Figures from the Paper

Microarrays: A Global Network Model of the Arsenic Response

Figure 1. Arsenic-induced signaling and regulatory mechanisms involve transcriptional activators and the proteasome. [A]-[D]

Figure 1. Arsenic-induced signaling and regulatory mechanisms involve transcriptional activators and the proteasome. [A]-[D]

Significant network neighborhoods (p<0.005) uncovered by the ActiveModules algorithm, with the search performed at depth 1 (all nodes in the network are the nearest neighbors of one central node): FHL1 center [A]; PRE1 center and proteasome complex [B]; YAP1 and CAD1 (YAP2) centers [C]; HSF1 center [D]. Panel [F] provides an overview of the network relationships between major arsenic-responsive transcription factors. [E] An additional network centered on MET31 with functional relevance to the arsenic response, which, however, did not reach significance in this analysis, p<0.11. Induced = red; repressed = green; significant expression = blue boxed outline; protein-DNA interaction = yellow arrows; protein-protein interactions = blue lines. The 2h, 100uM AsIII condition was used for the visual mappings. Many of the genes mapped to the network neighborhoods and displayed in this figure are boxed for the sake of clarity and space, but are mostly significantly differentially expressed.

Download the PDF for Figure 1 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/model/docs/fig1b.pdf)   (329KB)

Figure 2. Yap1, but not Cad1, is important for mediating the cell’s adaptation to arsenic.

Figure 2. Yap1, but not Cad1, is important for mediating the cell’s adaptation to arsenic.

Induced = red, repressed = green. A) Self-organized heat map (dendrograms were removed and boxes 1-3 indicate specific clusters) of 6172 genes selected from the various indicated conditions: AsIII-treated Parent wildtype strain with normalized data values that are greater or less than those in condition(s)—knocked out Yap1, Cad1 (Yap2), Rpn4, Arr1 (Yap8) treated with AsIII--by a factor of 2 fold. All knockouts tested revealed altered profiles compared to the wildtype, except for cad1 Δ. B) Yap1 Δ (condition 2) loses induced expression of stress response genes found in Box1, such as SIR4, ISU2, MSN1, ATR1, CYT2, MDH1, AAD6, AAD4, TRR1, FLR1, GLR1, and GRE2. C). Rpn4 Δ (condition 4) loses induced expression of ubiquitinating and proteasomal genes found in Box3, UBP6, PRE8, PRE4, PRE7, PRE1. D) Arr1 Δ (condition 5) loses repressed expression of sulfur amino acid metabolism gene SAM3 and glutamate biosynthesis gene CIT2, among others (Box 2). Arr1 D also loses induced expression of serine biosynthesis gene, SER3, sulfur amino acid metabolism gene, SAM4, cell cycle regulator, ZPR1, spindle checkpoint subunit, MAD2, ribonucleotide reductase RNR1, and RNA Pol1 transcription factor RRN9, to name a few (Box 3). For a comprehensive list of genes affected in all knockout experiments, go to Supplemental Figures and Tables.

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Figure 3. The ubiquitin and proteasome system responds to arsenic-mediated toxicity.

Figure 3. The ubiquitin and proteasome system responds to arsenic-mediated toxicity.

S. cerevisiae ubiquitin and proteasome pathways show differential expression in a number of key genes, including the proteasomal activator, RPN4. Induction is denoted by red-colored boxes with fold-change ranges representing the 2h, 100uM AsIII and 0.5h, 1mM AsIII experiments, respectively.

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Figure 4. Gene expression profiling links sulfur assimilation, methionine, and glutathione pathways.

Figure 4. Gene expression profiling links sulfur assimilation, methionine, and glutathione pathways.

Selected genes in these pathways are represented as red for induced (2h, 100uM AsIII and 0.5h, 1mM AsIII, respectively) and green for repressed. Genes in white boxes are not differentially expressed. The pathways in the blue ovals are upstream of methionine, cysteine, and glutathione and sensitive to arsenic. The downstream pathways employ numerous redundant enzymes which are differentially expressed, but not sensitive. LT = late time-point, 4h, 100uM AsIII experiment; h = human; y = yeast.

Download the PDF for Figure 4 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/model/docs/fig3b.pdf)   (152KB)

Figures 5a and 5b. LinearActivePaths analysis finds that virtually all genes in active metabolic networks confer sensitivity to arsenic when deleted.

Figures 5a and 5b. LinearActivePaths analysis finds that virtually all genes in active metabolic networks confer sensitivity to arsenic when deleted.

A) Serine, threonine, glutamate amino acid synthetic pathways; B) Shikimate pathway. The paths that compose these networks all have individual p-values of < 0.05. The coloration for these figures is based on red for any gene ranked in the top 50 significant genes, yellow for 51-100, and green for > 101.

Download the PDF for Figure 5a (http://www.niehs.nih.gov/research/atniehs/core/microarrays/model/docs/fig5a.pdf)   (71KB) or Figure 5b (http://www.niehs.nih.gov/research/atniehs/core/microarrays/model/docs/fig5b.pdf)   (63KB)

Figure 6. Global model of the arsenic response: combining phenotypic data with gene expression profiles reveals synergistic pathways leading to yeast detoxification mechanisms.

Figure 6. Global model of the arsenic response: combining phenotypic data with gene expression profiles reveals synergistic pathways leading to yeast detoxification mechanisms.

Serine, Threonine, Aspartate, and Arginine, as well as, Shikimate metabolisms, in light blue, represent pathways that are sensitive by phenotypic profiling. Yap1, colored light blue and red, is an example of a transcription factor that is both sensitive and confers induced gene expression. Deletion analysis confirms its role in arsenic-mediated control of the stress response. Red and green represent pathways or genes that are differentially expressed but not sensitive by phenotypic profiling. This schematic diagram demonstrates how the deletion of an individual gene leads to a change in sensitivity if the protein product of that gene is important in a biological process for adaptation to arsenic. On the other hand, expression profiling shows the end product of the cell’s response to arsenic. Many of these downstream targets share redundant functions and are not vulnerable in the phenotypic profiling. The expression changes lead to the cell’s response to indirect oxidative stress and mechanisms for detoxification. The arrows A, B, C, and D represent the multiple branch points between redundant pathways. Note that the transport protein, Arr3, which extrudes AsIII out of the cell, is both sensitive and highly differentially expressed.

Download the PDF for Figure 6 (http://www.niehs.nih.gov/research/atniehs/core/microarrays/model/docs/fig5a.pdf)   (22KB)

Download Pathways Enriched for Genes Significantly Expressed in Response to Arsenic (http://www.niehs.nih.gov/research/atniehs/core/microarrays/model/docs/table1.pdf)   (36KB)

Download Sulfur Metabolism Affiliated Genes (http://www.niehs.nih.gov/research/atniehs/core/microarrays/model/docs/table2.pdf)   (33KB)

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