Limits...
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.

Show MeSH

Related in: MedlinePlus

Frequencies of core promoter elements in TFIIB target promoters. Pie charts showing the relative frequencies of (a) TATA and TATA-like motifs, (b) BREu, and (c) INR consensus in the top 100 TFIIB-bound promoters (left chart), high-TFIIB promoters (middle chart) and low-TFIIB promoters (right chart). Motif sequences and positions that were requested for a hit are shown below the charts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2864573&req=5

Figure 3: Frequencies of core promoter elements in TFIIB target promoters. Pie charts showing the relative frequencies of (a) TATA and TATA-like motifs, (b) BREu, and (c) INR consensus in the top 100 TFIIB-bound promoters (left chart), high-TFIIB promoters (middle chart) and low-TFIIB promoters (right chart). Motif sequences and positions that were requested for a hit are shown below the charts.

Mentions: General features of high-TFIIB promoters (upper 5th percentile) were compared to low-TFIIB promoters (45th to 50th percentile) and no-TFIIB promoters (lower 5th percentile). For each group the core promoter sequences from position -50 to +50 were extracted, aligned at the major TSS and represented in a nucleotide frequency plot [28] (Additional file 1). High- and low-TFIIB promoters have 61% and 62% GC content compared to 54% of the no-TFIIB promoter set, well above the 38% for the whole human genome [10]. An exception is the region surrounding the TSS, where, consistent with previous CAGE data, pyrimidine (Py) at -1 and purine (Pu) at +1 (with G as the most frequently base at +1) is seen [15]. We next searched for core promoter elements in the different promoter groups, including a block of 100 genes with the highest levels of TFIIB binding. In the latter group, referred to as 'top 100', 24% of all promoters contained a TATA consensus motif (TATAW, with the first T at position -31 relative to the TSS). The number decreased in the less frequently bound groups, reaching an overall 5% in high-TFIIB and 1.4% in low-TFIIB promoters (Figure 3a). TATA-like sequences (WWWW) within position -20 to -40 were found in 66% of the top 100 genes, and decreased to 29% and 20% in high- and low-TFIIB promoters (Figure 3a). In contrast, the frequency of the BREu motif (SRCGCC positioned immediately upstream of TATA) was around 2 to 3% and independent of TFIIB occupancy (Figure 3b). Relaxation of the BREu sequence constraints by allowing for one mismatch elevated frequencies to 17%, 19% and 21% in the top 100, high-TFIIB and low-TFIIB genes, respectively. Thus, unlike TATA, BREu and BREu-like sequences do not correlate with TFIIB occupancy. For BREd, we analyzed only TATA consensus promoters within high-TFIIB promoters to allow accurate location of the motif downstream of TATA as described [5]. Despite its degenerated consensus (RTDKKKK) we did not find a single TATA promoter containing a full match to this sequence in this subgroup. Allowing for one mismatch did not reveal enrichment of BREd above stochastic levels. Hence, BREd is essentially absent in TATA consensus promoters with high TFIIB levels. Finally, we found that 17% of the top 100 genes contained a full match to the initiator sequence (YYANWY) around the TSS (with the central A between position -4 and +5). INR frequency was slightly decreased in high-TFIIB promoters (12%) and low-TFIIB genes (10%) (Figure 3c). Like TATA, initiator was readily discovered using the ab initio motif discovery program MEME [29] in the top 100 TFIIB-bound promoters (data not shown). No other motifs with reasonable E-values (measuring significance of enrichment) and/or specific positioning in the core region could be identified. Most notably, MEME uncover neither BREu nor BREd from these TFIIB-bound promoters.


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)

Frequencies of core promoter elements in TFIIB target promoters. Pie charts showing the relative frequencies of (a) TATA and TATA-like motifs, (b) BREu, and (c) INR consensus in the top 100 TFIIB-bound promoters (left chart), high-TFIIB promoters (middle chart) and low-TFIIB promoters (right chart). Motif sequences and positions that were requested for a hit are shown below the charts.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Frequencies of core promoter elements in TFIIB target promoters. Pie charts showing the relative frequencies of (a) TATA and TATA-like motifs, (b) BREu, and (c) INR consensus in the top 100 TFIIB-bound promoters (left chart), high-TFIIB promoters (middle chart) and low-TFIIB promoters (right chart). Motif sequences and positions that were requested for a hit are shown below the charts.
Mentions: General features of high-TFIIB promoters (upper 5th percentile) were compared to low-TFIIB promoters (45th to 50th percentile) and no-TFIIB promoters (lower 5th percentile). For each group the core promoter sequences from position -50 to +50 were extracted, aligned at the major TSS and represented in a nucleotide frequency plot [28] (Additional file 1). High- and low-TFIIB promoters have 61% and 62% GC content compared to 54% of the no-TFIIB promoter set, well above the 38% for the whole human genome [10]. An exception is the region surrounding the TSS, where, consistent with previous CAGE data, pyrimidine (Py) at -1 and purine (Pu) at +1 (with G as the most frequently base at +1) is seen [15]. We next searched for core promoter elements in the different promoter groups, including a block of 100 genes with the highest levels of TFIIB binding. In the latter group, referred to as 'top 100', 24% of all promoters contained a TATA consensus motif (TATAW, with the first T at position -31 relative to the TSS). The number decreased in the less frequently bound groups, reaching an overall 5% in high-TFIIB and 1.4% in low-TFIIB promoters (Figure 3a). TATA-like sequences (WWWW) within position -20 to -40 were found in 66% of the top 100 genes, and decreased to 29% and 20% in high- and low-TFIIB promoters (Figure 3a). In contrast, the frequency of the BREu motif (SRCGCC positioned immediately upstream of TATA) was around 2 to 3% and independent of TFIIB occupancy (Figure 3b). Relaxation of the BREu sequence constraints by allowing for one mismatch elevated frequencies to 17%, 19% and 21% in the top 100, high-TFIIB and low-TFIIB genes, respectively. Thus, unlike TATA, BREu and BREu-like sequences do not correlate with TFIIB occupancy. For BREd, we analyzed only TATA consensus promoters within high-TFIIB promoters to allow accurate location of the motif downstream of TATA as described [5]. Despite its degenerated consensus (RTDKKKK) we did not find a single TATA promoter containing a full match to this sequence in this subgroup. Allowing for one mismatch did not reveal enrichment of BREd above stochastic levels. Hence, BREd is essentially absent in TATA consensus promoters with high TFIIB levels. Finally, we found that 17% of the top 100 genes contained a full match to the initiator sequence (YYANWY) around the TSS (with the central A between position -4 and +5). INR frequency was slightly decreased in high-TFIIB promoters (12%) and low-TFIIB genes (10%) (Figure 3c). Like TATA, initiator was readily discovered using the ab initio motif discovery program MEME [29] in the top 100 TFIIB-bound promoters (data not shown). No other motifs with reasonable E-values (measuring significance of enrichment) and/or specific positioning in the core region could be identified. Most notably, MEME uncover neither BREu nor BREd from these TFIIB-bound promoters.

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