Loss of LINE-1 Activity in the Megabats

Abstract

LINE-1 (L1) retrotransposons are the most abundant type of mammalian retroelement. They have profound effects on genome plasticity and have been proposed to fulfill essential host functions, yet it remains unclear where they lie on the spectrum from parasitism to mutualism. Their ubiquity makes it difficult to determine the extent of their effects on genome evolution and gene expression because of the relative dearth of animal models lacking L1 activity. We have isolated L1 sequences from 11 megabat species by a method that enriches for recently inserted L1s and have done a bioinformatic examination of L1 sequences from a 12th species whose genome was recently shotgun sequenced. An L1 extinction event appears to have occurred at least 24 million years ago (MYA) in an ancestor of the megabats. The ancestor was unusual in having maintained two highly divergent long-term L1 lineages with different levels of activity, which appear, on an evolutionary scale, to have simultaneously lost that activity. These megabat species can serve as new animal models to ask what effect loss of L1 activity has on mammalian genome evolution and gene expression.

Genetic conflicts: the usual suspects and beyond

“…Consistent with this notion, only a few transposable element copies account for the bulk of transposition activity in human genomes (Beck et al, 2011;Brouha et al, 2003). Further, there are well-documented examples of extinction of entire families of transposons in host genomes (Cantrell et al, 2008;Grahn et al, 2005), which could reflect especially potent host restriction or perhaps the random loss of these elements.…”

Origin and evolution of SINEs in eukaryotic genomes

“…Clearly, a decline in LINE activity makes the further amplification of the dependent SINE impossible. Thus, activity correlation is observed for many SINE/LINE partners, for example, Ther-1 and L2 in human and mouse (Human Genome Sequencing Consortium, 2001; Mouse Genome Sequencing Consortium, 2002); MEG and L1 in fruit bats (Cantrell et al, 2008;Gogolevsky et al, 2009) or Alu and L1 subfamilies in human (Ohshima et al, 2003).…”

Retrofitting the Genome: L1 Extinction Follows Endogenous Retroviral Expansion in a Group of Muroid Rodents

“…There are only two known instances of L1 extinction-loss of copies of L1 that can transpose autonomously. Both occurred in the ancestors of speciose groups and thus appear to affect most species of sigmodontine rodents and all species of megabats (15,16,32).…”