Abstract
BackgroundThe general structure and action of all eukaryotic and archaeal RNA polymerases machinery have an astonishing similarity despite the diversity of core promoter sequences in different species. The goal of our work is to find common characteristics of DNA region that define it as a promoter for the RNA polymerase II (Pol II).ResultsThe profiles of a large number of physical and structural characteristics, averaged over representative sets of the Pol II minimal core promoters of the evolutionary divergent species from animals, plants and unicellular fungi were analysed. In addition to the characteristics defined at the base-pair steps, we, for the first time, use profiles of the ultrasonic cleavage and DNase I cleavage indexes, informative for internal properties of each complementary strand.ConclusionsDNA of the core promoters of metazoans and Schizosaccharomyces pombe has similar structural organization. Its mechanical and 3D structural characteristics have singular properties at the positions of TATA-box. The minor groove is broadened and conformational motion is decreased in that region. Special characteristics of conformational behavior are revealed in metazoans at the region, which connects the end of TATA-box and the transcription start site (TSS). The intensities of conformational motions in the complementary strands are periodically changed in opposite phases. They are noticeable, best of all, in mammals. Such conformational features are lacking in the core promoters of S. pombe. The profiles of Saccharomyces cerevisiae core promoters significantly differ: their singular region is shifted down thus pointing to the uniqueness of their structural organization. Obtained results may be useful in genetic engineering for artificial modulation of the promoter strength.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3292-z) contains supplementary material, which is available to authorized users.
Highlights
The general structure and action of all eukaryotic and archaeal RNA polymerases machinery have an astonishing similarity despite the diversity of core promoter sequences in different species
We have used sets of the animal promoters (23,360 promoters for H. sapiens, 21,239 promoters for M. musculus, 15,073 promoters for D. melanogaster, 10,726 promoters for D. rerio, 7120 promoters for C. elegans; plant promoters (10,229 promoters for A. thaliana) and fungi promoters (4324 promoters for S. cerevisae and 3440 promoters for S. pombe)
The present study was aimed to elucidate the special structural organization of the naked DNA in minimal core promoters of RNA polymerase II, which could be important for their functioning
Summary
The general structure and action of all eukaryotic and archaeal RNA polymerases machinery have an astonishing similarity despite the diversity of core promoter sequences in different species. TATA box binding protein (TBP) subunit of the transcription factor II D (TFIID) initiates the assembly of a transcription complex It binds to the eight base-pair TATA-element and induces local structural changes, previously characterized as a formation of the novel form of the double helix, the so-called TA-form of DNA, remarkable feature of which is extremely high base-pair inclination [4]. X-ray structures of the complexes of TBP from A. thaliana, S. cerevisiae and H. sapiens with oligonucleotides that contain octanucleotides TATAAAAG or TATAAAAA in their center show that eight base-pair TATA-element binds to the concave surface of TBP by bending towards the major groove [5,6,7,8] This causes wide opening of the shallow minor groove, which forms predominantly hydrophobic interface with the entire under-surface of the TBP saddle. Fine analysis of 8 base-pair TATA box [8] has revealed remarkable structural inhomogeneity of DNA in the complex and lead to the assumption that binding polarity of TBP could be due to the asymmetry
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.
