ArticleGenome biology2004
Prediction of Saccharomyces cerevisiae replication origins.
Article in Genome biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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70 citing papers in PubMed, 110 citations in OpenAlex.
- Engineering iridoviruses: development of reverse genetics and virus rescue systems.Journal of virology · 2025Article
- Identification of 1600 replication origins ineLife · 2024Article
- Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes.Nucleus (Austin, Tex.) · 2023Review
- The conserved histone chaperone Spt6 is strongly required for DNA replication and genome stability.Cell reports · 2023Article
- Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon.BMC biology · 2023Article
- The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors.BMC biology · 2022Article
- Origin recognition complex harbors an intrinsic nucleosome remodeling activity.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Using multi-layer perceptron to identify origins of replication in eukaryotes via informative features.BMC bioinformatics · 2021Article
- Disruption of origin chromatin structure by helicase activation in the absence of DNA replication.Genes & development · 2021Article
- Methylation of histone H3 at lysine 37 by Set1 and Set2 prevents spurious DNA replication.Molecular cell · 2021Article
- Humanizing the yeast origin recognition complex.Nature communications · 2021Article
- Bioinformatical dissection of fission yeast DNA replication origins.Open biology · 2020Article
- Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork.Genome research · 2019Article
- Comprehensive Analysis of Replication Origins inFrontiers in microbiology · 2019Article
- Article
- Recent Advances on the Machine Learning Methods in Identifying DNA Replication Origins in Eukaryotic Genomics.Frontiers in genetics · 2018Review
- Bidirectional eukaryotic DNA replication is established by quasi-symmetrical helicase loading.Science (New York, N.Y.) · 2017Article
- Chromosome Duplication in Saccharomyces cerevisiae.Genetics · 2016Review
- Article
- Eukaryotic replication origins: Strength in flexibility.Nucleus (Austin, Tex.) · 2016Review
10 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAutonomously replicating sequences (ARSs) function as replication origins in Saccharomyces cerevisiae. ARSs contain the 17 bp ARS consensus sequence (ACS), which binds the origin recognition complex. The yeast genome contains more than 10,000 ACS matches, but there are only a few hundred origins, and little flanking sequence similarity has been found. Thus, identification of origins by sequence alone has not been possible.
resultsWe developed an algorithm, Oriscan, to predict yeast origins using similarity to 26 characterized origins. Oriscan used 268 bp of sequence, including the T-rich ACS and a 3' A-rich region. The predictions identified the exact location of the ACS. A total of 84 of the top 100 Oriscan predictions, and 56% of the top 350, matched known ARSs or replication protein binding sites. The true accuracy was even higher because we tested 25 discrepancies, and 15 were in fact ARSs. Thus, 94% of the top 100 predictions and an estimated 70% of the top 350 were correct. We compared the predictions to corresponding sequences in related Saccharomyces species and found that the ACSs of experimentally supported predictions show significant conservation.
conclusionsThe high accuracy of the predictions indicates that we have defined near-sufficient conditions for ARS activity, the A-rich region is a recognizable feature of ARS elements with a probable role in replication initiation, and nucleotide sequence is a reliable predictor of yeast origins. Oriscan detected most origins in the genome, demonstrating previously unrecognized generality in yeast replication origins and significant discriminatory power in the algorithm.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.