Nucleotide Composition of Ultra-Conserved Elements Shows Excess of GpC and Depletion of GG and CC Dinucleotides

Abstract

The public UCNEbase database, comprising 4273 human ultra-conserved noncoding elements (UCNEs), was thoroughly investigated with the aim to find any nucleotide signals or motifs that have made these DNA sequences practically unchanged over three hundred million years of evolution. Each UCNE comprises over 200 nucleotides and has at least 95% identity between humans and chickens. A total of 31,046 SNPs were found within the UCNE database. We demonstrated that every human has over 300 mutations within 4273 UCNEs. No association of UCNEs with non-coding RNAs, nor preference of a particular meiotic recombination rate within them were found. No sequence motifs associated with UCNEs nor their flanking regions have been found. However, we demonstrated that UCNEs have strong nucleotide and dinucleotide sequence abnormalities compared to genome averages. Specifically, UCNEs are depleted for CC and GG dinucleotides, while GC dinucleotides are in excess of 28%. Importantly, GC dinucleotides have extraordinarily strong stacking free-energy inside the DNA helix and unique resistance to dissociation. Based on the adjacent nucleotide stacking abnormalities within UCNEs, we conjecture that peculiarities in dinucleotide distribution within UCNEs may create unique 3D conformation and specificity to bind proteins. We also discuss the strange dynamics of multiple SNPs inside UCNEs and reasons why these sequences are extraordinarily conserved.

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

“…Last year, our team demonstrated that UCNEs have unusual DN frequencies and contain higher amounts of GpC DNs [ 4 ]. In this paper, we hypothesized that unique DN arrangements may exist within UCNEs, contributing to their evolutionary conservation and investigated this conjecture.…”

“…We used our purified set of 4272 UCNE sequences described and available form Fedorova et al [ 4 ]. This set was created from the human UCNE database ( (accessed on 6 August 2023)) [ 23 ].…”

“…This paper is the next step in our long-term project on deciphering DNA biomarkers that make UCNEs unchangeable over hundreds of millions of years. Thousands of these long (300 bp, on average) UCNEs, found within the intergenic and intronic regions of mammals, birds, and other vertebrates, demonstrate identical orthologous sequences across species despite undergoing numerous mutations [ 1 , 2 , 3 , 4 ]. Interestingly, individual UCNEs show no sequence similarity to all other UCNE members within the same species.…”

“…Interestingly, individual UCNEs show no sequence similarity to all other UCNE members within the same species. Recently, our team revealed that UCNEs are characterized by a higher abundance of GpC dinucleotides (DNs) and a depletion of GpG and CpC DNs [ 4 ]. Currently, this is the only reported distinction in nucleotide sequence between UCNEs and the rest of the genome.…”

Croizat’s form-making, RNA networks, and biogeography

“…Such molecular structures were described by Aloni and Lancet ( 2005 , p. 115): “Any human sequence that can reliably be aligned to chicken or fish sequence, therefore, strongly suggests functional constraints”. The “freezing” of such DNA sequences suggests that they are involved in regulatory functions that are fundamental to ontogeny and physiology (e.g., Bejerano et al, 2004 ; Simons et al, 2006 ; Fedorova et al, 2022 ).…”