Abstract
BackgroundExperimental investigation of transcription is still a very labor- and time-consuming process. Only a few transcription initiation scenarios have been studied in detail. The mechanism of interaction between basal machinery and promoter, in particular core promoter elements, is not known for the majority of identified promoters. In this study, we reveal various transcription initiation mechanisms by statistical analysis of 3393 nonredundant Drosophila promoters.ResultsUsing Drosophila-specific position-weight matrices, we identified promoters containing TATA box, Initiator, Downstream Promoter Element (DPE), and Motif Ten Element (MTE), as well as core elements discovered in Human (TFIIB Recognition Element (BRE) and Downstream Core Element (DCE)). Promoters utilizing known synergetic combinations of two core elements (TATA_Inr, Inr_MTE, Inr_DPE, and DPE_MTE) were identified. We also establish the existence of promoters with potentially novel synergetic combinations: TATA_DPE and TATA_MTE. Our analysis revealed several motifs with the features of promoter elements, including possible novel core promoter element(s). Comparison of Human and Drosophila showed consistent percentages of promoters with TATA, Inr, DPE, and synergetic combinations thereof, as well as most of the same functional and mutual positions of the core elements. No statistical evidence of MTE utilization in Human was found. Distinct nucleosome positioning in particular promoter classes was revealed.ConclusionWe present lists of promoters that potentially utilize the aforementioned elements/combinations. The number of these promoters is two orders of magnitude larger than the number of promoters in which transcription initiation was experimentally studied. The sequences are ready to be experimentally tested or used for further statistical analysis. The developed approach may be utilized for other species.
Highlights
Experimental investigation of transcription is still a very labor- and time-consuming process
We examined the Downstream Core Element (DCE) and BRE elements in Drosophila promoters, the biological function of those elements has only been observed in human promoters [3,14,17,19]
That if we apply our position weight matrix (PWM) to Drosophila Core Promoter Database at the region from -45 to -15 bp we find that 40.0% of promoters have the TATA box, which is close to their estimate (42.4%)
Summary
Experimental investigation of transcription is still a very labor- and time-consuming process. In the absence of the TATA box (TATA-less promoters), TAFs bind to DNA and/or to other TFs in order to involve TBP in pre-initiation complex [9,12,13,14]. Strong synergism between DPE and Inr, MTE and Inr, DCE and Inr, MTE and DPE, BRE and TATA, and Inr and TATA has been experimentally established [9,14,15,16,17,18,19] It is peculiar, that in spite of the considerable improvement of our knowledge of the transcriptional regulation processes due to emergence of new experimental techniques and computational approaches, the scenarios of the interaction between basal transcription machinery and the core promoter are not known for the majority of identified promoters [20]
Sign-in/Register to view highlights & summary 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 callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
