Genome-wide identification of replication origins in yeast by comparative genomics

Nieduszynski, Conrad A.; Knox, Yvonne; Donaldson, Anne

doi:10.1101/gad.385306

Cited by 180 publications

(236 citation statements)

References 32 publications

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“…Phylogenetic sequence conservation allowed the precise identification of functional ACS motifs. Although the majority of ACS elements were found to be conserved in at least one other sensu stricto species, we found that only 18% were conserved in the five species investigated (Nieduszynski et al 2006). The lack of sequence conservation could reflect genuine divergence between the species or could be a consequence of limited sequence data, poor sequence alignment, or the definition of sequence conservation.…”

Section: Resultsmentioning

confidence: 53%

“…Comparative genomic approaches in the sensu stricto group of Saccharomyces yeasts revealed phylogenetic conservation of the ORC-binding site and facilitated the identification of functional ACS motifs (Theis et al 1999;Nieduszynski et al 2006;Chang et al 2008). Other studies have investigated genome replication in a wider range of Saccharomycotina species.…”

mentioning

confidence: 99%

“…Saccharomyces cerevisiae replication origins are called autonomously replicating sequences (ARS) and are primarily defined by sequence (Nieduszynski et al 2006). Each origin contains an essential sequence element (the ARS consensus sequence or ACS) that is responsible for recruiting the Origin Recognition Complex (ORC).…”

mentioning

confidence: 99%

“…A match to the ACS motif is necessary, but not sufficient for origin function. Additional factors involved in the recruitment of ORC and subsequent origin activity include proximal nucleosomes (Lipford and Bell 2001;Nieduszynski et al 2006;Berbenetz et al 2010;Eaton et al 2010;Müller et al 2010) and a region of helical instability (Umek and Kowalski 1988).…”

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confidence: 99%

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Conservation of replication timing reveals global and local regulation of replication origin activity

2012

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DNA replication initiates from defined locations called replication origins; some origins are highly active, whereas others are dormant and rarely used. Origins also differ in their activation time, resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. paradoxus, S. arboricolus, and S. bayanus. First, we find that the locations of active origins are predominantly conserved between species, whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also in activation time. Only a minority of these conserved origins show differences in activation time between these species. To gain insight as to the mechanisms by which origin activation time is regulated we generated replication profiles for a S. cerevisiae/S. bayanus hybrid strain and find that there are both local and global regulators of origin function.

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Section: Resultsmentioning

confidence: 53%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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Conservation of replication timing reveals global and local regulation of replication origin activity

2012

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“…Another study took advantage of the presence of singlestranded DNA at replication forks to map replication origins in budding yeast and in fission yeast (Feng et al 2007). Finally, a comparative analysis of phylogenetic conservation of sequences between five related Saccharomyces species was used to map S. cerevisiae origins at base pair resolution (Nieduszynski et al 2006). These origins appear in OriDB, a web-based catalogue gathering all the genome-wide datasets available for S. cerevisiae (Nieduszynski et al 2007).…”

Section: Dna Replication Programs: the Yeast Paradigmmentioning

confidence: 99%

Defining replication origin efficiency using DNA fiber assays

2009

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The timely duplication of eukaryotic genomes depends on the coordinated activation of thousands of replication origins distributed along the chromosomes. Origin activation follows a temporal program that is imposed by the chromosomal context and is under the control of S-phase checkpoints. Although the general mechanisms regulating DNA replication are now well-understood at the level of individual origins, little is known on the coordination of thousands of initiation events at a genome-wide level. Recent studies using DNA combing and other single-molecule assays have shown that eukaryotic genomes contain a large excess of replication origins. Most of these origins remain "dormant" in normal growth conditions but are activated when fork progression is impeded. In this review, we discuss how DNA fiber technologies have changed our view of eukaryotic replication programs and how origin redundancy contributes to the maintenance of genome integrity in eukaryotic cells.

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Origin plasticity during budding yeast DNA replication in vitro

2014

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The separation of DNA replication origin licensing and activation in the cell cycle is essential for genome stability across generations in eukaryotic cells. Pre-replicative complexes (pre-RCs) license origins by loading Mcm2-7 complexes in inactive form around DNA. During origin firing in S phase, replisomes assemble around the activated Mcm2-7 DNA helicase. Budding yeast pre-RCs have previously been reconstituted in vitro with purified proteins. Here, we show that reconstituted pre-RCs support replication of plasmid DNA in yeast cell extracts in a reaction that exhibits hallmarks of cellular replication initiation. Plasmid replication in vitro results in the generation of covalently closed circular daughter molecules, indicating that the system recapitulates the initiation, elongation, and termination stages of DNA replication. Unexpectedly, yeast origin DNA is not strictly required for DNA replication in vitro, as heterologous DNA sequences could support replication of plasmid molecules. Our findings support the notion that epigenetic mechanisms are important for determining replication origin sites in budding yeast, highlighting mechanistic principles of replication origin specification that are common among eukaryotes.

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Genome-wide identification of replication origins in yeast by comparative genomics

Cited by 180 publications

References 32 publications

Conservation of replication timing reveals global and local regulation of replication origin activity

Conservation of replication timing reveals global and local regulation of replication origin activity

Defining replication origin efficiency using DNA fiber assays

Origin plasticity during budding yeast DNA replication in vitro

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