NEW YORK (GenomeWeb News) – Enhancer elements that regulate and bump up the expression of some genes can arise de novo in vertebrate genomes, a new study suggests.
As they reported online last night in PLoS Biology, a pair of researchers from University of Heidelberg's Centre for Organismal Studies tracked down these enhancer sequences in the genomes of teleost fish such as the stickleback or the medaka by looking for non-coding orthologues to protein-coding genes found in other vertebrates. Their results suggest that subtle tweaks can sometimes produce enhancers from sequences that did not previously have a regulatory role.
"By revealing that minor changes in non-regulatory sequences are sufficient to generate new enhancers, our study highlights an important playground for creating new regulatory variability and evolutionary innovation," corresponding author Laurence Ettwiller and co-author Michael Eichenlaub wrote.
Previous studies suggest that new enhancers arise in the genome as a consequence of duplications, modifications and/or relocations of existing enhancers, the duo explained. Even so, there is also evidence of poor conservation between some of these regulatory elements sequenced in related species, hinting that existing enhancers may not be the sole source of new enhancers.
"[C]omplete autonomous enhancer elements containing all the necessary binding sites in the correct arrangement can be lineage specific," the researchers wrote, adding, "it is currently unclear whether these apparent lineage-specific enhancers appear de novo or are derived from pre-existing enhancers whose sequences have diverged too much to be identifiable."
To try to distinguish between these possibilities, the researchers looked for what they called "recycled regions" in the genome, sequences that act as enhancers in one vertebrate lineage but are conserved due to another reason — for instance, because of a protein-coding role — in other lineages.
Because these recycled regions are predicted to be rare in most stable genomes, they explained, they decided to start by looking at the genome of fish in the teleost lineage, which have experienced recent whole genome duplication and subsequent losses of many duplicated protein-coding genes.
Though numerous nucleotide alterations sometimes turn up in genes that are no longer needed after such genome duplication, they explained, some of these duplicated but non-coding sequences might continue to share orthology with the original gene sequences if they take on an alternate function that leads to sequence constraint.
"[W]e used the ancestral coding function as an evolutionary trap to identify orthologous sequences of the enhancer across lineages … and assessed whether these enhancers are generated de novo in the teleost lineage," the researchers wrote.
Using a computational approach, they were able to find examples of conserved, non-coding sequences in the genomes of either stickleback or medaka fish that are orthologous with protein-coding genes in the mammalian lineage.
Three of the four recycled regions detected in the medaka genome seemed to be authentic enhancers based on in vivo reporter assays for enhancer activity and other experiments. On the other hand, the researchers did not find enhancer activity related to the protein-coding orthologues of these enhancers in other vertebrate lineages, suggesting their regulatory role is relatively new.
Based on their findings so far, the pair argued that enhancer elements that have formed de novo in the genome may be an unappreciated source of gene expression differences in vertebrates, including humans.
"The results of this study have significant implications, notably in the gene regulation and medical genetic fields by pointing out that genomic variation could lead to the generation of enhancers in regions with no apparent regulatory function," the study authors concluded. "As such variation may also lead to altered gene expression, more attention should be devoted to variation in so-called 'neutral' DNA."