Asymmetry in the distributions of the four nucleotides at mRNA initiation and 3′ termini sites: Some geometrical implications

All mammalian and non-mammalian vertebrate sequences in the database have been aligned by their transcription initiation sites, and separately, by their mRNA 3′ termini. A simple analysis of the distribution of single nucleotide composition in the 1000 nucleotides around these sites yields surprising results. An asymmetric pattern in the behaviour of complementary nucleotides, i.e., C vs. G and A vs. T, in both these sites is observed. The four nucleotides also behave in an opposite manner around mRNA transcription initiation and 3′ termini. This may suggest that these are signals affecting the intrinsic dynamics of the DNA structure and as such facilitate the first stages of the recognition process of the RNA polymerase in the neighbourhood of transcription initiation. These signals may also play a role in transcription termination rather than serve as signals for the mRNA cleavage/processing machinery.