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Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.

Albert TK, Grote K, Boeing S, Meisterernst M - Genome Biol. (2010)

Bottom Line: We compare target genes of TFIIB and NC2 in human B cells and analyze associated core promoter architectures.TATA and TATA-like elements dictate TFIIB occupancy at a subset of genes.Biochemical data support a model in which preinitiation complex but not TBP-NC2 complex formation is regulated.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Molecular Tumor Biology (IMTB), University of Muenster, Robert-Koch-Str, Muenster, Germany. albertt@uni-muenster.de

ABSTRACT

Background: The general transcription factor TFIIB and its antagonist negative cofactor 2 (NC2) are hallmarks of RNA polymerase II (RNAPII) transcription. Both factors bind TATA box-binding protein (TBP) at promoters in a mutually exclusive manner. Dissociation of NC2 is thought to be followed by TFIIB association and subsequent preinitiation complex formation. TFIIB dissociates upon RNAPII promoter clearance, thereby providing a specific measure for steady-state preinitiation complex levels. As yet, genome-scale promoter mapping of human TFIIB has not been reported. It thus remains elusive how human core promoters contribute to preinitiation complex formation in vivo.

Results: We compare target genes of TFIIB and NC2 in human B cells and analyze associated core promoter architectures. TFIIB occupancy is positively correlated with gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA elements, but not the previously in vitro defined TFIIB recognition elements, are enriched in some 4 to 5% of the genes. NC2 binds to a highly related target gene set. Nonetheless, subpopulations show strong variations in factor ratios: whereas high TFIIB/NC2 ratios select for promoters with focused start sites and conserved core elements, high NC2/TFIIB ratios correlate to multiple start-site promoters lacking defined core elements.

Conclusions: TFIIB and NC2 are global players that occupy active genes. Preinitiation complex formation is independent of core elements at the majority of genes. TATA and TATA-like elements dictate TFIIB occupancy at a subset of genes. Biochemical data support a model in which preinitiation complex but not TBP-NC2 complex formation is regulated.

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TFIIB versus NC2 binding to human promoters. (a) Genome-wide correlation of TFIIB and NC2 binding levels on promoter regions. r, Pearson's correlation. (b) Pie chart showing the overlap of high-occupancy promoters (upper 10th percentile) recovered in TFIIB and NC2 ChIP-chip samples. (c) Comparison of the frequencies of TATA and BREu consensus sequences in high-TFIIB versus high-NC2 promoters.
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Figure 4: TFIIB versus NC2 binding to human promoters. (a) Genome-wide correlation of TFIIB and NC2 binding levels on promoter regions. r, Pearson's correlation. (b) Pie chart showing the overlap of high-occupancy promoters (upper 10th percentile) recovered in TFIIB and NC2 ChIP-chip samples. (c) Comparison of the frequencies of TATA and BREu consensus sequences in high-TFIIB versus high-NC2 promoters.

Mentions: NC2 ChIP-chip was conducted in parallel to TFIIB and as described previously [22]. The two data sets proved to be closely related (Pearson's coefficient of 0.8; Figure 4a). Nearly three-quarters of TFIIB target promoters from the upper 10th percentile were also identified in the upper 10th percentile of NC2 targets (Figure 4b). Binding of the repressor NC2 to active genes and overlap in targets is not unexpected given that both factors target exclusively active genes bound by TBP. TATA frequency was slightly higher in TFIIB target promoters (4.8% versus 3.3% in NC2 target promoters), whereas BREu frequency in the two sets was identical (Figure 4c). The limited preference of NC2 for TATA confirms previous biochemical analyses conducted on model promoters in vitro ([30]; see also below).


Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.

Albert TK, Grote K, Boeing S, Meisterernst M - Genome Biol. (2010)

TFIIB versus NC2 binding to human promoters. (a) Genome-wide correlation of TFIIB and NC2 binding levels on promoter regions. r, Pearson's correlation. (b) Pie chart showing the overlap of high-occupancy promoters (upper 10th percentile) recovered in TFIIB and NC2 ChIP-chip samples. (c) Comparison of the frequencies of TATA and BREu consensus sequences in high-TFIIB versus high-NC2 promoters.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864573&req=5

Figure 4: TFIIB versus NC2 binding to human promoters. (a) Genome-wide correlation of TFIIB and NC2 binding levels on promoter regions. r, Pearson's correlation. (b) Pie chart showing the overlap of high-occupancy promoters (upper 10th percentile) recovered in TFIIB and NC2 ChIP-chip samples. (c) Comparison of the frequencies of TATA and BREu consensus sequences in high-TFIIB versus high-NC2 promoters.
Mentions: NC2 ChIP-chip was conducted in parallel to TFIIB and as described previously [22]. The two data sets proved to be closely related (Pearson's coefficient of 0.8; Figure 4a). Nearly three-quarters of TFIIB target promoters from the upper 10th percentile were also identified in the upper 10th percentile of NC2 targets (Figure 4b). Binding of the repressor NC2 to active genes and overlap in targets is not unexpected given that both factors target exclusively active genes bound by TBP. TATA frequency was slightly higher in TFIIB target promoters (4.8% versus 3.3% in NC2 target promoters), whereas BREu frequency in the two sets was identical (Figure 4c). The limited preference of NC2 for TATA confirms previous biochemical analyses conducted on model promoters in vitro ([30]; see also below).

Bottom Line: We compare target genes of TFIIB and NC2 in human B cells and analyze associated core promoter architectures.TATA and TATA-like elements dictate TFIIB occupancy at a subset of genes.Biochemical data support a model in which preinitiation complex but not TBP-NC2 complex formation is regulated.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Molecular Tumor Biology (IMTB), University of Muenster, Robert-Koch-Str, Muenster, Germany. albertt@uni-muenster.de

ABSTRACT

Background: The general transcription factor TFIIB and its antagonist negative cofactor 2 (NC2) are hallmarks of RNA polymerase II (RNAPII) transcription. Both factors bind TATA box-binding protein (TBP) at promoters in a mutually exclusive manner. Dissociation of NC2 is thought to be followed by TFIIB association and subsequent preinitiation complex formation. TFIIB dissociates upon RNAPII promoter clearance, thereby providing a specific measure for steady-state preinitiation complex levels. As yet, genome-scale promoter mapping of human TFIIB has not been reported. It thus remains elusive how human core promoters contribute to preinitiation complex formation in vivo.

Results: We compare target genes of TFIIB and NC2 in human B cells and analyze associated core promoter architectures. TFIIB occupancy is positively correlated with gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA elements, but not the previously in vitro defined TFIIB recognition elements, are enriched in some 4 to 5% of the genes. NC2 binds to a highly related target gene set. Nonetheless, subpopulations show strong variations in factor ratios: whereas high TFIIB/NC2 ratios select for promoters with focused start sites and conserved core elements, high NC2/TFIIB ratios correlate to multiple start-site promoters lacking defined core elements.

Conclusions: TFIIB and NC2 are global players that occupy active genes. Preinitiation complex formation is independent of core elements at the majority of genes. TATA and TATA-like elements dictate TFIIB occupancy at a subset of genes. Biochemical data support a model in which preinitiation complex but not TBP-NC2 complex formation is regulated.

Show MeSH
Related in: MedlinePlus