Study : Arabidopsis thaliana RNA Seq


Arabidopsis thaliana RNA Seq
Genomes of higher eukaryotes, including plants, comprise a large amount of transposable elements (TEs), which are often silenced by epigenetic mechanisms such as histone posttranslational modifications and DNA methylation. Although silencing of TEs imposes deleterious effects on expression of nearby genes, recent studies reveal the presence of intragenic TEs marked by repressive epigenetic marks within actively transcribed genes. However, even for the well-studied plant model Arabidopsis thaliana, the abundance of intragenic TEs, how they are epigenetically regulated, and their potential impacts on host gene expression, remain unexplored. In this study, we comprehensively analyzed genome-wide distribution and epigenetic regulation of intragenic TEs in A.thaliana. Our analysis revealed that about 7% of TEs are located within gene bodies, almost equally distributed between intronic and exonic regions. Most of them are short and less methylated than their intergenic copies. Interestingly, while exonic TEs are epigenetically targeted in the same manner as genes, intronic TEs are regulated similarly to intergenic TEs. Moreover, expression analysis showed that heterochromatic epigenetic marks associated with intronic TEs are critical for proper transcription of the associated genes. Our study provides the first insight into how epigenetic regulation of intragenic TEs affects transcriptional landscape of the A.thaliana genome, and suggests the importance of epigenetic mechanisms for regulation of TEs within transcriptional gene units.


Accession number Name Taxon