Examples for validation by individual bisulfite sequencing.

<p>The plots show the correlation between calculated and validated methylation levels (C/(C+T)) from regions selected for congruency (A) or disagreement (B–D) between BiSS and A3M. Each point represents one cytosine position. The x-axis corresponds to the methylation levels calculated from either BiSS (filled circles and black regression lines) or A3M (open circles and dotted regression lines); the y-axis shows the result of individual bisulfite sequencing. The legends show the Pearson correlation coefficients. (A) Methylated region according to both methods (M/M). (B) A region called methylated by BiSS but not by A3M (M/U); the rectangles indicate experimentally validated Cs congruent to BiSS (filled) and discrepant to A3M (open). (C) A region called methylated by BiSS but not by A3M due to insufficient sequencing coverage (M/X). (D) A region called methylated by A3M but not by BiSS (U/M), the rectangle symbols are the same as in (B).</p

Comparison of mapping results for BiSS and selected other aligning programs¹.

<p>Default parameters unless otherwise specified.</p>1<p>A3M – results reported by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041528#pone.0041528-Lister1" target="_blank">[4]</a>.</p>2<p>BSMAPv1 parameters: -p 8 -s 12 -r 2 -w 100 -n 1 -v 5 -g 5, recommended by the authors, maximal 5 mismatches.</p>3<p>RMAP parameters: -m 5 –v, default parameters.</p

Congruency between methylation calling by A3M and BiSS.

<p>M: methylated, U: unmethylated, X: not determined due to lack of sufficient sequencing coverage. Percentages refer to the total number of genomic cytosines.</p

Global methylation level.

<p>Ratio of the number of mapped Cs divided by the number of mapped C plus T for all classified Cs. Black: Cs that are called methylated, White: C that are not called methylated.</p

Distribution of cytosine sequence context.

<p>(A) Frequency of sequence context in the reference genome. (B) Frequency of sequence context of methylated C according to BiSS and A3M.</p

Example for an asymmetric look-up table for 8 k-mers.

<p>The 8-mer ACGTCGCT (corresponds to key 7015) generates 7 other keys. The 8-mer ATGTCGTT (key 15215) from the BS-read can be looked up to find its referenced key as ACGTCGCT (key 7015), ACGTCGTT (key 7023), ATGTCGCT (key 15207) and ATGTCGTT (key 15215) but no others.</p

Cells lacking Hat1 show reduced virulence but persist in mouse kidneys.

<p>(A) Reduced growth rate of the <i>hat1</i>Δ/Δ strain was determined by measuring the OD₆₀₀ of cells growing in YPD at 30°C. (B) Cells lacking Hat1 are not cleared efficiently from kidneys. At the indicated time points, fungal burdens in kidneys of mice infected with <i>C</i>. <i>albicans</i> strains were determined and expressed as CFUs per gram kidney. Groups of 5–10 mice were analyzed at each time point and statistical significance was determined using the non-parametric Mann-Whitney-test. n.s.: not significant, *P<0.05 and **P<0.01 relative to the corresponding wild-type. (C) <i>hat1</i>Δ/Δ cells are defective in killing the host. Survival of mice infected with the indicated strains was monitored over 32 days post infection (p.i.). The data are presented as Kaplan-Meier survival curves. Groups of 6 mice were infected per <i>C</i>. <i>albicans</i> strain. Statistical significance was determined using the Log-rank test. ns: not significant; (D) Fungal burdens in kidneys of surviving mice from panel C were determined and expressed as CFUs per gram organ. One mouse infected with the <i>hat1</i>Δ/Δ strain was able to clear <i>Candida</i>. (E) The <i>cac2</i>Δ/Δ strain is not cleared efficiently from kidneys. Experiment was performed as described in (B). Groups of 4–5 mice were analyzed at each time point. (F) Infection with <i>hat1</i>Δ/Δ cells causes reduced kidney damage. Urea levels were determined in sera of infected mice at day 3 and 7 post infection. n.s.: not significant, *P<0.05, **P<0.01 relative to the wild-type (Student's t-test).</p

Deletion of <i>HAT1</i> primarily leads to upregulation of genes.

