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A 5'-3' terminal stem in small non-coding RNAs extends their lifetime.

Anastasia P Koval1, Irina K Gogolevskaya1, Karina A Tatosyan1

  • 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.

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Creating a double-stranded stem in short non-coding RNAs significantly extends their lifespan. This finding suggests a general mechanism for stabilizing small RNAs, impacting gene regulation and RNA stability research.

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4.5S RNARNA lifetimeSINESecondary structureSmall non-coding RNA

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Genomics

Background:

  • 4.5SI and 4.5SH are non-coding RNAs synthesized by RNA polymerase III in rodents.
  • 4.5SI RNA has a long half-life attributed to its terminal double-stranded stem, while 4.5SH RNA decays rapidly due to the absence of this structure.

Purpose of the Study:

  • To investigate if creating a terminal double-stranded structure can prolong the half-life of other short-lived non-coding RNAs.
  • To explore the role of stem length and location in RNA stability.

Main Methods:

  • Engineered terminal double-stranded stems in short interspersed elements (SINEs) B2 and Rhin-1 RNAs.
  • Assessed RNA half-life changes after structural modifications.
  • Investigated the impact of stem length and internal stem disruption on RNA stability.

Main Results:

  • Replacing terminal regions of B2 and Rhin-1 RNAs with complementary sequences increased their half-life over fourfold.
  • Shortening the terminal stem of 4.5SI RNA from 16bp to 8bp only slightly decreased its lifetime.
  • Disrupting an internal stem in 4.5SI RNA did not accelerate its decay.

Conclusions:

  • A terminal double-stranded stem is a key factor in extending the half-life of small non-coding RNAs.
  • The length of the terminal stem influences RNA stability, but even shorter stems provide significant stabilization.
  • Internal stem structures do not appear to be critical for the stability of 4.5SI RNA.