Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes

Abstract

During the process of transcription, RNA polymerase can exactly locate a promoter sequence in the complex maze of a genome. Several experimental studies and computational analyses have shown that the promoter sequences apparently possess some special properties, such as unusual DNA structures and low stability, which make them distinct from the rest of the genome. But most of these studies have been carried out on a particular set of promoter sequences or on promoter sequences from similar organisms. To examine whether the promoters from a wide variety of organisms share these special properties, we have carried out an analysis of sets of promoters from bacteria, vertebrates and plants. These promoters were analyzed with respect to the prediction of three different properties, such as DNA curvature, bendability and stability, which are relevant to transcription. All the promoter sequences are predicted to share certain features, such as stability and bendability profiles, but there are significant differences in DNA curvature profiles and nucleotide composition between the different organisms. These similarities and differences are correlated with some of the known facts about transcription process in the promoters from the three groups of organisms.

Figure 1

Distribution of free energy of duplex formation, near the TSSs. The figure shows the average free energy profiles (black) with respect to the relative base position (x-axis), in the case of (A) vertebrate, (B) plant, (C) E.coli and (D) B.subtilis promoters. More negative values indicate greater stability (indicated by black arrow on the top right hand corner of the figure). The profiles in this, and in subsequent Figures 2–4, extend from 500 nt upstream to 500 nt downstream of TSS (shown as dashed vertical line at 0 position). The profiles calculated for the shuffled sequences in the upstream and downstream regions are shown (gray) in each case.

Figure 2

Distribution of curvature around TSSs. The figure shows the average predicted curvature (d/l_max) profile (black) against the relative base position (x-axis), in the case of (A) vertebrate, (B) plant, (C) E.coli and (D) B.subtilis promoters. Smaller values indicate higher curvature (indicated by black arrow on the top right hand corner of the figure).

Figure 3

Bendability distribution around TSSs calculated using trinucleotide parameters based on nucleosomal positioning preferences. The figure shows the bendability profiles (black) with respect to the relative base position (x-axis), in the case of (A) vertebrate, (B) plant, (C) E.coli and (D) B.subtilis promoters. For the sake of clarity, the profiles are smoothed using a 50 nt window. Smaller values indicate greater bendability (indicated by black arrow on the top right hand corner of the figure).

Figure 4

Bendability distribution in the vicinity of TSSs calculated using DNase I sensitivity parameters. The figure shows the bendability profiles (black) with respect to the relative base position (x-axis), in the case of (A) vertebrate, (B) plant, (C) E.coli and (D) B.subtilis promoters. For the sake of clarity, the profiles are smoothed using a 50 nt window. Less negative values indicate higher bendability (indicated by black arrow on the top right hand corner of the figure).

Figure 5

The percentage occurrence of each dinucleotide in upstream (y-axis) versus downstream (x-axis) region in the near vicinity of TSS, i.e. −150 to −50 and 100 to 200 in the case of (A) vertebrate, (B) plant, (C) E. coli and (D) B. subtilis. The dinucleotides, which are present more often in downstream region than in the upstream region, appear below the diagonal and vice versa.

Figure 6

The percentage occurrence of trinucleotides in upstream (y-axis) versus downstream (x-axis) region in the near vicinity of TSS, i.e. −150 to −50 and 100 to 200 in the case of (A) vertebrate, (B) plant, (C) E. coli and (D) B. subtilis. The trinucleotides, which are found more often in the downstream region than in the upstream region, appear below the diagonal and vice versa. For the sake of clarity, only some trinucleotides, which show significantly large differences in their upstream and downstream frequencies, are labeled.