Epigenetic regulation of intragenic transposable elements: a two-edged sword

Genomes of animals and plants contain a large number of transposable elements (TEs). TEs often transpose into genic regions, affecting expression of surrounding genes. Intragenic TEs mostly reside in introns, and in much the same way as intergenic TEs, they are targeted by repressive epigenetic marks for transcriptional silencing. Silenced intragenic TEs generally co-repress expression of associated genes, while in some cases they significantly enhance splicing and transcript elongation. Genomes have evolved molecular mechanisms that allow the presence of silenced TEs within transcriptionally permissive chromatin environments. Epigenetic modulation of intragenic TEs often contributes to gene regulation, phenotypic expression, and genome evolution.