Functional characterization of RNA fragments using high-throughput interactome screening.

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Small RNA fragments (RFs) from non-coding RNAs are increasingly recognized but their biogenesis and function are unclear.
• RF formation is cell/tissue-specific and influenced by internal/external stimuli.
• Novel RNA-protein interactions are revealing new regulatory mechanisms.

Purpose of the Study:

• To investigate the protein interaction partners of seven selected RFs derived from tRNA, snoRNA, and snRNA.
• To construct an RF interactome network and compare it to the interactome of full-length parental RNAs.
• To explore the potential of RFs as endogenous aptamer-like molecules in RNA-protein regulatory networks.

Main Methods:

• RNA pull-down assays coupled with mass spectrometry to identify RF-interacting proteins.
• Integration of experimental data with publicly available protein-protein interaction databases.
• Construction and analysis of an RF interactome network.

Main Results:

• Seven RFs from tRNA, snoRNA, and snRNA were characterized for protein interactions.
• The RF interactome network revealed proteins involved in mRNA splicing, tRNA processing, DNA replication, protein biosynthesis, and metabolism.
• RFs interact with a distinct set of proteins compared to their parental full-length RNAs.

Conclusions:

• RNA fragments (RFs) exhibit unique protein-binding profiles, differing from their parent RNAs.
• RFs may function as endogenous aptamer-like molecules, engaging in unconventional RNA-protein interactions.
• These findings highlight RFs as significant components of newly discovered RNA-protein regulatory networks.