Transfecting RNA quadruplexes results in few transcriptome perturbations

Area of Science:

• Molecular Biology
• Genomics
• RNA Biology

Background:

• Guanine-rich sequences form G-quadruplexes, with DNA versions inhibiting cancer cell proliferation.
• The impact of transfecting RNA quadruplexes on cellular gene expression remains largely unexplored.

Purpose of the Study:

• To investigate the effects of transfecting a G-quadruplex RNA oligonucleotide (GqRNA) into human cells.
• To identify specific genes and pathways affected by GqRNA transfection.

Main Methods:

• HEK293T cells were transfected with a GqRNA oligonucleotide.
• Transcriptome-wide expression profiling was performed to analyze gene expression changes.
• Bioinformatic analysis was used to identify putative quadruplex sequences (PQS) in gene 3'-UTRs.

Main Results:

• GqRNA transfection did not affect cell viability.
• Only EGR1 and FOS gene expression levels were significantly altered (2- to 4-fold upregulation).
• Putative quadruplex sequences were identified in the 3'-UTRs of EGR1 and FOS, adjacent to stop codons.

Conclusions:

• Transfecting RNA quadruplexes leads to limited alterations in the transcriptome.
• Specific RNA G-quadruplex motifs near stop codons may influence gene expression, warranting further investigation.