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Updated: Jun 8, 2026
09:12
Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
Published on: February 27, 2026
RNA folding during transcription: protocols and studies.
1Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois, USA.
Methods in Enzymology
|October 16, 2010
Summary
Cotranscriptional RNA folding studies mimic cellular RNA folding. Researchers identified key folding intermediates and pathways by mapping paused transcription complexes, offering insights into RNA structure formation during synthesis.
Area of Science:
- Molecular Biology
- Biochemistry
- Structural Biology
Background:
- In vitro studies often focus on refolding completed RNA transcripts, which differs from the in-cell environment.
- RNA folding occurs during transcription (cotranscriptional folding), influenced by factors like RNA polymerase activity and associated proteins.
Purpose of the Study:
- To investigate RNA folding as it occurs during transcription, providing a more biologically relevant model.
- To identify and characterize folding intermediates and pathways of nascent RNA transcripts.
Main Methods:
- Utilizing cotranscriptional folding studies that consider the 5' to 3' polarity and transcriptional dynamics.
- Employing structural mapping of paused transcription complexes to reveal folding intermediates.
- Monitoring cotranscriptional folding using oligohybridization assays and ribozyme catalytic activity (in cis or trans).
Main Results:
- Strategic pause sites in transcription provide insights into RNA folding pathways.
- Structural mapping identified crucial folding intermediates during nascent RNA synthesis.
- Methodologies were successfully applied to diverse RNAs, including RNase P, SRP, tmRNA, riboswitches, and ribozymes.
Conclusions:
- Cotranscriptional folding studies offer a more accurate representation of RNA folding in vivo.
- Understanding cotranscriptional folding is essential for elucidating RNA function and structure.
- The developed methodologies enable comprehensive analysis of RNA folding pathways for various RNA molecules.
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