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Related Concept Videos

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Related Experiment Video

Updated: Feb 24, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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HCR-Proxy resolves site-specific proximal RNA microenvironments at subcompartmental resolution.

Anja Trupej1,2,3,4, Valter Bergant1,5, Jona Novljan1,2,3,6

  • 1National Institute of Chemistry, Ljubljana, SIovenia.

Nucleic Acids Research
|February 23, 2026
PubMed
Summary
This summary is machine-generated.

A new technique, HCR-Proxy, maps protein architecture within RNA condensates at high resolution. This reveals how RNA sequence dictates protein organization in cellular compartments like the nucleolus.

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Area of Science:

  • Cell Biology
  • Molecular Biology
  • Biochemistry

Background:

  • RNA-scaffolded condensates are crucial for cellular functions and disease.
  • Mapping protein architecture within these condensates at subcompartmental resolution is challenging.

Purpose of the Study:

  • To develop a novel technology for high-resolution mapping of RNA-proximal proteomes.
  • To investigate the spatial organization and protein partitioning within nucleolar subcompartments.

Main Methods:

  • Introduced HCR-Proxy, a proximity labeling technique combining hybridization chain reaction (HCR) signal amplification with in situ proximity biotinylation (Proxy).
  • Applied HCR-Proxy to nascent pre-rRNA targets in the nucleolus.
  • Integrated results with deep learning frameworks.

Main Results:

  • HCR-Proxy enabled proteomic profiling of RNA-proximal proteomes at subcompartmental resolution.
  • Revealed distinct proteomic signatures of nucleolar subcompartments.
  • Uncovered RNA sequence-driven spatial logic of protein partitioning based on charge, molecular weight, and RNA-binding domains.

Conclusions:

  • HCR-Proxy provides spatially resolved maps of RNA interactomes within the nucleolus.
  • Demonstrated a sequence-encoded basis for protein organization in nested condensate subcompartments.
  • Established HCR-Proxy as a scalable platform for RNA interactome discovery, linking transcript localization with proteomic context.