Title: Rehabilitating junk DNA
Description: A study to investigate whether conserved non-coding sequences (CNSs) account for the balance of functional non-coding positions was made. Whole-genome sequence data from four nonhuman species (chimp, dog, mouse and rat) and human polymorphism data were employed to analyze selection at single-nucleotide resolution. A significant fraction of functional positions were found to lie outside of CNSs, suggesting that many such positions are diffusely distributed across the genome. To facilitate the identification of functional positions, a program to score sequence conservation at the single-nucleotide level (SCONE - Sequence CONservation Evaluation) was developed. Application of SCONE to the ENCODE regions confirmed a diffuse distribution of functional positions. Analysis of the distribution of positions within annotated functional regions (coding and non-coding) suggests that the majority of conserved functional positions lie outside of CNS elements. In addition the overall fraction of conserved nucleotides in annotated functional non-coding regions is low, suggesting that sequence conservation has limited utility in identifying functional non-coding elements.

Finally, an analysis of chromatin accessibility (as assessed by DNAse-I hypersensitivity) in the non-coding portion of the Drosophila genome reveals a strong relationship between accessibility and the raw mutation rate. Furthermore, putative regulatory regions identified on the basis of extremely high accessibility (DNAse-I Hypersensitive Sites) show signals of purifying and adaptive selection. Collectively these results highlight the influence of accessibility on evolution and the role played by non-coding regulatory sequences in functional divergence.