Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome

Abstract

Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composition and arrangements compared to the rest of the genome. A total of 4272 human UCNE sequences were analyzed computationally and compared with the whole genomes of human, chicken, zebrafish, and fly. Statistical analysis was performed to assess the non-randomness in DN spacing arrangements within the entire human genome and within UCNEs. Significant non-randomness in DN spacing arrangements was observed in the entire human genome. Additionally, UCNEs exhibited distinct patterns in DN arrangements compared to the rest of the genome. Approximately 83% of all DN pairs within UCNEs showed significant (>10%) non-random genomic arrangements at short distances (2-6 nucleotides) relative to each other. At the extremes, non-randomness in DN spacing distances deviated up to 40% from expected values and were frequently associated with GpC, CpG, ApT, and GpG/CpC dinucleotides. The described peculiarities in DN arrangements have persisted for hundreds of millions of years in vertebrates. These distinctive patterns may suggest that UCNEs have specific DNA conformations.

Keywords: DNA structure; bioinformatics; genomics; inhomogeneity; polymorphism; stacking.

Figure 1

Algorithm for calculation of distances between DNs. (A) delineates the distances for the same type of DN that forms GpC -> GpC pairs. (B) delineates on the same sequence the distances for two different DN types that form the closest GpC -> TpC pairs. DNs are shown in red (GpC) and green (TpC) colors and have numbers above them. The distances are measured in nucleotides (nts). Note that examined DN pairs have direction on DNA sequence. For GpC -> TpC pairs, the GpC should always be at the 5′-end and TpC on the 3′-end (B).

Figure 2

Distribution of the DN spacing distances for UCNE (red), WG (green), randUCNE (yellow), and randWG (gray). The 99.7% confidence intervals (±3σ) are demonstrated for UCNE datasets as vertical bars. Statistical errors for averaged WG, randWG, and randUCNE are 30 times less than standard deviation for UCNE, and are invisible in these graphs.

Figure 3

Fractions of DN pairs for which most prominent peaks or dips were observed for a specific spacing distance L in the range from 2 to 6 nucleotides.

Figure 4

Distribution of the DN spacing distances for human WG (green), chicken WG (blue), zebrafish WG (yellow), and Drosophila melanogaster WG (orange). The results are averaged from the 1000 random WG subsets of these species, so the standard error is 31 times smaller than standard deviation.