Limits...
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.

Show MeSH

Related in: MedlinePlus

Positions of sites assessed in genomic and functional data. (A) Binding sites are enriched for conservation between human–mouse and human–rat. The fold enrichment (expressed with respect to randomized site locations) is plotted versus a conservation score taken as the quantile of pairwise alignment scores taken from UCSC genome database. For each conservation threshold, the number of sites falling in conserved islands is divided by its expected number, assuming random sites positions. Genome-wide alignments and scoring is described in (42). (B–C). Overlap with TFIID sites (15) and modified chromatin islands (17). In all cases the positions for c-Myc or sp1 sites are taken as the location of the Gaussian profiles (cf. Figure. S2, methods section). The TFIID- binding sites and the modified histone islands are given as genomic intervals. Their coordinates were taken from the original publications and mapped to the build hg17 of the human genome (Materials and Methods Section). (B) c-Myc and sp1 bind preferentially to TSSs also bound by TFIID (15). Such TSSs (255) are defined as having a TFIID island in a window of [−1 kb, +1 kb] around the TSS position and amount to 21% of all unique TSS region on chromosomes 21 and 22. Such TSSs also bound by c-Myc or sp1 are nearly 65% while this fraction is well below 20% for TFIID free sites. The relative fraction of dual sites is clearly higher when TFIID binds: the green fraction (dual) is larger than the combined blue (Myc) and yellow (sp1), whereas all three are approximately equal for TSS regions without TFIID. We find that 33% of all sp1 sites coincide with TFIID and 27% for the c-Myc sites. (C) c-Myc-only and dual sites are enriched near permissive chromatin islands (tri-methylated (Tri) and acetylated H3-K4 residues (Ace), 2 right bars). Bars represent the fraction of modified histone islands measured in HepG2 cells (17), (supplementary material) also bound by TFIID, and which contain either c-Myc, sp1, dual or no sites. We counted 125 such di-methylated (Di), 241 tri-methylated (Tri) and 259 acetylated (Ace) islands. Whereas the fractions c-Myc-only and dual sites is increased in the permissive state, sp1 fractions is unchanged from the facultative to the permissive states.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1851645&req=5

Figure 2: Positions of sites assessed in genomic and functional data. (A) Binding sites are enriched for conservation between human–mouse and human–rat. The fold enrichment (expressed with respect to randomized site locations) is plotted versus a conservation score taken as the quantile of pairwise alignment scores taken from UCSC genome database. For each conservation threshold, the number of sites falling in conserved islands is divided by its expected number, assuming random sites positions. Genome-wide alignments and scoring is described in (42). (B–C). Overlap with TFIID sites (15) and modified chromatin islands (17). In all cases the positions for c-Myc or sp1 sites are taken as the location of the Gaussian profiles (cf. Figure. S2, methods section). The TFIID- binding sites and the modified histone islands are given as genomic intervals. Their coordinates were taken from the original publications and mapped to the build hg17 of the human genome (Materials and Methods Section). (B) c-Myc and sp1 bind preferentially to TSSs also bound by TFIID (15). Such TSSs (255) are defined as having a TFIID island in a window of [−1 kb, +1 kb] around the TSS position and amount to 21% of all unique TSS region on chromosomes 21 and 22. Such TSSs also bound by c-Myc or sp1 are nearly 65% while this fraction is well below 20% for TFIID free sites. The relative fraction of dual sites is clearly higher when TFIID binds: the green fraction (dual) is larger than the combined blue (Myc) and yellow (sp1), whereas all three are approximately equal for TSS regions without TFIID. We find that 33% of all sp1 sites coincide with TFIID and 27% for the c-Myc sites. (C) c-Myc-only and dual sites are enriched near permissive chromatin islands (tri-methylated (Tri) and acetylated H3-K4 residues (Ace), 2 right bars). Bars represent the fraction of modified histone islands measured in HepG2 cells (17), (supplementary material) also bound by TFIID, and which contain either c-Myc, sp1, dual or no sites. We counted 125 such di-methylated (Di), 241 tri-methylated (Tri) and 259 acetylated (Ace) islands. Whereas the fractions c-Myc-only and dual sites is increased in the permissive state, sp1 fractions is unchanged from the facultative to the permissive states.

Mentions: 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.


