Abstract
Nucleosomes, which consist of DNA wrapped around histone octamers, are dynamic, and their structure, including their location, size, and occupancy, can be transformed. Nucleosomes can regulate gene expression by controlling the DNA accessibility of proteins. Using next-generation sequencing techniques along with such laboratory methods as micrococcal nuclease digestion, predicting the genomic locations of nucleosomes is possible. However, the true locations of nucleosomes are unknown, and it is difficult to determine their exact locations using next-generation sequencing data. This paper proposes a novel voting algorithm, NucVoter, for the reliable prediction of nucleosome locations. Multiple models verify the consensus areas in which nucleosomes are placed by the model with the highest priority. NucVoter significantly improves the performance of nucleosome prediction.
Highlights
Genes within DNA are transcribed into an RNA product [1]
The forward/reverse tags for both stable and fuzzy nucleosomes were randomly generated in the range of 1 to the C coverage at the starting/ending locations of nucleosomes
Stable tags were randomly shifted in the range of +/−20 bp and fuzzy tags in the range of +/−50 bp
Summary
Genes within DNA are transcribed into an RNA product [1]. The DNA region encoding a gene must be accessible to proteins such as transcription factors and RNA polymerase [2]. If the DNA region is wrapped compactly to prevent proteins from binding to the DNA, the corresponding gene is not transcribed [4]. Nucleosomes can regulate gene expression by restricting or facilitating the DNA accessibility of proteins. The area downstream of the −1 nucleosome is the nucleosome-free region (NFR) which shows very low nucleosome occupancies over approximately 150 bp on average [5]. While the +1 nucleosome is stable, its upstream and downstream nucleosomes show declines in occupancy and stability and become fuzzy
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