Epigenetic regulation of intragenic transposons and gene transcription in plant genomes

par Hidetoshi Saze, Plant Epigenetics Unit, Okinawa,Japan

Genomes of higher eukaryotes contain many transposable elements (TEs) that are often silenced by epigenetic mechanisms, such as histone modifications and DNA methylation. Although TE silencing adversely affects the expression of nearby genes, recent studies revealed the presence of intragenic TEs marked with repressive epigenetic marks within transcriptionally permissive chromatin environments. However, the molecular mechanisms underlying the regulation of intragenic TEs and their potential impacts on gene expression are still poorly understood. We analyzed the genome-wide distribution and epigenetic regulation of intragenic TEs in the genomes of Arabidopsis and rice and revealed that the repressive chromatin state of intragenic TEs is critical for proper transcription and splicing of associated genes. In addition, our recent long-read RNA sequencing analysis of Arabidopsis transcriptome identified a global production of chimeric TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. Our study provides new insights into how intragenic TEs affect the transcriptional landscape of the plant genomes and suggests the importance of epigenetic mechanisms regulating TEs within transcriptional gene units.