17 Results
for term "sites"
- The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae...Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908 ABSTRACT Transcriptional silencing in Saccharomyces cerevisiae occurs at several genomic sites including the silent mating-type loci, telomeres, and the ribosomal DNA (rDNA) tandem array. Epigenetic silencing at each ~~~
- Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae...and are normally prevented. Remarkably, eukaryotic genomes are normally quite stable, despite the fact that they includemany features that are at risk for causing the formation of GCRs, including duplicated sequences and double-strand break (DSB)-inducing sites (Gordenin and Resnick 1998; Lambert et al. 2005 ~~~
- Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)...(Cromie et al. 2013; Arana-Sanchez et al. 2015; Ludlow et al. 2016) are clean lineages or mosaics, though admixture was detected using genome-wide analysis of variants using restriction site associated DNA sequencing (Cromie et al. 2013; Ludlow et al. 2016). It would be very interesting if some ~~~
- Mechanisms and Regulation of Mitotic Recombination in Saccharomyces cerevisiae...of the Recombinogenic DNA Lesion 812 A. Induction of recombination by DSBs and nicks 812 B. Replication-coupled recombination 813 C. Fragile sites and noncanonical structures 813 D. Transcription-stimulated recombination 814 V. Cell Biology of Recombination 814 A. Recombination foci 814 B. Choreography of focus ~~~
- Chromosome Duplication in Saccharomyces cerevisiae...during the cell cycle, and to reveal the temporal regulation of origin usage during S phase. The dened sites of initiation also revealed the location and direction of replication forks, facilitating studies of their composition and function. Identication and characterization of replication origins ~~~
- The Composition, Functions, and Regulation of the Budding Yeast Kinetochore...a kinetochore is either attached or unattached to a microtubule at any given time. In contrast, most eukaryotic kinetochores have from 3 to 30 microtubule binding sites, which can be partially occupied (Walczak et al. 2010). Replication creates sister chromatids, which become physically linked together ~~~
Figure 8Genetic assays. (A) Direct-repeat recombination. Spontaneous homologous recombination between ade2-n and ade2-a alleles can occur by gene conversion to produce Ade+ Ura+ cells or by SSA to produce Ade+ Ura− cells (Fung et al. 2009). (B) Inverted repeat recombination. Inverted repeat recombination assays exclusively Ade+ recombinants arising from gene conversion since SSA will not produce viable recombinants. CO and NCO events will lead to inversion and noninversion of the TRP1 marker, respectively (Mott and Symington 2011). (C) Plasmid gap repair assay. The efficiency of plasmid–chromosome recombination, crossover frequency, and conversion tract length is assayed by transformation of the gapped pSB110 plasmid into yeast containing the chromosomal met17-sna mutant allele in which a SnaBI site is eliminated 216 bp downstream of the gap in the plasmid (Symington et al. 2000). When the plasmid gap is repaired by noncrossover gene conversion, the result is unstable (u) Ura+ transformants, which will be Met+ (class I) or Met− (class II), depending on the absence or presence of co-conversion of the met17-sna mutation, respectively. If the gene conversion event is associated with a crossover, the result is a stable (s) Ura+ phenotype (classes III and IV). ARS, autonomously replicating sequence. (D) Break-induced replication. In this assay, BIR is initiated by induction of an HO-mediated DSB adjacent to a 3′ truncated lys2 gene (lys) on chromosome V. The lys fragment has 2.1 kb of homology to a 5′ truncation of lys2 (ys2) close to the telomere on chromosome XI (Donnianni and Symington 2013), which serves as a donor for BIR. BIR results in deletion of the KanMX gene and all nonessential genes telomere proximal to the HO cut site and loss of G418 resistance (G418R). The strain has the MATa-inc allele to prevent cleavage at the endogenous HO cut site.
Figure 1Structure of S. cerevisiae replicator. The general structure of budding yeast replicators and the surrounding nucleosomes is illustrated. Although the precise nucleosome positions vary, the key elements of the replicator are located within a nucleosome-free region with the ORC binding site located asymmetrically within this region. The ORC-ACS consensus sequence shown is derived from Eaton et al. 2010.
Figure 8Evolution of mating-type switching. Left: same as Figure 7. Red lightning bolts refer to capture of site-specific nucleases. Right: MAT cassettes (colored boxes) are symbolized on chromosomes (gray bars) with MATa (horizontal black stripes) or MATα (vertical black stripes) idiomorphs. Silenced cassettes are shaded. Shown are the topologies observed in S. cerevisiae (for the Saccharomycetaceae) and K. phaffii (for the methylotrophs), but significant variations are found in both subgroups (see text). The α3 and Kat1 transposases of K. lactis are shown acting at the same place as the HO endonuclease of S. cerevisiae, despite important mechanistic differences.
Figure 2Local and long-range interactions of silent chromatin. (A) The arrangements of components within a typical locus of silent chromatin. Sir2 (2), Sir3 (3) and Sir4 (4) form the Sir2/3/4 complex that binds histones throughout the silenced domain. Histones within the domain lack post-translational modifications with the exception of H2AS129 phosphorylation and some H4K12 acetylation. ORC, Rap1 (R), Abf1 (A) and Sir1 (1) bind to cis-acting silencer elements and interact with proteins of the Sir2/3/4 complex. Specific interactions between these components are documented in subsequent figures. Ac, acetylation. (B) The folded-back structure of silent chromatin at a telomere. (C) The long-range interactions between the silent chromatin domains at HML and HMR cause chromosome III to fold back upon itself. (D) Interactions between the silent chromatin domains of different telomeres and interactions between silent chromatin and docking sites at the nuclear membrane cause chromosome ends to cluster at the nuclear periphery.