Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Transposable elements (TEs) are major drivers of human genome evolution.
• Post-transcriptional gene regulation by TE-derived sequences is incompletely understood.

Purpose of the Study:

• To systematically investigate the role of TEs in post-transcriptional regulation via RNA-protein interactions.
• To explore TE-derived sequence interactions with RNA binding proteins (RBPs) in human mRNAs and lncRNAs.

Main Methods:

• Analysis of 75 CLIP-Seq experiments.
• Mapping RNA binding sites for 51 human RBPs.
• Investigating TE-specific RBP binding motifs and conservation.

Main Results:

• Widespread interactions detected between RBPs and TE-derived sequences.
• Identification of diverse TE-specific RBP binding motifs, often conserved in the nonrepetitive transcriptome.
• TE-derived sites affect transcript abundance and splicing, with some RBP-TE interactions showing unique regulatory effects (e.g., HuR and Alu elements).

Conclusions:

• Transposable elements play a significant and widespread role in shaping RNA-protein regulatory networks in the human genome.