Three periods of regulatory innovation during vertebrate evolution

Abstract

The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.

Fig. 1

Regulatory innovation. Each panel shows data for the frequency of regulatory innovations near genes in a different GO category (panel title). Colors indicate the five lineages studied. Each data point (colored circle) represents the relative frequency of regulatory innovations on a specific lineage (color) as determined by analysis using the reference genome for that lineage. The relative frequency (enrichment factor) for a specific GO category is defined as the frequency of innovations in genes of this GO category as compared to what would be expected by selecting genomic regions at random (denoted by the horizontal line at the relative frequency of 1.0). Each data point is an estimate from at least 2800 putative regulatory innovations. The time associated with each data point, indicated on the horizontal axis, is the midpoint of the branch of the phylogenetic tree on which these innovations are inferred to have occurred by comparative genome analysis (Fig. S3 and Tables S1 and S2). The horizontal axis is annotated with both geologic time periods as well as speciation events for the lineages analyzed.

Fig. 2

A comparative history of innovations in regulatory regions and genes. Each panel shows data for the frequency of regulatory innovations near genes in a different GO category (panel title) as well as the frequency of genic innovations for that GO category. Each data point for regulatory innovations (red circle) represents the percent of regulatory innovations appearing on a branch in the human lineage that are associated with a gene annotated with the given GO category. Each data point for protein-coding genes (red x) represents the percent of protein-coding genes appearing on a branch that are associated with the given GO category. The time associated with each data point is as described in Fig. 1.

Fig. 3

Enrichment for regulatory regions originating near genes involved in hair development during the time hair originated in evolution. For each branch we plot the percentage of genes or regulatory elements created on that branch that are associated with hair development.