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Ewing Sarcoma Related protein 1 recognizes R-loops by binding DNA forks.

Michelle A Lay1,2,3, Valery F Thompson1,2, Ajibola D Adelakun1,2,4

  • 1Department of Pharmacology, University of Arizona, Tucson, Arizona, USA.

Biopolymers
|March 21, 2024
PubMed
Summary
This summary is machine-generated.

Ewing Sarcoma Related protein 1 (EWSR1) binds R-loops, structures causing genomic stress. Its Zinc-finger and RNA recognition motifs specifically target DNA forks in R-loops, explaining its role in preventing genomic instability.

Keywords:
DNA bindingEWSR1Ewing sarcomaRNA bindingR‐loop

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • EWSR1 (Ewing Sarcoma Related protein 1) is a ubiquitous RNA-binding protein involved in RNA processing.
  • EWSR1 plays a role in regulating R-loop formation; aberrant R-loops cause genomic and transcriptional stress.
  • Loss of EWSR1 function is linked to increased R-loop abundance, particularly in Ewing Sarcoma.

Purpose of the Study:

  • To elucidate the specific mechanism by which EWSR1 recognizes and binds to R-loop structures.
  • To identify the molecular domains responsible for EWSR1's high-affinity binding and specificity to R-loops.

Main Methods:

  • Electrophoretic mobility shift assays (EMSA) were employed to assess EWSR1 binding to R-loop-related substrates.
  • Analysis focused on identifying the specific DNA regions within R-loops that EWSR1 interacts with.

Main Results:

  • EWSR1 demonstrated high-affinity binding to substrates mimicking R-loop components.
  • Specificity was mapped to the DNA fork region, the transition zone between double- and single-stranded DNA.
  • The Zinc-finger (ZnF) and RNA recognition motif (RRM) domains, along with flanking RGG domains, were identified as critical for binding affinity and specificity.

Conclusions:

  • EWSR1 utilizes its ZnF and RRM domains to specifically recognize and bind the DNA fork structures characteristic of R-loops.
  • This specific binding mechanism provides a rationale for EWSR1's role in mitigating R-loop-associated genomic stress across various cellular contexts.