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Related Concept Videos

Translational Regulation01:29

Translational Regulation

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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mRNA Interactome Capture from Plant Protoplasts
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Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.

Mason W Eisenhauer1, Abdelraouf O Dapour2, Warren B Rouse1

  • 1Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States.

Frontiers in Plant Science
|December 12, 2025
PubMed
Summary

Global temperature rise impacts agriculture. This study reveals how RNA secondary structures in maize (Zea mays) change with heat, offering insights into plant thermotolerance and food security.

Keywords:
RNA structureScanFoldZea mayscovariationheat shock factorsheat stress

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Area of Science:

  • Plant Biology
  • Genomics
  • Computational Biology

Background:

  • Rising global temperatures pose significant threats to agriculture and food security.
  • Plant responses to heat stress are regulated at transcriptional and post-transcriptional levels.
  • RNA secondary structure is an emerging key regulator in plant heat stress responses.

Purpose of the Study:

  • To characterize RNA secondary structure-function relationships in *Zea mays* (maize).
  • To identify temperature-sensitive RNA structures in the maize transcriptome.
  • To analyze the role of RNA structure in maize thermotolerance using heat shock factors as a case study.

Main Methods:

  • Computational approach (ScanFold) to build a transcriptome-wide database of RNA secondary structures.
  • Analysis of RNA structures across a temperature range (28°C to 42°C).
  • In-depth analysis of two maize heat shock factors (*ZmHsf04* and *ZmHsf17*).

Main Results:

  • Identified evolutionarily conserved, temperature-sensitive RNA structures in the maize transcriptome.
  • Many predicted RNA structures show sequence covariation, indicating functional importance.
  • Several key RNA structures exhibited significant conformational changes with increasing temperatures, particularly in *ZmHsf04* and *ZmHsf17*.

Conclusions:

  • Identified RNA structures in *ZmHsf04* and *ZmHsf17* may regulate gene expression via dynamic conformational changes.
  • These findings provide a framework for understanding RNA structure's role in maize heat response.
  • The developed dataset and methodology offer a robust approach for plant abiotic stress research.