<p>(A) Lack of Hat1 causes mainly induction of genes in logarithmically growing cells. Each dot corresponds to one protein-coding gene. The fold change in RNA expression between untreated wild-type and <i>hat1</i>Δ/Δ cells (y-axis) is plotted against the expression level of each gene in this dataset (x-axis). Differentially expressed genes in the <i>hat1</i>Δ/Δ mutant are depicted in red. logCPM: log2 counts per million reads; logFC: log2 fold change; (B+C) Loss of Cac2 or Rtt109 causes almost exclusively upregulation of genes in logarithmically growing cells. Plots were created as described in (A). (D) Venn diagram showing the overlaps of upregulated genes in the <i>hat1</i>Δ/Δ, <i>cac2</i>Δ/Δ and <i>rtt109</i>Δ/Δ mutants in the absence of H₂O₂. (E) Venn diagram showing the overlaps of upregulated genes in the <i>hat1</i>Δ/Δ, <i>cac2</i>Δ/Δ and <i>rtt109</i>Δ/Δ mutants upon treatment with H₂O₂. (F) H₂O₂ repressed genes are upregulated in the <i>hat1</i>Δ/Δ mutant upon peroxide treatment. Each dot corresponds to one protein-coding gene. The -fold change in RNA expression between H₂O₂ treated wild-type and <i>hat1</i>Δ/Δ strains (y-axis) is plotted against the fold change between the wild-type without and with treatment (x-axis). Differentially expressed genes in the <i>hat1</i>Δ/Δ mutant are depicted in red. logFC: log2 fold change; (A-F) Differentially regulated genes were defined by a fold change > = 2 and p-value <0.05.</p

Lack of histone chaperones mimics deletion of <i>HAT1</i>.

<p>(A) Loss of Cac2 increases H₂O₂ resistance. Deletion of <i>RTT106</i> or <i>HIR1</i> does not affect susceptibility to hydrogen peroxide. Fivefold serial dilutions of the indicated strains were spotted on agar plates containing the indicated substances and pictures were taken after incubation at 30°C for 3 days. (B) Deletion of <i>HAT1</i> or <i>CAC2</i> increases survival to transient hydrogen peroxide treatment. Exponentially growing cells were treated with the indicated concentrations of H₂O₂ for 2 hours. Cells were plated and colonies counted after 3 days of incubation on YPD plates at 30°C to determine viability. Data are shown as mean + SD from three independent experiments. (C) Deletion of <i>HIR1</i> reduces voriconazole (Voric.) susceptibility. The <i>hat1hir1</i>Δ/Δ double deletion strain mimics lack of Hat1. Loss of Cac2 has only a minor effect and deletion of <i>RTT106</i> does not alter azole susceptibility. Experiment was performed as described in (A). (D) Increased azole tolerance of <i>hat1</i>Δ/Δ, <i>hir1</i>Δ/Δ and <i>hat1hir1</i>Δ/Δ was confirmed using a liquid growth inhibition assay. Logarithmically growing cells were diluted into medium containing the indicated concentrations of voriconazole (Voric.) and incubated at 30°C for 18 hours. OD₆₀₀ was determined and growth inhibition relative to untreated samples was calculated. Data are shown as mean + SD from three independent experiments. (E) Lack of Spt6 reduces H₂O₂ susceptibility. Experiment was performed as described in (B). Cells were treated with 10 mM H₂O₂. Data are shown as mean + SD from two independent experiments. (F) Deletion of <i>SPT6</i> increases H₂O₂ resistance and azole tolerance. Fivefold serial dilutions of the indicated strains were spotted on agar plates containing the indicated substances and pictures were taken after incubation at 30°C for 5 days. (G) Reduction of histone gene dosage decreases H₂O₂ and azole susceptibility. Experiment was performed as described in (A). (B, D, E) *P<0.05, **P<0.01 and ***P<0.001 relative to the corresponding wild-type (Student's t-test).</p

Specific functional gene groups are upregulated in cells lacking Hat1.

<p>(A) GO terms enriched among 2-fold significantly upregulated genes in logarithmically growing <i>hat1</i>Δ/Δ cells are shown. (B) The plot shows GO terms found within genes significantly upregulated in the <i>hat1</i>Δ/Δ and <i>rtt109</i>Δ/Δ strains only. (C) GO terms enriched within genes significantly upregulated in the <i>hat1</i>Δ/Δ and <i>cac2</i>Δ/Δ strains only. (D) The panel shows GO terms found among genes significantly upregulated in the <i>hat1</i>Δ/Δ mutant only and not in the <i>rtt109</i>Δ/Δ and the <i>cac2</i>Δ/Δ strains. (E) GO terms enriched among significantly upregulated genes in <i>hat1</i>Δ/Δ cells after treatment with H₂O₂ are shown. (F) The plot shows GO terms found within genes significantly upregulated in the <i>hat1</i>Δ/Δ strain only and not in the <i>rtt109</i>Δ/Δ and the <i>cac2</i>Δ/Δ strains upon H₂O₂ treatment. (A-F) The corresponding p-values for the enrichment (empty bars) and the percentage of genes changed within the GO group (filled bars) are presented. The absolute number of regulated genes within a GO group is presented in brackets. Groups containing identical genes are depicted in the same color. Significantly regulated genes were defined by a p-value <0.05.</p