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| Status |
Public on Dec 19, 2009 |
| Title |
Comparative ChIP-chip analysis of general transcription factor TFIIB and negative cofactor NC2 in human B cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
A comparative ChIP-chip analysis of TFIIB and NC2 in human B cells reveals that basal core promoter architectures control the equilibrium between NC2 and preinitiation complexes. We conducted a comparative ChIP-chip and gene expression analysis of TFIIB in human B cells and analyze associated core promoter architectures. TFIIB occupancy relates well to gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA consensus and TATA-like motifs but not the previously in vitro defined TFIIB recognition elements (BREs) are enriched in approximately 5% of the genes. Further insight was obtained by performing a parallel ChIP-chip analysis of the TFIIB antagonist NC2. The latter identifies a highly related target gene set. Nonetheless, subpopulations show strong variations in TFIIB/NC2 ratios, with high NC2/TFIIB ratios correlating to promoters that show dispersed transcription start site patterns and lacking defined core elements. Conversely, high TFIIB/NC2 ratios select for conserved core promoter elements that include TATA and INR (initiator), the upstream TFIIB recognition element (BREu) and the downstream promoter element (DPE).
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| Overall design |
Two biological samples from LCL 721 lymphoblastoid human B cells were subjected to ChIP-chip analysis of TFIIB and NC2 using a Nimblegen human promoter array (based on the HG17 genome build) covering 1.5 kb DNA around transcription start sites.
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| Contributor(s) |
Albert TK, Grote K, Boeing S, Meisterernst M |
| Citation(s) |
20230619 |
| Submission date |
Dec 18, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Thomas Karl Albert |
| E-mail(s) |
albertt@uni-muenster.de
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| Phone |
+49-251-8353349
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| Organization name |
University Muenster
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| Department |
IMTB - Institute of Molecular Tumor Biology
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| Street address |
Robert-Koch-Strasse 43
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| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
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| Platforms (1) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA122407 |
