High-copy-number
transposable elements comprise the majority of eukaryotic genomes where they are major contributors to gene and genome evolution. However, it remains unclear how a host genome can survive a rapid burst of hundreds or thousands of insertions because such bursts are exceedingly rare in nature and therefore difficult to observe in real time. In a previous study we reported that in a few
rice strains the
DNA transposon mPing was increasing its
copy number by approximately 40 per plant per generation. Here we exploit the completely
sequenced rice genome to determine 1,664 insertion sites using
high-throughput sequencing of 24 individual
rice plants and assess the impact of insertion on the expression of 710 genes by comparative
microarray analysis. We find that the vast majority of
transposable element insertions either upregulate or have no detectable effect on
gene transcription. This modest impact reflects a surprising avoidance of
exon insertions by mPing and a preference for insertion into
5' flanking sequences of genes. Furthermore, we document the generation of new regulatory networks by a subset of mPing insertions that render adjacent genes stress inducible. As such, this study provides evidence for models first proposed previously for the involvement of
transposable elements and other repetitive sequences in genome restructuring and
gene regulation.
