Specification of DNA Replication Origins and Genomic Base Composition in Fission Yeasts

Mojardín, Laura; Vázquez, Enrique; Antequera, Francisco

doi:10.1016/j.jmb.2013.09.023

Cited by 13 publications

(10 citation statements)

References 43 publications

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“…In S. pombe , higher instability in the dyad region is consistent with the fact that its A + T composition is higher than that of the linker DNA . This is probably a consequence of the general bias of the S. pombe genome toward increasing its A + T content .…”

Section: Nucleosome Repositioning On the Dna Lagging Strand Compromissupporting

confidence: 59%

Replication dynamics in fission and budding yeasts through DNA polymerase tracking

Vázquez

Antequera

2015

BioEssays

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The dynamics of eukaryotic DNA polymerases has been difficult to establish because of the difficulty of tracking them along the chromosomes during DNA replication. Recent work has addressed this problem in the yeasts Schizosaccharomyces pombe and Saccharomyces cerevisiae through the engineering of replicative polymerases to render them prone to incorporating ribonucleotides at high rates. Their use as tracers of the passage of each polymerase has provided a picture of unprecedented resolution of the organization of replicons and replication origins in the two yeasts and has uncovered important differences between them. Additional studies have found an overlapping distribution of DNA polymorphisms and the junctions of Okazaki fragments along mononucleosomal DNA. This sequence instability is caused by the premature release of polymerase δ and the retention of non proof‐read DNA tracts replicated by polymerase α. The possible implementation of these new experimental approaches in multicellular organisms opens the door to the analysis of replication dynamics under a broad range of genetic backgrounds and physiological or pathological conditions.

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Section: Nucleosome Repositioning On the Dna Lagging Strand Compromissupporting

confidence: 59%

Replication dynamics in fission and budding yeasts through DNA polymerase tracking

Vázquez

Antequera

2015

BioEssays

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“…Current studies are examining the locations of origins of replication, the timing of origin firing, the regulation of replication fork movement, and the response to events such as replication fork stalling. S. pombe origins of replication are somewhat like those of higher eukaryotes in their lack of a conserved sequence element ( Mojardin et al 2013 ), thus making S. cerevisiae an outlier in this regard. Along with studies of DNA replication mechanisms, it has been shown that gene expression is affected by whether a DNA replication fork passes through the gene in the sense or antisense direction and that this is controlled by the location of surrounding origins, the timing of origin firing, and the presence of binding sites for the Sap1 or Reb1 proteins that block replication fork progression ( Sanchez-Gorostiaga et al 2004 ; Krings and Bastia 2005 ; Mejia-Ramirez et al 2005 ).…”

Section: Notable Advances From Research On Fission Yeastmentioning

confidence: 99%

An Ancient Yeast for Young Geneticists: A Primer on theSchizosaccharomyces pombeModel System

2015

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The fission yeast Schizosaccharomyces pombe is an important model organism for the study of eukaryotic molecular and cellular biology. Studies of S. pombe, together with studies of its distant cousin, Saccharomyces cerevisiae, have led to the discovery of genes involved in fundamental mechanisms of transcription, translation, DNA replication, cell cycle control, and signal transduction, to name but a few processes. However, since the divergence of the two species approximately 350 million years ago, S. pombe appears to have evolved less rapidly than S. cerevisiae so that it retains more characteristics of the common ancient yeast ancestor, causing it to share more features with metazoan cells. This Primer introduces S. pombe by describing the yeast itself, providing a brief description of the origins of fission yeast research, and illustrating some genetic and bioinformatics tools used to study protein function in fission yeast. In addition, a section on some key differences between S. pombe and S. cerevisiae is included for readers with some familiarity with budding yeast research but who may have an interest in developing research projects using S. pombe.

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“…It has been reported that ORIs contain some AT-rich elements for interactions with regulatory proteins ( Reeves and Beckerbauer, 2001 ; Takahashi et al, 2003 ). Previous research demonstrated that the information encoded in the high AT content can be recognized by the Orc4 subunit of ORC ( Mojardin et al, 2013 ). This can be attributed to the enrichment of the ACS around ORIs in S. cerevisiae , which is an AT-rich motif that contains the binding site for ORC.…”

Section: Resultsmentioning

confidence: 99%

Sequence analysis of origins of replication in the Saccharomyces cerevisiae genomes

Zhong

Zhu

et al. 2014

Front. Microbiol.

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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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Specification of DNA Replication Origins and Genomic Base Composition in Fission Yeasts

Cited by 13 publications

References 43 publications

Replication dynamics in fission and budding yeasts through DNA polymerase tracking

Replication dynamics in fission and budding yeasts through DNA polymerase tracking

An Ancient Yeast for Young Geneticists: A Primer on theSchizosaccharomyces pombeModel System

Sequence analysis of origins of replication in the Saccharomyces cerevisiae genomes

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