The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity

Deborah I. Ritter1, Qiang Li, Dennis Kostka, Katherine S. Pollard, Su Guo,
Jeffrey H. Chuang

• "Identified 41 zebrafish mutual best BLAST hits to orthologous enhancer sequences in the human genome. Zebrafish sequences were tested for enhancer activity in a Tol2 transposon GFP assay; human sequences had been assayed for enhancer activity in mouse embryos."
• "A minority of the enhancer pairs showed conserved anatomical activity (13/41, 31.7%)."
• "Correspondence between CNE activity patterns and target gene expression was irregular, with 14 zebrafish CNEs driving expression at least partially overlapping the expression of the predicted target gene."
• "Sequence Conservation is a Weak Predictor of Conserved Enhancer Activity. By calculating the true positive rate and false positive rate at each threshold of sequence conservation, we computed a receiver operating characteristic (ROC) curve (Figure 3A2). The area under the curve is 0.684, indicating a small improvement over random guessing."
• "an enhancer with accelerated primate evolution has been shown to have lineage-specific human activity"
• "We found that mammalian PAB has similar discriminative power as human-zebrafish
  sequence percent identity"
• "we compared the ZZ, HZ, and HM activity patterns simultaneously. In 4/13 (31%) of the cases, all three experiments drive similar anatomical expression in homologous tissues. This is a higher fraction than expected if cis- and trans- evolution were independent ((1- 0.39) × (1-0.69) = 19%), suggesting concerted cis- and trans- evolution to maintain function in each species. In other words, positive selection has likely acted on ~10% of our tested enhancer sequences to optimize them for species-specific trans- regulatory factors."