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

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

Positions of sites assessed in genomic and functional data. (A) Binding sites are enriched for conservation between human–mouse and human–rat. The fold enrichment (expressed with respect to randomized site locations) is plotted versus a conservation score taken as the quantile of pairwise alignment scores taken from UCSC genome database. For each conservation threshold, the number of sites falling in conserved islands is divided by its expected number, assuming random sites positions. Genome-wide alignments and scoring is described in (42). (B–C). Overlap with TFIID sites (15) and modified chromatin islands (17). In all cases the positions for c-Myc or sp1 sites are taken as the location of the Gaussian profiles (cf. Figure. S2, methods section). The TFIID- binding sites and the modified histone islands are given as genomic intervals. Their coordinates were taken from the original publications and mapped to the build hg17 of the human genome (Materials and Methods Section). (B) c-Myc and sp1 bind preferentially to TSSs also bound by TFIID (15). Such TSSs (255) are defined as having a TFIID island in a window of [−1 kb, +1 kb] around the TSS position and amount to 21% of all unique TSS region on chromosomes 21 and 22. Such TSSs also bound by c-Myc or sp1 are nearly 65% while this fraction is well below 20% for TFIID free sites. The relative fraction of dual sites is clearly higher when TFIID binds: the green fraction (dual) is larger than the combined blue (Myc) and yellow (sp1), whereas all three are approximately equal for TSS regions without TFIID. We find that 33% of all sp1 sites coincide with TFIID and 27% for the c-Myc sites. (C) c-Myc-only and dual sites are enriched near permissive chromatin islands (tri-methylated (Tri) and acetylated H3-K4 residues (Ace), 2 right bars). Bars represent the fraction of modified histone islands measured in HepG2 cells (17), (supplementary material) also bound by TFIID, and which contain either c-Myc, sp1, dual or no sites. We counted 125 such di-methylated (Di), 241 tri-methylated (Tri) and 259 acetylated (Ace) islands. Whereas the fractions c-Myc-only and dual sites is increased in the permissive state, sp1 fractions is unchanged from the facultative to the permissive states.
© Copyright Policy - openaccess
Related In: Results  -  Collection

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

Figure 2: Positions of sites assessed in genomic and functional data. (A) Binding sites are enriched for conservation between human–mouse and human–rat. The fold enrichment (expressed with respect to randomized site locations) is plotted versus a conservation score taken as the quantile of pairwise alignment scores taken from UCSC genome database. For each conservation threshold, the number of sites falling in conserved islands is divided by its expected number, assuming random sites positions. Genome-wide alignments and scoring is described in (42). (B–C). Overlap with TFIID sites (15) and modified chromatin islands (17). In all cases the positions for c-Myc or sp1 sites are taken as the location of the Gaussian profiles (cf. Figure. S2, methods section). The TFIID- binding sites and the modified histone islands are given as genomic intervals. Their coordinates were taken from the original publications and mapped to the build hg17 of the human genome (Materials and Methods Section). (B) c-Myc and sp1 bind preferentially to TSSs also bound by TFIID (15). Such TSSs (255) are defined as having a TFIID island in a window of [−1 kb, +1 kb] around the TSS position and amount to 21% of all unique TSS region on chromosomes 21 and 22. Such TSSs also bound by c-Myc or sp1 are nearly 65% while this fraction is well below 20% for TFIID free sites. The relative fraction of dual sites is clearly higher when TFIID binds: the green fraction (dual) is larger than the combined blue (Myc) and yellow (sp1), whereas all three are approximately equal for TSS regions without TFIID. We find that 33% of all sp1 sites coincide with TFIID and 27% for the c-Myc sites. (C) c-Myc-only and dual sites are enriched near permissive chromatin islands (tri-methylated (Tri) and acetylated H3-K4 residues (Ace), 2 right bars). Bars represent the fraction of modified histone islands measured in HepG2 cells (17), (supplementary material) also bound by TFIID, and which contain either c-Myc, sp1, dual or no sites. We counted 125 such di-methylated (Di), 241 tri-methylated (Tri) and 259 acetylated (Ace) islands. Whereas the fractions c-Myc-only and dual sites is increased in the permissive state, sp1 fractions is unchanged from the facultative to the permissive states.
Mentions: 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.

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