title: Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?
abstract: Transposable elements (TEs) are mobile genetic sequences that can jump around the genome from one location to another, behaving as genomic parasites. TEs have been particularly effective in colonizing mammalian genomes, and such heavy TE load is expected to have conditioned genome evolution. Indeed, studies conducted both at the gene and genome levels have uncovered TE insertions that seem to have been co-opted--or exapted--by providing transcription factor binding sites (TFBSs) that serve as promoters and enhancers, leading to the hypothesis that TE exaptation is a major factor in the evolution of gene regulation. Here, we critically review the evidence for exaptation of TE-derived sequences as TFBSs, promoters, enhancers, and silencers/insulators both at the gene and genome levels. We classify the functional impact attributed to TE insertions into four categories of increasing complexity and argue that so far very few studies have conclusively demonstrated exaptation of TEs as transcriptional regulatory regions. We also contend that many genome-wide studies dealing with TE exaptation in recent lineages of mammals are still inconclusive and that the hypothesis of rapid transcriptional regulatory rewiring mediated by TE mobilization must be taken with caution. Finally, we suggest experimental approaches that may help attributing higher-order functions to candidate exapted TEs.
authors.affiliation: Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina. fsouza.ingebi@gmail.com
authors.forename: Flávio S J
authors.initials: FS
authors.lastname: de Souza
authors.forename: Lucía F
authors.initials: LF
authors.lastname: Franchini
authors.forename: Marcelo
authors.initials: M
authors.lastname: Rubinstein
mesh_terms: D000818:Animals; D002460:Cell Line; D004251:DNA Transposable Elements; D004622:Embryo, Mammalian; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid
chemical_list: D004251:DNA Transposable Elements
keywords: enhancer; exaptation; gene expression; mobile element