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Identifying synergistic regulation involving c-Myc and sp1 in human tissues.

Parisi F, Wirapati P, Naef F - Nucleic Acids Res. (2007)

Bottom Line: Dual sites show several distinct features compared to the single regulator sites: specifically, they exhibit overall higher degree of conservation between human and rodents, stronger correlation with TFIID-bound promoters, and preference for permissive chromatin state.Namely, the correlation with c-Myc expression in promoters harboring dual-sites is increased for stronger sp1 sites by strong sp1 binding and the effect is largest in proliferating tissues.Our approach shows how integrated functional analyses can uncover tissue-specific and combinatorial regulatory dependencies in mammals.

View Article: PubMed Central - PubMed

Affiliation: Swiss Institute for Experimental Cancer Research (ISREC) and NCCR Molecular Oncology, Lausanne, Switzerland.

ABSTRACT
Combinatorial gene regulation largely contributes to phenotypic versatility in higher eukaryotes. Genome-wide chromatin immuno-precipitation (ChIP) combined with expression profiling can dissect regulatory circuits around transcriptional regulators. Here, we integrate tiling array measurements of DNA-binding sites for c-Myc, sp1, TFIID and modified histones with a tissue expression atlas to establish the functional correspondence between physical binding, promoter activity and transcriptional regulation. For this we develop SLM, a methodology to map c-Myc and sp1-binding sites and then classify sites as sp1-only, c-Myc-only or dual. Dual sites show several distinct features compared to the single regulator sites: specifically, they exhibit overall higher degree of conservation between human and rodents, stronger correlation with TFIID-bound promoters, and preference for permissive chromatin state. By applying regression models to an expression atlas we identified a functionally distinct signature for strong dual c-Myc/sp1 sites. Namely, the correlation with c-Myc expression in promoters harboring dual-sites is increased for stronger sp1 sites by strong sp1 binding and the effect is largest in proliferating tissues. Our approach shows how integrated functional analyses can uncover tissue-specific and combinatorial regulatory dependencies in mammals.

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Localization of binding sites with respect to annotated genes. Annotation is from UCSC build hg17 (on chromosome 21 and 22 these sum to 1255 TSSs, including alternative TSSs for some genes). (A) More than 70% of the 633 (360 for c-Myc, 221 for sp1) fall close to genes (black), defined here as spanning from −1.5 kb upstream of the TSS to 1 kb downstream of the PAS (this represents ∼30% of total genomic sequence). Very few sites are found in distal promoters (−10 kb to −1.5 kb, gray). The remaining 20–25% of sites (white) are thus far from genes. (B) Refined mapping for the sites near genes (black fraction in Figure 2A) shows a strong preference for the 5′ regions. Sites are classified as either 5′ regions (from −1.5 kb to +0.5 kb of the TSS; green), exons (light green), intron (pink) or 3′UTR (−1 kb to +1 kb of PAS; red). Color scheme for panels A and B is explained below the panels. (C) Distribution of distances from TSSs for sites mapped in the 5′ regions. We find a tight co-localization with the TSS (defined as 0) for both factors, coordinates are taken positive in the transcript direction.
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Figure 1: Localization of binding sites with respect to annotated genes. Annotation is from UCSC build hg17 (on chromosome 21 and 22 these sum to 1255 TSSs, including alternative TSSs for some genes). (A) More than 70% of the 633 (360 for c-Myc, 221 for sp1) fall close to genes (black), defined here as spanning from −1.5 kb upstream of the TSS to 1 kb downstream of the PAS (this represents ∼30% of total genomic sequence). Very few sites are found in distal promoters (−10 kb to −1.5 kb, gray). The remaining 20–25% of sites (white) are thus far from genes. (B) Refined mapping for the sites near genes (black fraction in Figure 2A) shows a strong preference for the 5′ regions. Sites are classified as either 5′ regions (from −1.5 kb to +0.5 kb of the TSS; green), exons (light green), intron (pink) or 3′UTR (−1 kb to +1 kb of PAS; red). Color scheme for panels A and B is explained below the panels. (C) Distribution of distances from TSSs for sites mapped in the 5′ regions. We find a tight co-localization with the TSS (defined as 0) for both factors, coordinates are taken positive in the transcript direction.

Mentions: Genomic sequence, annotations, chromosomal coordinates of TSSs, genes structure and alignments between human, mouse and rat are publicly available from the UCSC Genome Table browser (41). Based on these coordinates, we define ‘genes’ as the genomic regions from −1.5 kb upstream of the transcription start site (TSS) to +1 kb downstream of the polyadenylation site (PAS), accounting for roughly 30% of the chromosomes length. Additionally we define distal promoters stretching from −10 kb and −1.5 kb of the TSS (Figure 1A). The intragenic mapping follows the annotation, except for the 5′ regions defined as −1.5 kb to +0.5 kb of TSS, and 3′UTR, −1 kb to +1 kb of polyadenylation site (PAS).Figure 1.


