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Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs.

Grigory Stepanov1,2, Evgenii Zhuravlev3, Victoria Shender4,5

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Summary
This summary is machine-generated.

Synthetic small nucleolar RNAs (snoRNAs) and small nuclear RNAs (snRNAs) with modified bases were studied for their immune effects. Nucleotide modifications influence gene expression and RNA recognition by PKR, aiding in the development of gene regulation agents.

Keywords:
PKRRNA modificationRNA-Seqinnate immune responsesmall nuclear RNAssmall nucleolar RNAssynthetic RNA analogs

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Gene Regulation

Background:

  • Short nuclear regulatory RNAs, including small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs), are crucial for RNA processing and modification.
  • Synthetic non-coding RNAs (ncRNAs) incorporating natural modified nucleotides offer a strategy for developing novel RNA-based therapeutics.
  • Pseudouridine (Ψ) and 5-methylcytidine (m⁵C) are common modifications found in natural ncRNAs.

Purpose of the Study:

  • To investigate the impact of pseudouridine (Ψ) and 5-methylcytidine (m⁵C) modifications on the immune-stimulating and cytotoxic properties of synthetic snoRNA and snRNA analogs.
  • To perform a whole-transcriptome analysis of gene expression changes induced by modified synthetic snoRNA analogs in human cells.
  • To confirm the involvement of Protein Kinase R (PKR) in the cellular recognition of these synthetic RNA analogs.

Main Methods:

  • Synthesis of snoRNA and snRNA analogs with specific base modifications (Ψ, m⁵C).
  • Whole-transcriptome sequencing to assess gene expression profiles in human cells treated with modified analogs.
  • Short hairpin RNA (shRNA) mediated knockdown of PKR to evaluate its role in RNA analog recognition.

Main Results:

  • Synthetic snoRNA and snRNA analogs with Ψ and m⁵C modifications exhibit distinct immune-stimulating and cytotoxic effects.
  • Modified snoRNA analogs significantly alter global gene expression in human cells.
  • PKR plays a critical role in the cellular response to both snoRNA and snRNA analogs, as demonstrated by shRNA experiments.

Conclusions:

  • Nucleotide modifications in synthetic snoRNAs and snRNAs significantly influence their biological activity and gene expression profiles.
  • PKR is a key mediator in the recognition and response to these synthetic RNA molecules.
  • The findings provide valuable insights for designing RNA-based agents for gene regulation utilizing natural snoRNA and snRNA structures.