Email this article Updating nucleosome positions within individual genes using molecular modeling methods and mnase sequencing data
- Authors: Vasilev V.A1, Ryabov D.M1, Shaytan A.K1, Armeev G.A1
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Affiliations:
- Lomonosov Moscow State University
- Issue: Vol 68, No 5 (2023)
- Pages: 911-919
- Section: Articles
- URL: https://journals.rcsi.science/0006-3029/article/view/233457
- DOI: https://doi.org/10.31857/S0006302923050101
- EDN: https://elibrary.ru/PHCUCE
- ID: 233457
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Abstract
Organization of chromatin plays an important role in regulating the genetic machinery of the cell. The basic unit of chromatin packaging is a nucleosome, which harbors DNA of about 145 base pairs in length. The packaging of genetic material and its accessibility to transcription enzymes and other regulatory chromatin proteins depends on the positions of nucleosomes. MNase sequencing is used to examine nucleosome positions in a genome. MNase sequencing data are sufficient for detecting the presence of nucleosomes on the sequence, but a determination of the precise locations of nucleosomes can be problematic. Accurate determination of nucleosome positions requires additional data filtering and processing. In this study, using MNase sequencing data, a combined method based on geometric analysis of nucleosome chain molecular models is proposed for selecting possible nucleosome positions. The developed algorithm efficiently eliminates inaccessible nucleosome chain combinations and conformationally prohibited nucleosome positions.
Keywords
About the authors
V. A Vasilev
Lomonosov Moscow State UniversityMoscow, Russia
D. M Ryabov
Lomonosov Moscow State UniversityMoscow, Russia
A. K Shaytan
Lomonosov Moscow State UniversityMoscow, Russia
G. A Armeev
Lomonosov Moscow State University
Email: armeev@intbio.org
Moscow, Russia
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