Structural features of DNA that determine RNA polymerase II core promoter

Abstract

Background: 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. 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).

Results: The 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.

Conclusions: DNA 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.

Keywords: Local DNA structure; RNA polymerase II promoter sequences; Sequence-specific ultrasonic cleavage.

Fig. 1

Profiles of core promoter sequences as the mononucleotides frequencies of occurrence (in percentages) at each position along the strand, complementary to template for data sets of A. thaliana, D. melanogaster, C. elegans, D. rerio, M. musculus and H. sapiens

Fig. 2

Profiles of core promoter sequences as the mononucleotides frequencies of occurrence (in percentages) at each position along the strand, complementary to template for data sets of S. cerevisiae and S. pombe

Fig. 3

a Standard deviations of dinucleotide distributions at each position of core promoter sequences of A. thaliana, D. melanogaster, C. elegans, D. rerio, M. musculus, H. sapiens, S. cerevisiae and S. pombe. b Frequencies of occurrence of tetranucleotide TATA in core promoter sequences of A. thaliana, D. melanogaster, C. elegans, D. rerio, M. musculus, H. sapiens, S. cerevisiae and S. pombe. c Frequencies of occurrence of tetranucleotide AAAA in core promoter sequences of A. thaliana, D. melanogaster, C. elegans, D. rerio, M. musculus, H. sapiens, S. cerevisiae and S. pombe

Fig. 4

Local variations of the values of physical and structural parameters in core promoter regions of A. thaliana, D. melanogaster, C. elegans, D. rerio, M. musculus and H. sapiens. a Stacking energy (in kcal/mol). b Roll (in degrees). c Stiffness of the duplex structure to Roll alteration (in kcal/mol degree). d Slide (in angstroms). e Stiffness of the duplex structure to Slide alteration (in kcal/mol angstrom). f Mobility to bend towards major groove (in mobility units)

Fig. 5

Local variations of the values of physical and structural parameters in core promoter regions of S. cerevisiae and S. pombe. a Stacking energy (in kcal/mol). b Roll (in degrees). c Stiffness of the duplex structure to Roll alteration (in kcal/mol degree). d Slide (in angstroms). e Stiffness of the duplex structure to Slide alteration (in kcal/mol angstrom). f Mobility to bend towards major groove (in mobility units)

Fig. 6

a–h Profiles of ultrasonic cleavage indexes and DNase I cleavage indexes for H. sapiens core promoters

Fig. 7

a–h Profiles of ultrasonic cleavage indexes and DNase I cleavage indexes for S. cerevisiae core promoters

Fig. 8

a–h Profiles of ultrasonic cleavage indexes and DNase I cleavage indexes for S. pombe core promoters

Fig. 9

Differences between complementary strands profiles for ultrasonic cleavage indexes and DNase I cleavage indexes in core promoters A. thaliana, D. melanogaster, C. elegans, D. rerio, M. musculus and H. sapiens

Fig. 10

a-d Profiles of T- and S-indexes in two subsets of promotors of H. sapiens

Fig. 11

a-d Profiles of T- and S-indexes in two subsets of promotors of S. cerevisiae

Fig. 12

a-d Profiles of T- and S-indexes in two subsets of promotors of S. pombe