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