RNA Double Helix with Modified Nucleotides

Decoding RNA: How Modifications Can Optimize Gene Regulation Therapies

Reese Marlowe in Science & Nature June 2025 • 4 min read.

"Scientists are one step closer to understanding how modified nucleotides can reduce immune responses and improve synthetic RNA design for gene regulation"

In the dynamic world of molecular biology, short regulatory RNAs are pivotal in guiding the maturation of major RNA species. Among these, small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) stand out. SnRNAs are central to the spliceosome, orchestrating the critical process of pre-mRNA splicing. SnoRNAs, on the other hand, direct post-transcriptional modifications of pre-rRNAs, fine-tuning the protein synthesis machinery.

A promising avenue for creating molecules that mimic the function of non-coding RNAs (ncRNAs) involves strategically introducing modified nucleotides—those naturally present in ncRNAs—into synthetic RNA structures. This approach has the potential to revolutionize therapeutic strategies, but it's not without its challenges. One significant hurdle is the non-specific activation of the cellular innate immune response system, often leading to an unwanted interferon response.

This article explores recent breakthroughs in understanding how nucleotide modifications impact the immune-stimulating activity of synthetic snRNA and snoRNA analogs. By delving into a whole-transcriptome study, we uncover how specific base modifications, such as pseudouridine (Y) and 5-methylcytidine (m5C), influence gene expression. Moreover, we'll examine the role of PKR, a key player in recognizing these RNA analogs, and how this knowledge can be harnessed to create more effective and safer gene regulation agents.

Tuning the Immune Response: The Role of Nucleotide Modifications

RNA Double Helix with Modified Nucleotides

One of the key challenges in harnessing synthetic RNAs for therapeutic purposes is their tendency to trigger a non-specific immune response. This response, characterized by the activation of interferon-dependent transcription, can alter the expression of numerous genes, obscuring the intended effects of the synthetic RNA. Researchers have been actively seeking ways to minimize this unwanted immune stimulation.

A pivotal study by Kariko et al. illuminated the importance of nucleotide modifications in modulating immune responses. They demonstrated that RNA isolated from the nucleus of mammalian cells induced a lower innate immune response compared to RNA from the cytoplasm or total cellular RNA. Conversely, mitochondrial RNA transfection triggered a robust immune response. These findings suggest that nucleotide modifications act as key signals for distinguishing between endogenous and exogenous RNA molecules.

Modifications Matter: Altering the nucleotide composition of synthetic RNAs can significantly reduce their immunogenicity.
Nuclear Inspiration: Mimicking the structure of nuclear RNAs, which are naturally less prone to triggering immune responses, can be a successful strategy.
PKR's Role: The protein kinase R (PKR) plays a crucial role in recognizing both modified and unmodified RNA analogs, influencing the downstream immune response.

Building on these insights, researchers have explored the use of nuclear and nucleolar RNA structures to design gene-specific regulators. By incorporating modified nucleotides, they aim to fine-tune the immune-stimulating activity of these synthetic RNAs, paving the way for more precise and targeted gene regulation.

The Future of RNA-Based Therapies

These findings highlight the critical role of nucleotide modifications in modulating the immune response to synthetic RNAs. By understanding how these modifications influence RNA stability, receptor interactions, and downstream signaling pathways, scientists can design more effective and safer RNA-based therapies. The ability to fine-tune gene expression through synthetic RNA analogs holds immense potential for treating a wide range of diseases, from cancer to genetic disorders.

About this Article -

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This article is based on research published under:

DOI-LINK: 10.3390/genes9110531, Alternate LINK

Title: Nucleotide Modifications Decrease Innate Immune Response Induced By Synthetic Analogs Of Snrnas And Snornas

Subject: Genetics (clinical)

Journal: Genes

Publisher: MDPI AG

Authors: Grigory Stepanov, Evgenii Zhuravlev, Victoria Shender, Anna Nushtaeva, Evgenia Balakhonova, Elena Mozhaeva, Marat Kasakin, Vladimir Koval, Alexander Lomzov, Marat Pavlyukov, Irina Malyants, Mikhail Zhorov, Tatyana Kabilova, Elena Chernolovskaya, Vadim Govorun, Elena Kuligina, Dmitry Semenov, Vladimir Richter

Published: 2018-11-02

Everything You Need To Know

What are snRNAs and snoRNAs, and why are they important in gene regulation?

Small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) are crucial for RNA maturation. SnRNAs are vital to the spliceosome, which is responsible for pre-mRNA splicing. SnoRNAs guide post-transcriptional modifications of pre-rRNAs, which are essential for protein synthesis. Mimicking the function of non-coding RNAs (ncRNAs) by adding modified nucleotides into synthetic RNA has therapeutic potential. Challenges arise from the activation of the innate immune response system, leading to an interferon response.

How do nucleotide modifications affect the immune response to synthetic RNAs?

Nucleotide modifications are essential to modulating immune responses to synthetic RNAs. RNA isolated from the nucleus induces a lower innate immune response compared to RNA from the cytoplasm. Mitochondrial RNA transfection triggers a robust immune response. These findings suggest that nucleotide modifications act as key signals for distinguishing between endogenous and exogenous RNA molecules. Altering the nucleotide composition of synthetic RNAs can significantly reduce their immunogenicity.

What is PKR, and what role does it play in the context of modified RNA?

The protein kinase R (PKR) plays a crucial role in recognizing both modified and unmodified RNA analogs, influencing the downstream immune response. Understanding PKR's role is critical for designing safer and more effective gene regulation agents. Further research into PKR's interactions with modified nucleotides could lead to the development of synthetic RNAs that are less likely to trigger unwanted immune responses.

Can you elaborate on specific nucleotide modifications like pseudouridine and 5-methylcytidine and their impact?

Modified nucleotides, such as pseudouridine (Ψ) and 5-methylcytidine (m5C), play a significant role in influencing gene expression. Understanding how these specific base modifications impact gene expression is essential for creating more effective and safer gene regulation agents. Future research may uncover additional modifications and their specific effects, leading to even more precise control over gene expression.

What is the future potential for RNA-based therapies, considering the role of nucleotide modifications?

By understanding how nucleotide modifications influence RNA stability, receptor interactions, and downstream signaling pathways, scientists can design more effective and safer RNA-based therapies. Fine-tuning gene expression through synthetic RNA analogs holds immense potential for treating a wide range of diseases, from cancer to genetic disorders. Further advancements in this field could revolutionize therapeutic strategies and provide new hope for treating previously incurable conditions.