D error of the mean (SEM) from multiple independent experiments. For western blot and ChIP

D error of the mean (SEM) from multiple independent experiments. For western blot and ChIP assays, either monoclonal anti-myc (9B11, Cell Signaling) or monoclonal anti-FLAG (M2-F1804, Sigma) antibodies were utilised. Anti-Cdc2 antibody (y100.four, Abcam) was used in western blot analysis as a loading control. Ccq1 Thr93 phosphorylation was monitored working with phospho-(Ser/Thr) ATM/ ATR substrate antibody (2851, Cell Signaling) as previously described [10]. Although not especially raised against a Ccq1 Thr93 phosphopeptide, our previous evaluation indicated that the phospho(Ser/Thr) ATM/ATR substrate antibody can especially detect a Ccq1 Thr93 phosphopeptide, and detect a band corresponding to immunoprecipitated Ccq1 which is eliminated in ccq1-T93A mutant in western blot analysis [10]. Therefore, while we can not absolutely remove the possibility that this antibody recognizes phosphorylation on other web page(s) that may possibly be affected by ccq1-T93A mutation, for sake of simplicity, we denote the signal detected by this antibody as Ccq1 Thr93 phosphorylation within the text.blot-based asynchronous ChIP assays with telomeric DNA probe. (A) Telomere correction elements for Trt1-myc strains have been established by determining telomere/rDNA hybridization signal ratios relative to wt cells. Telomere correction components for other epitope tagged strains are shown in Supplementary Table S1. (B) Raw precipitated DNA values for dot blot-based Trt1-myc ChIP assays for the indicated genotypes. (C) Telomere length corrected ChIP information for Trt1-myc. (See Components and Procedures section for details.) Error bars correspond to SEM. (JPG)Figure S3 Raw information of dot blot-based cell cycle ChIP assays for Trt1TERT. (A, B) Cell cycle ChIP assays were performed with cdc25-22 synchronized cell cultures for wt, poz1D, rap1D or taz1D cells, and precipitated DNA was determined by hybridization of a telomeric probe to dot blotted input and ChIP samples. (C) septated cells were measured to monitor cell cycle progression of cdc25-22 synchronized cell cultures for the indicated genotypes. Error bars correspond to SEM. (JPG) Figure S4 DNA replication timing monitored by incorporation of BrdU in cdc25-22 synchronized cells for (A) ars2004 and (B) telomeres [25]. BrdU incorporation at telomeres is inhibited by addition of 15 mM HU for wt, poz1D and rap1D cells but not for taz1D cells. BrdU is incorporated into ars2004 with related kinetics 8-Hydroxy-DPAT Protocol inside the presence or absence of HU for all genetic backgrounds tested. (C) Pol1 (a) showed similar timing of recruitment to ars2004 in all genetic backgrounds tested. Error bars correspond to SEM. (JPG) Figure S5 Cell cycle ChIP assays for DNA polymerases. (A, B) Peak normalized cell cycle ChIP information for Pol1 (a) (A) and Pol2 (e) (B). For Pol2 (e), Student’s t-test identified a statistically significant difference in telomere binding at 80 min (p = 0.03) for wt vs. taz1DEstablishment of telomere length correction factorsCorrection things for telomere length have been established by measuring the hybridization signal intensity of telomere versus rDNA repeats (telomere/rDNA) for poz1D, rap1D and taz1D cells in comparison with wt cells (Figure S2A and Table S1), making use of NaOH denatured genomic DNA samples spotted on Nylon membrane by dot blot apparatus. “Telomere length corrected” ChIP values have been then calculated by multiplying the background subtracted precipitated DNA values (raw precipitated DNA no tag control precipitated DNA) with all the correction components, and normalizing the.