The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Long noncoding RNAs (lncRNAs) are abundant in the genome and possess regulatory functions.
• The functional domains of lncRNAs are not well understood.
• Transposable elements (TEs) are mobile genetic sequences that contribute to genome evolution via exaptation.

Purpose of the Study:

• To propose that exonic TEs in lncRNAs function as essential RNA domains.
• To introduce the concept of Repeat Insertion Domains of LncRNAs (RIDLs).
• To suggest that TEs are repurposed as recognition sites for nucleic acids and proteins during lncRNA evolution.

Main Methods:

• Review of existing literature on lncRNAs and TEs.
• Analysis of experimentally defined RIDLs.
• Discussion of potential genomic screening strategies for RIDL discovery.

Main Results:

• TE-derived fragments within lncRNAs, termed RIDLs, have been experimentally identified.
• RIDLs function as RNA-, DNA-, and protein-binding domains.
• The exaptation of TEs provides a mechanism for lncRNA functional evolution.

Conclusions:

• The RIDL hypothesis offers a framework for understanding lncRNA functional evolution.
• TEs can be repurposed as functional domains within lncRNAs.
• Genomic maps of TEs may predict lncRNA function.