Not long ago, much of the genome that doesn’t encode proteins was dismissed as junk DNA. But science has made it abundantly clear that long non-coding RNAs (IncRNAs) are far from junk.
In fact, their regulatory mechanisms make them promising therapeutic targets, as silencing a single lncRNA can lead to widespread biological effects.
lncRNAs are typically longer than 200 nucleotides, and while they do not code for proteins, they play crucial roles in regulating gene expression at the epigenetic, transcriptional, and post-transcriptional levels. They regulate gene expression by interacting with transcription factors, chromatin-modifying proteins, and microRNAs (miRNAs). Sometimes, IncRNAs form RNA-DNA triplex structures that physically block transcription or recruit methyltransferases to silence gene expression.
Because of their ability to control key regulatory networks and their tissue- and cell-specific expression patterns, lncRNAs have emerged as attractive targets for oligonucleotide-based therapeutics.
Targeting IncRNAs: Tools for therapeutic modulation
Several molecular tools are available to modulate IncRNA function for therapeutic purposes:
- Antisense oligonucleotides (ASOs): Short DNA-like molecules that bind to lncRNAs and trigger degradation or interfere with function.
- siRNA and shRNA: Small RNA molecules that guide the degradation of lncRNAs through RNA interference, either transiently (siRNA) or stably (shRNA).
- CRISPR/Cas9: Enables precise gene editing or knockout of lncRNA loci for functional studies or permanent modulation.
- Small molecules: Can bind lncRNAs to disrupt their secondary structure or block interactions with proteins or DNA.
These methods are particularly potent because lncRNAs often regulate entire networks of genes, meaning low doses of therapeutic agents can have strong biological effects.
Finding and validating IncRNA targets
Discovering promising lncRNA targets for drug development begins with deep RNA sequencing. RNA sequencing (RNA-seq) of healthy and diseased tissues or cells can reveal lncRNAs that are differentially expressed under specific conditions. Many lncRNAs also exhibit tissue-specific expression patterns, making them compelling candidates for precision medicine.
Standard technologies to evaluate the therapeutic potential of IncRNAs include:
- shRNA or CRISPR libraries to screen for IncRNAs that affect disease-relevant phenotypes.
- RNA-seq to monitor downstream effects through changes in gene expression profiles, identify biomarkers of target engagement and pharmacodynamic (PD) response, and assess potential off-target effects.
- qPCR and dPCR assays, using carefully designed primers, enable targeted quantification of the lncRNA itself, its silencing effect, or even detection of the therapeutic molecules (e.g., ASO, siRNA, or gRNA). Technologies like Two-Tailed PCR allow for absolute quantification of short RNA targets, which is especially valuable in biodistribution and pharmacokinetic (PK) studies.
- Gene expression analysis is also a critical tool for identifying novel lncRNAs and understanding how they influence regulatory networks, providing key insights into both mechanism of action and therapeutic safety.
IncRNA is the future of precision RNA therapeutics
While we still have much to learn about the full range of IncRNA functions, it’s clear they play essential regulatory roles in health and disease. They’re reported to be involved in cancer, cardiovascular disease, neurological disorders, diabetes, and more. Their tissue- and disease-specific expression and ability to control other regulatory molecules like transcription factors and miRNAs make them prime candidates for oligo therapeutics.
From once being considered genomic junk to being seen as key players in gene regulation and therapeutic innovation, lncRNAs represent a powerful and still largely untapped layer of biology.