A 13 kb resolution cosmid map of the 14 Mb fission yeast genome by nonrandom sequence-tagged site mapping

Mizukami, Toru; Chang, William I.; Garkavtsev, Igor; Kaplan, Nancy; Lombardi, D. Rachel; Matsumoto, Tomohiro; Niwa, Osami; Kounosu, Asako; Yanagida, Mitsuhiro; Marr, Thomas G.; Beach, David

doi:10.1016/0092-8674(93)90165-m

Cited by 145 publications

(104 citation statements)

References 17 publications

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“…Similar results were obtained in the generation of the map for Schizosaccharomyces pombe using a similar mapping strategy (Mizukami et al 1993). Three to four times as many STS markers would have been needed to reach this same state of completion if the STSs had been chosen in a random fashion.…”

Section: Strategic Choicessupporting

confidence: 67%

A P1-based physical map of the Drosophila euchromatic genome.

Kimmerly¹,

Stultz²,

Lewis³

et al. 1996

Genome Res.

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A PCR-based sequence-tagged site (STS) content mapping strategy has been used to generate a physical map with 90% coverage of the 120-Mb euchromatic portion of the Drosophila genome. To facilitate map completion, the bulk of the STS markers was chosen in a nonrandom fashion. To ensure that all contigs were localized in relation to each other and the genome, these contig-building procedures were performed in conjunction with a large-scale in situ hybridization analysis of randomly selected clones from a Drosophila genomic library that had been generated in a PI cloning vector. To date, the map consists of 649 contigs with an STS localized on average every 50 kb. This is the first whole genome that has been mapped based on a library constructed with large inserts in a vector that is maintained in Escherichia coli as a single-copy plasmid.

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Section: Strategic Choicessupporting

confidence: 67%

A P1-based physical map of the Drosophila euchromatic genome.

Kimmerly¹,

Stultz²,

Lewis³

et al. 1996

Genome Res.

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“…The PCR sequence thus obtained was used as the hybridization probe for screening of an S. pombe ordered cosmid DNA library (Mizukami et al 1993). Cosmids obtained were overlapping and mapped near the cdc25+ gene in chromosome I.…”

Section: Isolation Of the Pr55 Subunit Genementioning

confidence: 99%

The regulatory subunits of fission yeast protein phosphatase 2A (PP2A) affect cell morphogenesis, cell wall synthesis and cytokinesis

et al. 1996

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Backggvound: Protein phosphatase 2A (PP2A) holoenzymes have a trimeric structure, consisting of a catalytic subunit C and two regulatory subunits A (PR65) and B (PR55). In fission yeast the C subunits, being 80% identical to their mammalian counterparts, are essential for viability and negatively regulate the entry into mitosis. Genetic analyses in budding yeast and Drosophila show that the regulatory subunits are implicated in chromosome segregation, cell morphogenesis and/or cytokinesis. Results:We isolated fission yeast genes p a a l + and p a b l + encoding the regulatory subunits PR65 and PR55, respectively. Gene disruption showed that the paa1'-gene was essential for viability while p a b l + was not required at 26-33°C. Microtubule

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“…SfiI restriction enzyme has been chosen because of its ability to introduce three cuts in CIII outside of rDNA loci. After SfiI digestion, we monitored by Southern blotting the size of the chromosomal rDNA frag- ments (Fan et al, 1991;Mizukami et al, 1993) (Figure 6C). The rDNA fragments generated by SfiI digestion of slx1 genomic DNA were smaller than those obtained with wildtype genomic DNA, particularly for the slx1#2 strain.…”

Section: Slx1 and Rqh1 Maintain Rdnamentioning

confidence: 99%

Slx1-Slx4 Are Subunits of a Structure-specific Endonuclease That Maintains Ribosomal DNA in Fission Yeast

Coulon

Gaillard

Chahwan

et al. 2004

MBoC

109

173

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In most eukaryotes, genes encoding ribosomal RNAs (rDNA) are clustered in long tandem head-to-tail repeats. Studies of Saccharomyces cerevisiae have indicated that rDNA copy number is maintained through recombination events associated with site-specific blockage of replication forks (RFs). Here, we describe two Schizosaccharomyces pombe proteins, homologs of S. cerevisiae Slx1 and Slx4, as subunits of a novel type of endonuclease that maintains rDNA copy number. The Slx1-Slx4 -dependent endonuclease introduces single-strand cuts in duplex DNA on the 3 side of junctions with single-strand DNA. Deletion of Slx1 or Rqh1 RecQ-like DNA helicase provokes rDNA contraction, whereas simultaneous elimination of Slx1-Slx4 endonuclease and Rqh1 is lethal. Slx1 associates with chromatin at two foci characteristic of the two rDNA repeat loci in S. pombe. We propose a model in which the Slx1-Slx4 complex is involved in the control of the expansion and contraction of the rDNA loci by initiating recombination events at stalled RFs. INTRODUCTIONAccurate duplication of a eukaryotic genome depends on highly proficient DNA replication machinery acting in conjunction with DNA repair and checkpoint signaling pathways Osborn et al., 2002). Repair and checkpoint systems are vital because replisomes stall when they encounter DNA damage, protein complexes, or torsional stress. Arrested replication forks (RFs) are prone to rearrangement or collapse. Studies of bacteria have shown that stalled forks can be rescued through either recombinogenic or nonrecombinogenic pathways (Seigneur et al., 1998;Cox et al., 2000;Seigneur et al., 2000;Cox, 2001;McGlynn and Lloyd, 2002).Recent studies have indicated that eukaryotes rescue stalled forks by mechanisms similar to those proposed to act in prokaryotes (Doe et al., 2000;Cox, 2001). A conserved family of eukaryotic DNA helicases related to Escherichia coli RecQ helicase seems to play a central role in the rescue of stalled forks through a nonrecombinogenic mechanism (Doe et al., 2000;Cox, 2001;Hickson et al., 2001). The crucial role of these RecQ-related helicases in maintenance of genome integrity is underscored by the pleiotropic phenotypes of the human Bloom, Werner, and Rothmund-Thomson syndromes associated with defects in BLM, WRN, and RecQ4 proteins, respectively. These hereditary disorders are characterized by high genomic instability, cancer predisposition and, in the case of Werner syndrome, also premature aging (Shen and Loeb, 2000). In budding yeast, Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe, mutations in the genes encoding the RecQ-related helicases Sgs1 and Rqh1, respectively, are associated with hyper-recombination phenotypes. The sgs1 phenotype is characterized by an increase in intra-and interchromosomal recombination, especially at the tandem repeated ribosomal DNA (rDNA) loci (Watt et al., 1995;Sinclair and Guarente, 1997), whereas rqh1 mutants are unable to segregate their chromosomes properly under conditions that stall replication (Stewart et al., 1997...

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A 13 kb resolution cosmid map of the 14 Mb fission yeast genome by nonrandom sequence-tagged site mapping

Cited by 145 publications

References 17 publications

A P1-based physical map of the Drosophila euchromatic genome.

A P1-based physical map of the Drosophila euchromatic genome.

The regulatory subunits of fission yeast protein phosphatase 2A (PP2A) affect cell morphogenesis, cell wall synthesis and cytokinesis

Slx1-Slx4 Are Subunits of a Structure-specific Endonuclease That Maintains Ribosomal DNA in Fission Yeast

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