Abstract
As the fundamental unit of eukaryotic chromatin structure, nucleosome plays critical roles in gene expression and regulation by controlling physical access to transcription factors. In this paper, based on the geometrically transformed Tsallis entropy and two index-vectors, a valid nucleosome positioning information model is developed to describe the distribution of A/T-riched and G/C-riched dimeric and trimeric motifs along the DNA duplex. When applied to train the support vector machine, the model achieves high AUCs across five organisms, which have significantly outperformed the previous studies. Besides, we adopt the concept of relative distance to describe the probability of arbitrary DNA sequence covered by nucleosome. Thus, the average nucleosome occupancy profile over the S.cerevisiae genome is calculated. With our peak detection model, the isolated nucleosomes along genome sequence are located. When compared with some published results, it shows that our model is effective for nucleosome positioning. The index-vector component is identified to be an important influencing factor of nucleosome organizations.
Highlights
As the basic structural unit of eukaryotic chromatin, nucleosome is composed of DNA with 147 bp wrapped 1.65 turns around a protein complex of eight histones
Inspired by the pioneering work of Trifonov [15], which was the AT-riched and GC-riched dimeric and trimeric motifs were contributed to nucleosome organization, we would like to further explore the role that A/T-riched and G/C-riched dimeric and trimeric motifs plays in nucleosome positioning by defining two index-vectors
We have established a simple and efficient nucleosome positioning model consisting of nucleosome positioning information model, nucleosome occupancy model and peak detection model by describing the regularity of A/T-riched and G/C-riched dimeric and trimeric motifs along sequence
Summary
As the basic structural unit of eukaryotic chromatin, nucleosome is composed of DNA with 147 bp wrapped 1.65 turns around a protein complex of eight histones. The presence (absence) of nucleosomes directly (indirectly) affects a variety of processes of life, including recombination, replication, centromere formation and DNA repair. The developments of the high-thoughput techniques such as chromatin immunoprecipitation (CHIP) coupled with microarrays (CHIP-chip) and CHIP coupled with sequencing techniques (CHIP-Seq) have enabled landmark genome-wide studies of nucleosome positions for several model organisms, like Yeast, Caenorhabditis elegans, Drosophila and Human, which allow the researchers to establish models for nucleosome positioning as well as explore the internal relations between them and the expression and regulation among the whole genome. Nucleosome formation along genome depends on multiple factors, including perference of DNA sequence, physical constraints and epigenetic factors like activities of ATP-dependent remodeling complex.
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