Biochemical activity is the default DNA state in eukaryotes

Abstract

Genomes encode for genes and the regulatory signals that enable those genes to be transcribed, and are continually shaped by evolution. Genomes, including those of human and yeast, encode for numerous regulatory elements and transcripts that have limited evidence of conservation or function. Here, we sought to create a genomic null hypothesis by quantifying the gene regulatory activity of evolutionarily naive DNA, using RNA-seq of evolutionarily distant DNA expressed in yeast and computational predictions of random DNA activity in human cells and tissues. In yeast, we found that >99% of bases in naive DNA expressed as part of one or more transcripts. Naive transcripts are sometimes spliced, and are similar to evolved transcripts in length and expression distribution, indicating that stable expression and/or splicing are insufficient to indicate adaptation. However, naive transcripts do not achieve the extreme high expression levels as achieved by evolved genes, and frequently overlap with antisense transcription, suggesting that selection has shaped the yeast transcriptome to achieve high expression and coherent gene structures. In humans, we found that, while random DNA is predicted to have minimal activity, dinucleotide content-matched randomized DNA is predicted to have much of the regulatory activity of evolved sequences, including active chromatin marks at between half (DNase I and H3K4me3) and 1/16th (H3K27ac and H3K4me1) the rate of evolved DNA, and the repression-associated H3K27me3 at about twice the rate of evolved DNA. Naive human DNA is predicted to be more cell type-specific than evolved DNA and is predicted to generate co-occurring chromatin marks, indicating that these are not reliable indicators of selection. However, extreme high activity is rarely achieved by naive DNA, consistent with these arising via selection. Our results indicate that evolving regulatory activity from naive DNA is comparatively easy in both yeast and humans, and we expect to see many biochemically active and cell type-specific DNA sequences in the absence of selection. Such naive biochemically active sequences have the potential to evolve a function or, if sufficiently detrimental, selection may act to repress them.