Promoter influences transcription elongation: TATA-box element mediates the assembly of processive transcription complexes responsive to cyclin-dependent kinase 9

Abstract

Pausing of RNA polymerase II (RNAPII) during transcript elongation is an important mechanism for regulating gene expression at many genes. In this study we investigated the mechanism of regulated elongation of c-myc and human immunodeficiency virus-1 (HIV-1) using an in vitro elongation assay that reproduces the conditional block to elongation. We found that HIV-1 Tat can activate the RNAPII transcription complexes paused on c-myc by enhancing their elongation efficiency. We determined that cyclin-dependent kinase 9 (CDK9), the kinase subunit of positive transcription elongation factor b (P-TEFb) complex, regulates transcriptional elongation of c-myc and is present in transcription pre-initiation complexes formed on the c-myc promoter, which emphasizes a common mechanism of elongation control between HIV-1 and c-myc genes. We also investigated the roles of upstream elements of the HIV-1 and c-myc promoters in CDK9-activated transcriptional elongation. We found that the TATA-box element mediates the assembly of processive transcription complexes responsive to CDK9 and that specific combinations of upstream activation binding sites contribute to the recruitment of these complexes. We propose a common mechanism for elongation control at the c-myc and HIV-1 genes with an essential role for the TATA-box and specific modulatory contribution of upstream regulatory sequences, derived from the unique structure of the promoters, to form a composite surface for efficient recruitment of elongation-competent transcription complexes.