RT Journal Article
SR Electronic
T1 Similar evolutionary trajectories for retrotransposon accumulation in mammals
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 091652
DO 10.1101/091652
A1 Reuben M Buckley
A1 R Daniel Kortschak
A1 Joy M Raison
A1 David L Adelson
YR 2017
UL http://biorxiv.org/content/early/2017/01/15/091652.abstract
AB The factors guiding retrotransposon insertion site preference are not well understood. Different types of retrotransposons share common replication machinery and yet occupy distinct genomic domains. Autonomous long interspersed elements accumulate in gene-poor domains and their non-autonomous short interspersed elements accumulate in gene-rich domains. To determine genomic factors that contribute to this discrepancy we analysed the distribution of retrotransposons within the framework of chromosomal domains and regulatory elements. Using comparative genomics, we identified large-scale conserved patterns of retrotransposon accumulation across several mammalian genomes. Importantly, retrotransposons that were active after our sample-species diverged accumulated in orthologous regions. This suggested a conserved interaction between retrotransposon activity and conserved genome architecture. In addition, we found that retrotransposons accumulated at regulatory element boundaries in open chromatin, where accumulation of particular retrotransposon types depended on insertion size and local regulatory element density. From our results, we propose a model where density and distribution of genes and regulatory elements canalise the accumulation of retrotransposons. Through conservation of synteny, gene regulation and nuclear organisation, we have found that mammalian genomes follow similar evolutionary trajectories.