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. 2011 Feb 18;41(4):480-92.
doi: 10.1016/j.molcel.2011.01.015.

A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces

Bryan J Venters  1 , Shinichiro Wachi, Travis N Mavrich, Barbara E Andersen, Peony Jena, Andrew J Sinnamon, Priyanka Jain, Noah S Rolleri, Cizhong Jiang, Christine Hemeryck-Walsh, B Franklin Pugh
Affiliations

A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces

Bryan J Venters et al. Mol Cell. .

Abstract

Hundreds of different proteins regulate and implement transcription in Saccharomyces. Yet their interrelationships have not been investigated on a comprehensive scale. Here we determined the genome-wide binding locations of 200 transcription-related proteins, under normal and acute heat-shock conditions. This study distinguishes binding between distal versus proximal promoter regions as well as the 3' ends of genes for nearly all mRNA and tRNA genes. This study reveals (1) a greater diversity and specialization of regulation associated with the SAGA transcription pathway compared to the TFIID pathway, (2) new regulators enriched at tRNA genes, (3) a global co-occupancy network of >20,000 unique regulator combinations that show a high degree of regulatory interconnections among lowly expressed genes, (4) regulators of the SAGA pathway located largely distal to the core promoter and regulators of the TFIID pathway located proximally, and (5) distinct mobilization of SAGA- versus TFIID-linked regulators during acute heat shock.

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Figures

Figure 1
Figure 1. Scope and data display of genome-wide location analysis
(A) Illustration of the chromatin context of a stereotype promoter. The pie chart depicts the number of regulators analyzed from each stage, out of the total number of potential regulators in those stages (demarcated by dashed lines). Those not covered largely resided within complexes that contain regulators that were covered. (B) Approximate positions of microarray 60mer probes relative to a gene (arrow). Negative control probes were present at ~300 intergenic regions between two convergently transcribed genes. (C) Browser display of the occupancy and change in occupancy upon heat shock at the indicated probe locations (pointed bullets), for a selected number of regulators. The upper and lower probe tracks for each regulator reflect occupancy levels at 25°C (grayscale) and changes in occupancy during heat shock (red/green scale), respectively. Any region for the ~200 regulators can be queried at http://atlas.bx.psu.edu.
Figure 2
Figure 2. Promoter occupancy at 25°C for individual genes and groups of genes
(A) Number of promoters or 3' ORFs significantly occupied (5% FDR) by the number of regulators indicated along the x-axis. (B) Regulators significantly bound at the indicated genes are shown as a heatmap. Columns represent regulators. The color scale indicates the occupancy percent rank for those meeting a 5% FDR cutoff. Regulators are grouped by stage. Only those regulators having potentially meaningful occupancy are shown. (C) Regulator promoter occupancy for genes in the top 10th percentile of transcription frequency (Holstege et al., 1998) are shown, and filtered to be in one of the three following classes: 1) RP genes; 2) TFIID-dominated and TATA-less but not RP genes; 3) SAGA-dominated and TATA-containing (Basehoar et al., 2004; Huisinga and Pugh, 2004). Potentially meaningful occupancy levels are displayed by transcription stage, with the fraction of each gene group occupied also shown. The median values for each class of genes are shown to the right of each row.
Figure 3
Figure 3. Regulators that occupy tRNA genes
(A) The median 25°C occupancy for 202 regulators was computed for 274 tRNA genes and displayed as a bar graph. The vast majority of tRNA promoters are >200 bp from a Pol II promoter, and thus would not erroneously pick up signal from nearby genes. Such adjacent genes are also not enriched with these regulators (not shown). (B, C) Bar graph showing the occupancy level of the Pol III transcription machinery and other high occupancy regulators at tRNA genes. (D) Frequency distribution plot for the motifs of the three sequence-specific regulator occupying tRNA genes. (E) Hda1 frequency distribution plot for its interpolated binding location is shown along with nucleosome density (Mavrich et al., 2008) shown in gray fill. (F) Illustration depicting a composite organization of regulators at tRNA genes. Only the TFIIIB, TFIIIC, and Pol III are like to be present at all genes, with the remaining at a statistically-enriched subset.
Figure 4
Figure 4. Regulator co-occupancy matrices
Shown are promoter co-occupancies and other related properties between 20,301 unique combinations of 202 regulator pairs. (A) Percent overlap for the set of genes co-occupied by each regulator pair is displayed as a heatmap. Each pixel represents the overlap in a Venn diagram between two regulators, heatmap color-coded in accord with the extent of overlap, as indicated. Overlaps that did not meet a significance threshold of P <10-5, or represented a self-by-self comparison were drawn as white pixels. Rows and columns were hierarchically clustered using Cluster (Eisen et al., 1998). See Figure S1 for high resolution images. A blow-up of a portion of cluster a (8 × 8 matrix) is shown in upper portion of the panel. (B) Statistical significance (P-value determined by the Chi-test) of overlap for the set of genes co-occupied by each regulator pair is displayed as a heatmap. For panels B-D, pixels are in the same position as in A, and were colored white if they were white in panel A. (C) The corresponding median transcription frequency for the set of genes co-occupied by each regulator pair is displayed as a heat map. Data for mRNA/hr is from (Holstege et al., 1998). (D) If two compared regulators belonged to the same stage of the transcription cycle (Figure 1A), then the corresponding pixel was color-coded by the stage, as indicated. Otherwise they were colored white.
Figure 5
Figure 5. Composite distribution of regulators across promoter regions
(A) Complexes particularly enriched in the distal (<-120bp) versus proximal (>-120bp) promoter region based on panel B are listed. The consensus locations for the TATA box, the “-1” and “+1” nucleosomes are shown (Basehoar et al., 2004; Mavrich et al., 2008). The frequency distribution mode around the TSS for individual subunits shown in panel B defined the consensus binding location for each complex. If two or more subunits were available for a complex, then the modes for all subunits were averaged. (B) In the heat map, the ChIP-chip binding locations for each regulator (one regulator per line) were interpolated between the UAS and TSS probe at each gene, binned, and aligned by the TSS. Heatmap color was used to indicate bin counts. Data were filtered to have at least twofold occupancy levels. The upper-most track indicates the distribution of microarray probes. (C) For elongation regulators, ChIP-seq data were used to generate a heatmap display for the composite frequency distributions relative to the TSS. The ChIP-seq data for each regulator were binned in 25 bp intervals and normalized to an untagged control. Log2 values were centered so that the lowest quartile value was the same in all datasets. Genes with >2-fold normalized occupancy were plotted. See also Figures S5-6.
Figure 6
Figure 6. Assembly and disassembly of the transcription machinery in response to heat shock
Log2 ratios of 37°C/25°C occupancy changes for promoter regions that increased (red), decreased (green), did not change (black), or did not have data (black), the latter comprising <10% of the data. Rows representing promoter regions (A) were clustered alongside 3' ORF regions (B) by K-means (K = 8), and are ordered identically in the two panels. The data were filtered to include promoters having >75% data present and >3-fold change in occupancy in at least 7 datasets, which resulted in 934 genes. Columns represent ChIP-chip data for a given regulator, and were clustered hierarchically by stage. For clarity, only a subset of the 200 regulators are shown; the cluster of all regulators is shown in Figure S7. The changes in gene expression during heat shock are aligned to the right (Zanton and Pugh, 2004). The average transcription rate at 25°C (Holstege et al., 1998) for each cluster are indicated on the right of the panel.
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