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

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.