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for term "sites"
- DNA Repair Mechanisms and the Bypass of DNA Damage in Saccharomyces cerevisiae...27710. E-mail: sue. robertson@duke.edu Genetics, Vol. 193, 10251064 April 2013 1025 CONTENTS, continued AP endonucleases 1031 Apn1, AP endonuclease 1: 1031 Apn2, AP endonuclease 2: 1031 Origin, repair, and biological impact of endogenous AP sites: 1031 Single-strand break repair: dirty end processing ~~~
- Structure and Function in the Budding Yeast Nucleus...subcompartments is achieved in the nucleus without intranuclear membranes and depends instead on sequence elements, proteinprotein interactions, specic anchorage sites at the nuclear envelope or at pores, and long-range contacts between specic chromosomal loci, such as telomeres. Here we review the spatial ~~~
- Everything You Ever Wanted to Know About Saccharomyces cerevisiae Telomeres: Beginning to End...-stranded DNA breaks (DSBs), which create chromosome ends at internal sites on chromosomes. Thus, a central question is how cells distinguish natural ends or telomeres from DSBs. Telomeres on one hand are essential for the stable maintenance of chromosomes: they must be retainedthey cannot be lost ~~~
- Prions in Yeast...al. 2004; Glover and Lum 2009), solubilize aggregated stress-damaged proteins. Indeed, a modied version of Hsp104, HAP, or the modied Hsp104-ClpB chimera, 4BAP, which contains a docking site for the inactive bacterial protease ClpP and is able to capture protein molecules pulled from aggregates ~~~
Figure 5Outline of the proposed sequence of events leading to telomere maintenance via recombination after telomerase loss. DNA strand coloring is as above. Tick marks on the brown sequence indicate a conserved XhoI restriction enzyme site. Most cells die after ∼50–100 generations of growth, but rare cells with the indicated two types of DNA arrangements can continue to divide. Virtually all events are dependent on RAD52 and POL32. Bottom: Typical southern blot analysis using XhoI-digested DNA derived from indicated strains. The probe consisted of a 32P labeled DNA fragment specific for telomeric repeat sequences. M, molecular size standards; yku, DNA derived from a strain lacking YKU80 and harboring short terminal repeat tracts. WT, DNA from a wild-type strain; type I, DNA from type I survivors; type II, DNA derived from type II survivors. Red square, location of terminal XhoI fragments. Blue square, signal for the amplified Y′ elements in type I survivors. Note that the fragment pattern for type II survivors is highly variable and unstable; thus the patterns shown in the last two lanes should be taken as an example for illustration purposes only.
Figure 3Visualization of the dynamics of a chromosomal locus. (A) Through the binding of a GFP–LacI fusion to arrays of bacterial lacO sites inserted into the yeast genome (e.g., near a telomere), one can track the rapid chromatin movement in living cells. (B) The nuclear boundary is detected by expression of GFP-Nup49, which helps align sequential time-lapse frames. Three-dimensional stack of images are taken at 1.5-sec intervals for 5–7.5 min. Shown are 5-min tracks (in red) of a GFP-LacI-tagged silent Tel3L and a tagged Tel3L that is derepressed and released from the nuclear envelope, visualized by GFP-Nup49. The repressed and perinuclear telomere moves less frequently. (C) A GFP-tagged LYS2 locus and the same locus excised from Chr II by recombination (D) are shown. Both the tracking over 7.5 min and the xt and yt orthogonal portrayal of the movements are shown. (E) The movement of a given focus was analyzed by mean squared displacement (MSD) analysis (see formula in E), which yields both the diffusion coefficient and the radius of constraint (Rc = 0.6 µm) (Gasser 2002; Marshall 2002; Hubner and Spector 2010). Movement of the LYS2 chromosomal locus (black) is not quite identical to the constrained random walk modeled using averaged parameters of step size and movement from actual movement analysis (red). (F) Similar MSD analysis was performed on the LYS2 locus after excision as a large chromatin ring of 17 kb, which retains the lacO-binding sites. The excised ring moves with a higher diffusion constant and perfectly recapitulates a simulated random walk (red trace). Images and graphs are modified from Neumann et al. (2012).
Figure 5(A) DNA repair compartments within the yeast nucleus. The nucleoplasm is the site of Rad52-mediated homologous recombination, whereas sequestration at Mps3 or nuclear pores either suppresses recombination between telomeres or allows processing of a DSB for alternative repair pathways. For the rDNA binding to the INM protein, Heh1 (also known as Src1) prevents rDNA recombination. References are noted in A. (B) Model of Mec1/Tel1-dependent relocation of DSBs or collapsed replication forks to Nup84/Slx5/Slx8 complexes associated with nuclear pores. This complex may ubiquitylate a substrate for proteolysis, enabling fork-associated repair (Nagai et al. 2008; Kalocsay et al. 2009; Khadaroo et al. 2009; Oza et al. 2009). (C) Telomeres are anchored through redundant pathways as depicted in Figure 4. At long telomeres, Siz2-mediated SUMOylation (red circles) of Yku70/Yku80 and Sir4 favors telomere anchorage, which in turn may restrict elongation efficiency. When telomeres become critically short, loss of Siz2-mediated anchoring, perhaps through de-sumoylation by Ulp1, releases telomeres from the periphery, allowing efficient elongation (Ferreira et al. 2011). Control of telomerase through Cdc13 (Hang et al. 2011) is not included for simplicity. Symbols: green shapes 2 and 3 indicate Sir2 and Sir3; encircled 3 and gray shape 1 near Est2 indicate Est3 and Est1, respectively.
Figure 1The BER pathway. AP sites (red “O”) are generated either by spontaneous base loss or a DNA N-glycosylase. Apn1 and Apn2 nick the backbone on the 5′ side of an AP site to initiate the major pathway for repair; the resulting 5′-dRP is removed by the Rad27 5′-flap endonuclease. AP-site processing can also be initiated by the Ntg1 or Ntg2 lyase, which nicks on the 3′ side of lesion. The resulting 3′-dRP can be removed by the 3′-diesterase activity of Apn1/Apn2 or as part of a Rad1-Rad10 generated oligonucleotide. Finally, the gap is filled by DNA Pol ε, and the backbone is sealed by DNA ligase 1.
Figure 2The GO network. Reactive oxygen species attack guanine base-paired with cytosine to yield 8-oxoG (GO). Ogg1 excises 8-oxoG from the DNA backbone, and the resulting AP site is repaired via BER (“repair”). If encountered during replication, local sequence context will determine whether Pol δ/ε stalls at or bypasses the GO lesion. If Pol δ/ε stalls at 8-oxoG during replication, Pol η is recruited by ubiquitinated PCNA (Ub-PCNA) and preferentially incorporates C opposite the lesion (“error-free bypass”). During bypass by Pol δ/ε, adenine is frequently inserted instead of cytosine to create a GO:A mispair, which is recognized by the MMR machinery. The newly synthesized, A-containing strand is degraded to generate a single-strand gap containing the lesion, and C is incorporated opposite the lesion during a gap-filling reaction, which may involve Pol η. If not repaired, the GO:A mispair will yield a GC-to-TA transversion at the next round of replication (“mutagenesis”).
Figure 3Bypass of endogenous AP sites. dUTP levels in the nucleotide pool are reduced by Dut1 activity, thereby limiting the incorporation of dUMP into genomic DNA. Most endogenous AP sites (indicated by red “O”) are generated by Ung1 removal of uracil in DNA. The resulting AP site can be repaired by the BER pathway or bypassed by the concerted action of Rev1, which usually inserts cytosine opposite the AP site, and Pol ζ, which extends the O:C terminus.