title: Sequence analysis of origins of replication in the Saccharomyces cerevisiae genomes.
abstract: DNA replication is a highly precise process that is initiated from origins of replication (ORIs) and is regulated by a set of regulatory proteins. The mining of DNA sequence information will be not only beneficial for understanding the regulatory mechanism of replication initiation but also for accurately identifying ORIs. In this study, the GC profile and GC skew were calculated to analyze the compositional bias in the Saccharomyces cerevisiae genome. We found that the GC profile in the region of ORIs is significantly lower than that in the flanking regions. By calculating the information redundancy, an estimation of the correlation of nucleotides, we found that the intensity of adjoining correlation in ORIs is dramatically higher than that in flanking regions. Furthermore, the relationships between ORIs and nucleosomes as well as transcription start sites were investigated. Results showed that ORIs are usually not occupied by nucleosomes. Finally, we calculated the distribution of ORIs in yeast chromosomes and found that most ORIs are in transcription terminal regions. We hope that these results will contribute to the identification of ORIs and the study of DNA replication mechanisms.
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China Chengdu, China.
authors.forename: Wen-Chao
authors.initials: WC
authors.lastname: Li
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China Chengdu, China.
authors.forename: Zhe-Jin
authors.initials: ZJ
authors.lastname: Zhong
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China Chengdu, China.
authors.forename: Pan-Pan
authors.initials: PP
authors.lastname: Zhu
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China Chengdu, China.
authors.forename: En-Ze
authors.initials: EZ
authors.lastname: Deng
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China Chengdu, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Ding
authors.affiliation: Department of Physics, School of Sciences and Center for Genomics and Computational Biology, Hebei United University Tangshan, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China Chengdu, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
keywords: GC profile; GC skew; Saccharomyces cerevisiae; distribution of ORIs; information redundancy; origin of replication