Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae

TitleStructural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae
Publication TypeJournal Article
Year of Publication2010
AuthorsNikolaou C, Althammer S, Beato M, Guigo R
JournalEpigenetics & chromatin
Date PublishedNov

ABSTRACT: BACKGROUND: Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses aim towards providing a better understanding of the process of nucleosome positioning, for which a number of models have been suggested. Nevertheless, questions regarding the sequence constraints of nucleosomal DNA and how they may have been shaped through evolution remain open. Here we analyze in detail different experimental nucleosome datasets with the aim of providing a hypothesis for the emergence of nucleosome-forming sequences. RESULTS: We have compared the complete sets of nucleosome positions for the budding yeast (S. cerevisiae) as defined in the output of two independent experiments with the use of two different experimental techniques. We found that less than 10% of the experimentally defined nucleosome positions were consistently positioned in both datasets. This subset of well-positioned nucleosomes, when compared to the bulk, was shown to have particular properties at both sequence and structural levels. Consistently positioned nucleosomes were also shown to occur preferentially in pairs of di-nucleosomes and to be surprisingly less conserved when compared to their adjacent nucleosome-free linkers. CONCLUSION: Our findings may be combined into a hypothesis for the emergence of a weak nucleosome-positioning code. According to this hypothesis, consistent nucleosomes may be partly guided by nearby nucleosome-free regions through statistical positioning. Once established, a set of well-positioned consistent nucleosomes may impose secondary constraints which further shape the structure of the underlying DNA. We are able to capture these constraints through the application of a recently introduced structural property that is related to the symmetry of DNA curvature. Furthermore we show that both consistently-positioned nucleosomes and their adjacent nucleosome-free regions show an increased tendency for the conservation of this structural feature.