retroposition

Szcześniak MW, Ciomborowska J, Nowak W, Rogozin IB & Makałowska I 2011 Primate and rodent specific intron gains and the origin of retrogenes with splice variants. Mol Biol Evol 28:33-37.

  • many genome-wide comparisons of eukaryotic species demonstrated multiple intron losses and intron gains
  • intron gain is a very rare event in vertebrate evolution
  • no intron gains into intact conserved coding regions of mammalian genes are known
  • the only reported new introns were acquired, by and large, by either a fusion of retrogene with host genes or de novo from the genomic environment as a result of new exon capture
  • we report two retrogenes, RNF113B and DCAF12, where the exon sequence was split by creation of a new intron as the result of mutations and emergence of new splice sites
  • the first copy of RNF113 was retroposed into the intronic region of NDUFA1 gene in the genome of the mammalian ancestor
  • after the mammalian radiation the RNF113A retrogene was duplicated, by retropositions or segmental duplications, in several lineages
  • after the retroposition/duplication, the primate specific RNF113B gene underwent rapid evolution including intron gain
  • the intron of RNF113B is not a de novo insertion but rather originated from the exonic sequence
  • a double point mutation, AG → GT, generated the donor site
  • the origin of acceptor site is not so clear
  • one variant has two exons, as described above
  • the other one is a single exon transcript similar to RNF113A
  • most primates have three transcripts of RNF113: one from the RNF113A retrogene and two from the RNF113B
  • the presence of the splice variants in the retrogene is very surprising and has only been reported once before
  • a second case involves DCAF12
  • there were two events that changed the splicing pattern in DCAF12L2
  • first, an intronization event occurred in the common ancestor of primates and rodents
  • second, an alternative donor site emerged in rodents only
  • numerous studies revealed a tendency of retrogenes to be expressed exclusively in testis
  • the hypertranscription present in the meiotic and postmeiotic spermatogenic cells makes possible transcription of DNA that is usually not transcribed
  • the failure of previous studies to find intron gains can be explained by the fact that they were focused on different intron gain mechanisms and did not consider exon intronization