From 'JUNK' to just unexplored noncoding knowledge: the case of transcribed Alus

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Non-coding RNAs (ncRNAs) are crucial for diverse cellular functions.
• Repetitive elements, particularly primate-specific Alu repeats, constitute a significant portion of the human genome.
• Alu repeats are implicated in modulating gene expression and transcriptome complexity.

Purpose of the Study:

• To explore the functional roles of Alu repeats in the human genome.
• To understand how Alu repeats contribute to transcriptome modulation and primate-specific evolution.
• To investigate the interplay between RNA polymerase II (pol II) and RNA polymerase III (pol III) in Alu-mediated regulation.

Main Methods:

• Analysis of Alu repeat sequences for functional RNA Pol II transcription factor binding sites (TFBS).
• Investigation of Alu exonization events and their impact on RNA processing and miRNA targeting.
• Examination of Alu RNA expression levels under stress conditions.
• Review of recent findings on co-localization of pol II and pol III binding sites.

Main Results:

• Alu repeats harbor functional RNA Pol II TFBS, influence alternative splicing via exonization, and act as miRNA targets or sponges.
• Retro-transposition of Alu elements has shaped gene-specific regulatory networks.
• Alu exonized transcripts are substrates for RNA editing, affecting miRNA interactions and transcript localization.
• Co-localization of pol II and pol III sites suggests coordinated transcriptional regulation involving Alu elements.

Conclusions:

• Dynamic Alu repeats are central to modulating the human transcriptional landscape.
• Alu elements contribute significantly to the evolution of primate-specific regulatory repertoires and functions.
• Further research is needed to fully elucidate the functional significance of differential Alu RNA levels during stress.