Abstract
BackgroundMore than 80% of mammalian protein-coding genes are driven by TATA-less promoters which often show multiple transcriptional start sites (TSSs). However, little is known about the core promoter DNA sequences or mechanisms of transcriptional initiation for this class of promoters.Methodology/Principal FindingsHere we identify a new core promoter element XCPE2 (X core promoter element 2) (consensus sequence: A/C/G-C-C/T-C-G/A-T-T-G/A-C-C/A+1-C/T) that can direct specific transcription from the second TSS of hepatitis B virus X gene mRNA. XCPE2 sequences can also be found in human promoter regions and typically appear to drive one of the start sites within multiple TSS-containing TATA-less promoters. To gain insight into mechanisms of transcriptional initiation from this class of promoters, we examined requirements of several general transcription factors by in vitro transcription experiments using immunodepleted nuclear extracts and purified factors. Our results show that XCPE2-driven transcription uses at least TFIIB, either TFIID or free TBP, RNA polymerase II (RNA pol II) and the MED26-containing mediator complex but not Gcn5. Therefore, XCPE2-driven transcription can be carried out by a mechanism which differs from previously described TAF-dependent mechanisms for initiator (Inr)- or downstream promoter element (DPE)-containing promoters, the TBP- and SAGA (Spt-Ada-Gcn5-acetyltransferase)-dependent mechanism for yeast TATA-containing promoters, or the TFTC (TBP-free-TAF-containing complex)-dependent mechanism for certain Inr-containing TATA-less promoters. EMSA assays using XCPE2 promoter and purified factors further suggest that XCPE2 promoter recognition requires a set of factors different from those for TATA box, Inr, or DPE promoter recognition.Conclusions/SignificanceWe identified a new core promoter element XCPE2 that are found in multiple TSS-containing TATA-less promoters. Mechanisms of promoter recognition and transcriptional initiation for XCPE2-driven promoters appear different from previously shown mechanisms for classical promoters that show single “focused” TSSs. Our studies provide insight into novel mechanisms of RNA Pol II transcription from multiple TSS-containing TATA-less promoters.
Highlights
Recent bioinformatics studies have revealed that most mammalian genes do not conform to the simple model in which a TATA box directs transcription from a single defined nucleotide position –most genes have multiple promoters, within which there are multiple start sites, and that 72% of human promoters are associated with CpG islands [1,2,3]
It has been reported that the majority of strong human RNA polymerase II (RNA pol II) core promoters have an array of closely located transcriptional start sites (TSSs) that are spread over 50–100 bp [4], which is different from the traditional view that ‘‘true’’ or ’’truly specific’’ transcriptional initiations show single TSS
A number of questions remain regarding the mechanisms at play for promoters utilizing multiple start sites; (1) whether individual start sites are driven by definitive core promoter elements or whether a single ‘‘loose’’ element can drive transcription from multiple locations, (2) how transcription from different start sites within a promoter can be differently regulated, (3) which general transcription factors (GTFs) are used for transcription from different start sites at these types of promoters, and (4) whether a stable preinitiation complex is formed for transcriptional initiation from each start site
Summary
Recent bioinformatics studies have revealed that most mammalian genes do not conform to the simple model in which a TATA box directs transcription from a single defined nucleotide position –most genes have multiple promoters, within which there are multiple start sites, and that 72% of human promoters are associated with CpG islands [1,2,3]. A number of questions remain regarding the mechanisms at play for promoters utilizing multiple start sites; (1) whether individual start sites are driven by definitive core promoter elements or whether a single ‘‘loose’’ element can drive transcription from multiple locations, (2) how transcription from different start sites within a promoter can be differently regulated, (3) which general transcription factors (GTFs) are used for transcription from different start sites at these types of promoters, and (4) whether a stable preinitiation complex is formed for transcriptional initiation from each start site. Little is known about the core promoter DNA sequences or mechanisms of transcriptional initiation for this class of promoters
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
