ArticleFrontiers in microbiology2014
Sequence analysis of origins of replication in the Saccharomyces cerevisiae genomes.
Article in Frontiers in microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Computational prediction of replication origins: a comparative review of methods, benchmarks, and trends from heuristics to deep learning.Briefings in bioinformatics · 2026Review
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Identification of 1600 replication origins ineLife · 2024Article
- Article
- Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats.PLoS genetics · 2019Article
- iRO-PsekGCC: Identify DNA Replication Origins Based on Pseudo k-Tuple GC Composition.Frontiers in genetics · 2019Article
- Recent Advances on the Machine Learning Methods in Identifying DNA Replication Origins in Eukaryotic Genomics.Frontiers in genetics · 2018Review
- iRSpot-Pse6NC: Identifying recombination spots inInternational journal of biological sciences · 2018Article
- Euclidean Distance Analysis Enables Nucleotide Skew Analysis in Viral Genomes.Computational and mathematical methods in medicine · 2018Article
- Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.Genomics data · 2016Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Recent advances in the genome-wide study of DNA replication origins in yeast.Frontiers in microbiology · 2015Article
- Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico.BioMed research international · 2015Review
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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