%0 Journal Article
%T NucVoter: A Voting Algorithm for Reliable Nucleosome Prediction Using Next-Generation Sequencing Data
%A Boseon Byeon
%J ISRN Bioinformatics
%D 2013
%R 10.1155/2013/174064
%X 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. 1. Introduction Genes within DNA are transcribed into an RNA product [1]. To be transcribed, the DNA region encoding a gene must be accessible to proteins such as transcription factors and RNA polymerase [2]. As shown in Figure 1, a nucleosome is composed of a DNA sequence wrapped 1.65 times around a histone octamer [3]. If the DNA region is wrapped compactly to prevent proteins from binding to the DNA, the corresponding gene is not transcribed [4]. Therefore, nucleosomes can regulate gene expression by restricting or facilitating the DNA accessibility of proteins. Figure 1: Organization of nucleosomes and linkers, and DNA. A nucleosome is composed of DNA wrapped around a histone octamer. H indicates a histone octamer. Nucleosomes are connected by linker DNA. DNA is double stranded; the forward strand is in the 5¡ä to 3¡ä direction, while the reverse strand is in the opposite direction. Figure 2 shows the profile of typical nucleosomes around the transcription start sites (TSSs) of yeast genes. The most prevalent size of nucleosomes is approximately 147 base pairs (bp), and the length of linker DNA between nucleosomes is approximately 18£¿bp [3]. The occupancy of a nucleosome represents the possibility that a nucleosome resides at a particular genomic location. The so-called £¿1 nucleosome is the first nucleosome upstream of the TSS. 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]. The NFR contains transcription factor binding sites and is therefore important in transcription regulation [6]. The first nucleosome downstream of the NFR is the +1 nucleosome, followed by the +2, +3,
%U http://www.hindawi.com/journals/isrn.bioinformatics/2013/174064/