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Published on: May 24, 2017
Mapping RNA structure assembly and remodeling in biomolecular condensates.
Ritwika Bose1,2, Erik W Bergstrom3, Sovanny R Taylor1,4
1Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX.
Biorxiv : the Preprint Server for Biology
|June 4, 2026
Summary
Researchers developed RAID-MaP to measure RNA structure inside biomolecular condensates. This method revealed spatial regulation of RNA folding and structure, uncovering a new layer of gene regulation within cells.
Area of Science:
- Molecular Biology
- Biochemistry
- Cell Biology
Background:
- Biomolecular condensates are crucial for RNA processing and gene regulation.
- Measuring RNA structure within native condensates is a significant challenge.
- RNA structure plays a key role in its function and regulation.
Purpose of the Study:
- To develop a method for measuring RNA structure within subcellular compartments.
- To investigate RNA folding and maturation within the nucleolus.
- To explore the role of RNA structure in gene regulation by condensates.
Main Methods:
- Introduced RAID-MaP (RNA structure probing by APEX-proximity labeling and dimethyl sulfate probing).
- Combined APEX proximity labeling with dimethyl sulfate (DMS) chemical probing.
- Applied RAID-MaP to ribosomal RNA (rRNA) in the nucleolus and 7SK small nuclear RNA.
Main Results:
- Resolved late-stage rRNA folding within the nucleolar granular component, showing structural differences from mature ribosomes.
- Determined rRNA maturation kinetics, revealing domain-level ordering and stabilization by nucleolar factors.
- Demonstrated a link between rRNA folding, phase separation, and nucleolar phenotypes.
- Discovered spatially regulated structural switching of 7SK RNA linked to transcription factor release.
Conclusions:
- RAID-MaP enables measurement of RNA structure within native biomolecular condensates.
- Subcellular spatial control of RNA structure is a novel regulatory mechanism.
- RNA folding and structure within condensates are critical for RNA processing and gene regulation.
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