Global distribution of negative cofactor 2 subunit-alpha on human promoters.
Negative cofactor 2 (NC2) forms a stable complex with TATA-binding protein (TBP) on promoters in vitro. Its association with TBP prevents the binding of TFIIB and leads to inhibition of preinitiation complex formation. Here, we investigate the association of NC2 subunit-alpha with human RNA polymerase II promoter regions by using gene-specific ChIP and genome-wide promoter ChIPchip analyses. We find NC2alpha associated with a large number of human promoters, where it peaks close to the core regions. NC2 occupancy in vivo positively correlates with mRNA levels, which perhaps reflects its capacity to stabilize TBP on promoter regions. In single gene analyses, we confirm core promoter binding and in addition map the NC2 complex to enhancer proximal regions. High-occupancy histone genes display a stable NC2/TFIIB ratio during the cell cycle, which otherwise varies markedly from one gene to another. The latter is at least in part explained by an observed negative correlation of NC2 occupancy with the presence of the TFIIB recognition element in core promoter regions. Our data establish the genome-wide basis for general and gene-specific functions of NC2 in mammalian cells.
Albert
Thomas K
TK
Department of Gene Expression and Gene Vectors, GSF-National Research Center for Environment and Health, Marchioninistrasse 25, 81377 Munich, Germany.
Grote
Korbinian
K
Boeing
Stefan
S
Stelzer
Gertraud
G
Schepers
Aloys
A
Meisterernst
Michael
M
D001402:B-Lymphocytes / Q000378:metabolism; D002051:Burkitt Lymphoma / Q000473:pathology; D002461:Cell Line, Transformed; D045744:Cell Line, Tumor; D002472:Cell Transformation, Viral; D047369:Chromatin Immunoprecipitation; D015870:Gene Expression; D015894:Genome, Human; D006801:Humans; D019169:Jurkat Cells; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000032:analysis; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D035181:TATA-Box Binding Protein / Q000378:metabolism; D035581:Transcription Factor TFIIB / Q000037:antagonists & inhibitors / Q000235:genetics
C091514:BABAM2 protein, human; C099112:DRAP1 protein, human; D009419:Nerve Tissue Proteins; D012333:RNA, Messenger; D012097:Repressor Proteins; D035181:TATA-Box Binding Protein; D035581:Transcription Factor TFIIB; D012319:RNA Polymerase II