Roles of Transposable Elements in the Different Layers of Gene Expression Regulation

Abstract

The biology of transposable elements (TEs) is a fascinating and complex field of investigation. TEs represent a substantial fraction of many eukaryotic genomes and can influence many aspects of DNA function that range from the evolution of genetic information to duplication, stability, and gene expression. Their ability to move inside the genome has been largely recognized as a double-edged sword, as both useful and deleterious effects can result. A fundamental role has been played by the evolution of the molecular processes needed to properly control the expression of TEs. Today, we are far removed from the original reductive vision of TEs as "junk DNA", and are more convinced that TEs represent an essential element in the regulation of gene expression. In this review, we summarize some of the more recent findings, mainly in the animal kingdom, concerning the active roles that TEs play at every level of gene expression regulation, including chromatin modification, splicing, and protein translation.

Keywords: TEs co-option; gene expression regulation; transposable elements.

Figure 1

Effect of TE localization on the epigenetic regulation of gene expression. (A) The different distribution of TEs during evolution reshapes the epigenetic regulation of a specific gene. (B) The differential redistribution of TEs in different cells/tissues of the same organism during the development affects the expression of a specific gene. (C) The relocalization of TEs sequence in the same cell after a specific stimulus/condition affects the expression of a specific gene.

Figure 2

TE-dependent post-transcriptional regulation of gene expression. (1) TE inside the 5′-UTR cause the presence of an upstream ORF that participates in the regulation of the main ORF translation; (2) the exonization of a TE and thus its translation determines the presence of an additional domain inside the encoded protein; (3) the exonization of TE inside the coding region of an mRNA can result in the presence of a premature stop codon, thus resulting in Nonsense-mediated Decay process. (4) TE sequence can interact with RNA-binding proteins (RBP) and affects alternative splicing; (5) the presence of a TE sequence in the 3′-UTR of an mRNA can trigger STAU-mediated decay, (6) serves as a docking station for RBP involved in RNA stability such as HuR protein, (7) or triggers translational repression through the generation of a shorter mRNA without poly-A tail.