Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome

Nicolai K H Barth, Lifei Li, Leila Taher*

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

Many regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized to originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears to be counterintuitive to natural selection: Redundant sequences are expected to either diverge and acquire new functions or accumulate mutations and become nonfunctional. Nevertheless, we show that at least 31% of the redundant enhancer pairs in the human genome (and 17% in the mouse genome) indeed originated in this manner. Specifically, for virtually all transposon-derived redundant enhancer pairs, both enhancer partners have evolved independently, from the exaptation of two different transposons. In addition to conferring robustness to the system, redundant enhancers could provide an evolutionary advantage by fine-tuning gene expression. Consistent with this hypothesis, we observed that the target genes of redundant enhancers exhibit higher expression levels and tissue specificity as compared with other genes. Finally, we found that although enhancer redundancy appears to be an intrinsic property of certain mammalian regulatory networks, the corresponding enhancers are largely species-specific. In other words, the redundancy in these networks is most likely a result of convergent evolution.

Original languageEnglish
Article numberevaa004
Pages (from-to)1-17
Number of pages17
JournalGenome Biology and Evolution
Volume12
Issue number3
Early online date17 Jan 2020
DOIs
Publication statusPublished - 17 Mar 2020

Keywords

  • evolution
  • gene regulation
  • redundant enhancers
  • transposons

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics

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