Identifying synergistic regulation involving c-Myc and sp1 in human tissues.

Parisi F, Wirapati P, Naef F - Nucleic Acids Res. (2007)

Localization of binding sites with respect to annotated genes. Annotation is from UCSC build hg17 (on chromosome 21 and 22 these sum to 1255 TSSs, including alternative TSSs for some genes). (A) More than 70% of the 633 (360 for c-Myc, 221 for sp1) fall close to genes (black), defined here as spanning from −1.5 kb upstream of the TSS to 1 kb downstream of the PAS (this represents ∼30% of total genomic sequence). Very few sites are found in distal promoters (−10 kb to −1.5 kb, gray). The remaining 20–25% of sites (white) are thus far from genes. (B) Refined mapping for the sites near genes (black fraction in Figure 2A) shows a strong preference for the 5′ regions. Sites are classified as either 5′ regions (from −1.5 kb to +0.5 kb of the TSS; green), exons (light green), intron (pink) or 3′UTR (−1 kb to +1 kb of PAS; red). Color scheme for panels A and B is explained below the panels. (C) Distribution of distances from TSSs for sites mapped in the 5′ regions. We find a tight co-localization with the TSS (defined as 0) for both factors, coordinates are taken positive in the transcript direction.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1851645&req=5

Figure 1: Localization of binding sites with respect to annotated genes. Annotation is from UCSC build hg17 (on chromosome 21 and 22 these sum to 1255 TSSs, including alternative TSSs for some genes). (A) More than 70% of the 633 (360 for c-Myc, 221 for sp1) fall close to genes (black), defined here as spanning from −1.5 kb upstream of the TSS to 1 kb downstream of the PAS (this represents ∼30% of total genomic sequence). Very few sites are found in distal promoters (−10 kb to −1.5 kb, gray). The remaining 20–25% of sites (white) are thus far from genes. (B) Refined mapping for the sites near genes (black fraction in Figure 2A) shows a strong preference for the 5′ regions. Sites are classified as either 5′ regions (from −1.5 kb to +0.5 kb of the TSS; green), exons (light green), intron (pink) or 3′UTR (−1 kb to +1 kb of PAS; red). Color scheme for panels A and B is explained below the panels. (C) Distribution of distances from TSSs for sites mapped in the 5′ regions. We find a tight co-localization with the TSS (defined as 0) for both factors, coordinates are taken positive in the transcript direction.
Mentions: Genomic sequence, annotations, chromosomal coordinates of TSSs, genes structure and alignments between human, mouse and rat are publicly available from the UCSC Genome Table browser (41). Based on these coordinates, we define ‘genes’ as the genomic regions from −1.5 kb upstream of the transcription start site (TSS) to +1 kb downstream of the polyadenylation site (PAS), accounting for roughly 30% of the chromosomes length. Additionally we define distal promoters stretching from −10 kb and −1.5 kb of the TSS (Figure 1A). The intragenic mapping follows the annotation, except for the 5′ regions defined as −1.5 kb to +0.5 kb of TSS, and 3′UTR, −1 kb to +1 kb of polyadenylation site (PAS).Figure 1.

Bottom Line: Dual sites show several distinct features compared to the single regulator sites: specifically, they exhibit overall higher degree of conservation between human and rodents, stronger correlation with TFIID-bound promoters, and preference for permissive chromatin state.Namely, the correlation with c-Myc expression in promoters harboring dual-sites is increased for stronger sp1 sites by strong sp1 binding and the effect is largest in proliferating tissues.Our approach shows how integrated functional analyses can uncover tissue-specific and combinatorial regulatory dependencies in mammals.

View Article: PubMed Central - PubMed

Affiliation: Swiss Institute for Experimental Cancer Research (ISREC) and NCCR Molecular Oncology, Lausanne, Switzerland.

ABSTRACT
Combinatorial gene regulation largely contributes to phenotypic versatility in higher eukaryotes. Genome-wide chromatin immuno-precipitation (ChIP) combined with expression profiling can dissect regulatory circuits around transcriptional regulators. Here, we integrate tiling array measurements of DNA-binding sites for c-Myc, sp1, TFIID and modified histones with a tissue expression atlas to establish the functional correspondence between physical binding, promoter activity and transcriptional regulation. For this we develop SLM, a methodology to map c-Myc and sp1-binding sites and then classify sites as sp1-only, c-Myc-only or dual. Dual sites show several distinct features compared to the single regulator sites: specifically, they exhibit overall higher degree of conservation between human and rodents, stronger correlation with TFIID-bound promoters, and preference for permissive chromatin state. By applying regression models to an expression atlas we identified a functionally distinct signature for strong dual c-Myc/sp1 sites. Namely, the correlation with c-Myc expression in promoters harboring dual-sites is increased for stronger sp1 sites by strong sp1 binding and the effect is largest in proliferating tissues. Our approach shows how integrated functional analyses can uncover tissue-specific and combinatorial regulatory dependencies in mammals.

Show MeSH
Related in: MedlinePlus