- Transposable elements (TEs) are the single largest component of most eukaryote genomes. Rice and wheat offer ideal systems to study epigenetic regulation of TEs and to investigate the evolution of TEs following allopolyploidization. Almost 40% of the rice genome and ∼90% of the wheat genome are derived from TEs. Most elements contain inactivating mutations, but others are reversibly silenced by epigenetic mechanisms. The presence of TE sequences in EST and cDNA databases indicates that those elements escaped silencing and expressed. The transcriptional activation of TEs might impact the expression of adjacent host genes. Allopolyploidization in wheat activates long terminal repeat (LTR) retrotransposon promoters that initiate readout transcription into adjacent genes. Moreover, LTR methylation and readout transcription initiated from promoters in LTRs change during plant development. The power of whole genome analysis of TE methylation and transcription coupled with the availability of virtually a complete genome sequence for rice resulted in much higher resolution than in previously reported studies. The underlying mechanism(s) whereby TEs alter expression of adjacent genes through readout transcription and the potential significant biological role of transcriptional interference between retroelements and cellular genes are discussed.