mix_11yeasts

Files associated with the figure 2

mix_environmental_sample

Files associated with the figure 3

Le «pré-urbain» : un territoire entre urbain et rural théâtre de transferts culturels

Related to Fig. 3. Animated 3D reconstruction of the entire contact map of long-lived SP cells (isolated from a SP culture by density gradient). Same annotations as in Additional file 2. (GIF 12057 kb

Additional file 3: Figure S2. of Spatial reorganization of telomeres in long-lived quiescent cells

SIR-mediated telomere clustering drives chromosome conformation in the dense fraction of SP cells. a Mean contacts frequencies between 100-kb centromeres windows in G1 (blue) and G0 quiescent cells (red). Black and green curves: contacts between 100-kb segments randomly sampled in both conditions, to illustrate the absence of coverage biases after normalization. b Chromosome organization of WT and sir3∆ quiescent cells (the cryptic mating type locus HML was deleted to prevent pseudo-diploid effect). ii) Normalized contact matrix obtained for hml∆* (left) and hml∆ sir3∆ (right) cells. Color scale: contact frequencies from rare (white) to frequent (dark blue). Red arrowheads: centromeres contacts; green and yellow arrowheads: telomere–telomere contacts in hml∆ and hml∆ sir3∆ G0 cells, respectively. The 3D representations of the hml∆ and hml∆ sir3∆ matrices are represented next to the contact maps. Each chromosome is represented as a chain of beads (1 bead = 20 kb), with color code reflecting the chromosome arm lengths, from short (blue) to long (red) arms. Yellow beads: subtelomeric regions; black beads: centromeres; purple beads: boundaries of the rDNA cluster. c Contact maps of W303 strain during exponentially growth (EXPO, left) and quiescence (G0, right). Red arrowheads: centromere clustering; green and yellow arrowheads: telomere–telomere contacts of two chromosomes (XIII and XV) in expo and G0 cells, respectively. Because of the low sequencing coverage and quality, the signal is not as strong as for data in Fig. 3 and the bins are larger (1 vector: 80 DpnII RFs). d Quantification of colocalization of 30-kb telomeric regions (red dots) compared with the distribution of the colocalization scores (box plot, two standard deviations) computed for 1000 random sets of 32 windows of 30 kb in the genome (excluding centromeric regions). The colocalization score is normalized by the sequencing depth for each dataset

Additional file 1: Figure S1. of Spatial reorganization of telomeres in long-lived quiescent cells

Characterization of the SP silent chromatin hypercluster. a Western blot against Rap1 on crude extracts from exponential, respiratory, or stationary cultures of a WT strain (yAT1684). H2A antibody was used for the loading control. b Representative fluorescent images of wild-type (WT) strains tagged with Rap1-GFP “yAT 1684”, GFP-Sir2 “yAT405”, Sir3-GFP “yAT779” and GFP-Sir4 “yAT431” strains. Overnight liquid cultures were diluted to 0.2 OD600nm/ml and images were acquired after 5 h (1 OD600nm/ml, fermentation phase) and 7 days (40 OD600nm/ml, stationary phase). c Representative fluorescent image of a Rap1-GFP Sir3-mCherry-tagged strain “yAT194” from stationary phase cultures. We note that Sir3 associates with both telomeres and the rDNA in stationary phase cells. d Representative fluorescent images of Rap1-GFP in stationary cultures of WT “yAT1684” and sir4∆ “yAT2092” strains. e Representative fluorescent images of the nucleolar protein Sik1 tagged with mCherry during fermentation, respiration, and stationary phase (“yAT340”). f Representative fluorescent image of Rap1-GFP Dad2-mRFP (Duo1 And Dam1 interacting, an essential component of the microtubule–kinetochore interface) tagged stationary phase cells (“yAT2279”). g Representative fluorescent image of Sir3-mCherry Cse4-GFP-tagged strain “yAT2280” from stationary phase. Scale bar is 1 μm. (PDF 1343 kb

Additional file 5: Figure S3. of Spatial reorganization of telomeres in long-lived quiescent cells

Telomere hyperclustering is not due to slow growth. a Representative fluorescent image of Rap1-GFP tagged strain grown either at 30 °C or 25 °C in exponential phase (top) and then starved for 16 h in water before imaging (bottom). b Calcofluor staining of LD and HD fractions of a post DS culture after gradient separation. c Heat shock (HS) assay on the LD and HD fractions used in b. (PDF 11591 kb

Guidi et al. 2015

<p>Raw images corresponding to Guidi et al. 2015.</p> <p>For each figure of the manuscript Guidi et al. containing microscopy data we show Z projection (max intensity) of cropped images normalized to be comparable within each experiment. Here we provide for each crop the corresponding Z stack and the Z projection of the whole field image.</p

If That.

Plasmid replication efficacy of DNA regions surrounding identified replication origins. (DOC 40 kb

Additional file 5: of Genome-wide replication landscape of Candida glabrata

rDNA locus replication. Top: One tandem repeat unit of the S. cerevisiae rDNA locus on chromosome 12 is represented. Coordinates are shown in boxes, according to the Saccharomyces Genome Database (release 19 November 2012). The ARS present in each repeat unit is indicated as a blue diamond. Bottom: Same representation for the C. glabrata rDNA locus. Coordinates are shown according to GĂŠnolevures database (release 10 September 2008). The two ARSs captured are shown by blue diamonds. (PDF 65 kb

Additional file 4: of Genome-wide replication landscape of Candida glabrata

Additional experiment performed to confirm replication origins. The time course shown in this experiment was performed as described in “Methods” for the first experiment (Additional file 1). Top: FACS analyses and DNA content are shown. Time points T0 to T6 were sequenced on a MiSeq (Illumina) sequencer and 2.3–4.1 millions reads were obtained (175 bp single reads) for each time point. Bottom: Sequence coverage for time points T2, T3, T4, and T6, for each chromosome (smoothing span: 0.05–0.09, depending on chromosome size). Sequence mapping of two time points (T1 and T5) exhibited too many gaps to allow us to calculate non-linear regressions for each of the 12 millions nucleotides of the C. glabrata genome, in order to determine T50 values. However, using T6 and T0 coverage, which correspond respectively to S and G1 phases of the cell cycle, we were able to determine replication peak positions. A comparison of peaks detected in experiment #1 (Fig. 2) and experiment #2 (the present figure) was made in the bottom right table. Out of 83 bona fide origins, 73 were found in experiment #2 (88 %), and 241 replication origins were detected (instead of 253 in experiment #1). The average distance between bona fide replication peaks found in both experiments was 6.9 ± 2.4 kb (95 % confidence interval), consistent with what was deduced from comparisons between ARS positions and replication peaks (Fig. 5a). (PDF 1224 kb