Refinement of Nucleosome Positions within Individual Genes Using Molecular Modeling Methods and MNase Sequencing Data

IF 4.033 Q4 Biochemistry, Genetics and Molecular Biology Biophysics Pub Date : 2024-03-07 DOI:10.1134/S0006350923050317
V. A. Vasilev, D. M. Ryabov, A. K. Shaytan, G. A. Armeev
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Abstract

Chromatin organization plays an important role in regulating the genetic machinery of the cell. A nucleosome is a basic unit of chromatin packaging and harbors about 145 bp of DNA. The packaging of genetic material and its accessibility to transcription enzymes and other regulatory chromatin proteins depend on the positions of nucleosomes. MNase sequencing is used to examine the nucleosome positions in a genome. MNase sequencing data are sufficient for detecting the presence of nucleosomes on a sequence, but their precise locations can be problematic to establish. Additional data filtering and processing are required for accurate determination of nucleosome positions. A combined method was developed using a geometric analysis of the molecular models of nucleosome chains to select the possible nucleosome positions on the basis of MNase sequencing data. The algorithm efficiently eliminates the inaccessible nucleosome chain combinations and conformationally prohibited nucleosome positions.

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利用分子建模方法和 MNase 测序数据完善单个基因内的核小体位置
摘要 染色质组织在调节细胞遗传机制方面发挥着重要作用。核小体是染色质包装的基本单位,容纳约 145 bp 的 DNA。遗传物质的包装及其对转录酶和其他染色质调控蛋白的可及性取决于核小体的位置。MNase 测序用于检测基因组中核小体的位置。MNase 测序数据足以检测序列中核小体的存在,但要确定核小体的精确位置却很困难。要准确确定核小体的位置,还需要额外的数据过滤和处理。通过对核小体链的分子模型进行几何分析,开发出了一种综合方法,可根据 MNase 测序数据选择可能的核小体位置。该算法有效地排除了无法进入的核糖体链组合和构象禁用的核糖体位置。
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来源期刊
Biophysics
Biophysics Biochemistry, Genetics and Molecular Biology-Biophysics
CiteScore
1.20
自引率
0.00%
发文量
67
期刊介绍: Biophysics is a multidisciplinary international peer reviewed journal that covers a wide scope of problems related to the main physical mechanisms of processes taking place at different organization levels in biosystems. It includes structure and dynamics of macromolecules, cells and tissues; the influence of environment; energy transformation and transfer; thermodynamics; biological motility; population dynamics and cell differentiation modeling; biomechanics and tissue rheology; nonlinear phenomena, mathematical and cybernetics modeling of complex systems; and computational biology. The journal publishes short communications devoted and review articles.
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