Using Alu elements as polyadenylation sites: A case of retroposon exaptation

Mol Biol Evol. 2009 Feb;26(2):327-34. doi: 10.1093/molbev/msn249. Epub 2008 Nov 4.

Abstract

Of the 1.1 million Alu retroposons in the human genome, about 10,000 are inserted in the 3' untranslated regions (UTR) of protein-coding genes and 1% of these (107 events) are active as polyadenylation sites (PASs). Strikingly, although Alu's in 3' UTR are indifferently inserted in the forward or reverse direction, 99% of polyadenylation-active Alu sequences are forward oriented. Consensus Alu+ sequences contain sites that can give rise to polyadenylation signals and enhancers through a few point mutations. We found that the strand bias of polyadenylation-active Alu's reflects a radical difference in the fitness of sense and antisense Alu's toward cleavage/polyadenylation activity. In contrast to previous beliefs, Alu inserts do not necessarily represent weak or cryptic PASs; instead, they often constitute the major or the unique PAS in a gene, adding to the growing list of Alu exaptations. Finally, some Alu-borne PASs are intronic and produce truncated transcripts that may impact gene function and/or contribute to gene remodeling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alu Elements*
  • Animals
  • Base Sequence
  • Enhancer Elements, Genetic
  • Humans
  • Mice
  • Molecular Sequence Data
  • Polyadenylation*
  • RNA Splice Sites

Substances

  • RNA Splice Sites