مدل شبیه سازی برای توزیع نوکلئوزوم در مخمر ژنوم بر اساس موقعیت داده های یکپارچه کراس پلت فرم

In-depth analysis of six recent experimental nucleosome datasets in the yeast reveals broad disagreements between the final nucleosome positions detected by previous studies. Our results, which combine different types of data, suggest that cross-platform information, including discrepancy and consistency, reflects the mechanisms of nucleosome packaging in vivo more faithfully than individual studies. Furthermore, nucleosomes can be divided into two classes according to their stable and dynamic characteristics. By combining the nucleosome distribution information with a statistical positioning idea, we constructed a novel simulation model for nucleosome distributions in promoter regions.

In eukaryotic genomes, DNA is compacted through multiple steps into a protein–DNA complex known as chromatin. The first level of compaction involves wrapping the long genomic DNA strands into arrays of particles called nucleosomes, each containing a 146 bp long stretch of DNA that is sharply bent and tightly wrapped in nearly two superhelical turns around an octameric core of histone [1]. Any DNA sequence can be packaged into a nucleosome; however, homeostatic histone concentrations ensure that only 70–90% of the DNA is wrapped in nucleosomes, with consecutive nucleosomes typically separated by 15–50 bp of unwrapped linker DNA [2]. In particular, the histone components, as well as additional chromatin proteins, can interact to form higher-order chromosomal structures. Thus, nucleosomes are critical to the organization and maintenance of chromatin, and their position and modification state can significantly influence genetic activities, such as the plasticity or control of gene expression. As a result, studies of nucleosome positions, determined by either experimental measurements or computational methods, continue to be an active field of research. Six high-resolution genome-scale nucleosome positioning studies have recently been completed in Saccharomyces cerevisiae [3], [4], [5], [6], [7] and [8]. In these assays, either tiling arrays or direct sequencing technologies were used to map the positions of nucleosomes. However, it is clear from previous work that nucleosome positions are subtle and diffuse, which makes it difficult to distinguish their true position data from random noise in a single experiment. The dynamic changes and experimental errors that may be responsible for inconsistencies among these studies led us to develop a criterion to assess these studies effectively. In addition, inconsistent assignment of nucleosome positions, derived from different detection methods, highlights the need for careful and comprehensive comparison of these experimental datasets.

In eukaryotic genomes, DNA is compacted through multiple steps into a protein–DNA complex known as chromatin. The first level of compaction involves wrapping the long genomic DNA strands into arrays of particles called nucleosomes, each containing a 146 bp long stretch of DNA that is sharply bent and tightly wrapped in nearly two superhelical turns around an octameric core of histone [1]. Any DNA sequence can be packaged into a nucleosome; however, homeostatic histone concentrations ensure that only 70–90% of the DNA is wrapped in nucleosomes, with consecutive nucleosomes typically separated by 15–50 bp of unwrapped linker DNA [2]. In particular, the histone components, as well as additional chromatin proteins, can interact to form higher-order chromosomal structures. Thus, nucleosomes are critical to the organization and maintenance of chromatin, and their position and modification state can significantly influence genetic activities, such as the plasticity or control of gene expression. As a result, studies of nucleosome positions, determined by either experimental measurements or computational methods, continue to be an active field of research. Six high-resolution genome-scale nucleosome positioning studies have recently been completed in Saccharomyces cerevisiae [3], [4], [5], [6], [7] and [8]. In these assays, either tiling arrays or direct sequencing technologies were used to map the positions of nucleosomes. However, it is clear from previous work that nucleosome positions are subtle and diffuse, which makes it difficult to distinguish their true position data from random noise in a single experiment. The dynamic changes and experimental errors that may be responsible for inconsistencies among these studies led us to develop a criterion to assess these studies effectively. In addition, inconsistent assignment of nucleosome positions, derived from different detection methods, highlights the need for careful and comprehensive comparison of these experimental datasets.