin film of a dense resonant medium with allowance for the dipole-dipole interactions of atoms. It is shown that for certain values of intensity of an external field, there occurs in the film the light-induced first-kind phase transition which causes the emergence of regions (domains) with the high excitation of atoms. The switching effects of the system “dense resonant medium + periodically-modulated field” under consideration result in a hysteresis behaviour in the dependence of the diffraction efficiency on the adiabatically changing intensity of the external field. The predicted hysteresis offers additional potentialities in the investigation of the dynamics of the first-kind phase transition in dense media and outlook for usage of the film as a switching logical element.
    Type of Medium: Electronic Resource
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