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Related Experiment Video

Updated: Feb 15, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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Nucleotide-Resolution Mapping Reveals Specific MLE Binding Site on roX2 lncRNA.

Susmit Narayan Chaudhury1, Nathan Edward Jespersen1, Karissa Y Sanbonmatsu2

  • 1Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, United States.

Journal of Molecular Biology
|February 13, 2026
PubMed
Summary
This summary is machine-generated.

The RNA helicase MLE binds roX2 RNA, with ATP hydrolysis driving structural changes. This rearrangement exposes key motifs, influencing chromatin complex regulation during X-chromosome hyperactivation.

Keywords:
RNA-protein interactionX-chromosome inactivationchemical probinglncRNA structure

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • RNA Biology

Background:

  • Long noncoding RNAs (lncRNAs) function as scaffolds for chromatin complexes, but their structural dynamics and protein interactions are not well understood.
  • The RNA helicase MLE (Male-Less) is crucial for X-chromosome hyperactivation, incorporating roX RNAs into the MSL complex to increase X-linked gene expression.

Purpose of the Study:

  • To elucidate the nucleotide-level interactions between MLE and roX2 RNA.
  • To investigate how ATP hydrolysis influences MLE-mediated RNA remodeling.

Main Methods:

  • SHAPE chemical probing
  • Hydroxyl radical footprinting
  • Electrophoretic Mobility Shift Assay (EMSA)
  • Fluorescence polarization

Main Results:

  • MLE binds specific 5'-helices of roX2 RNA in an ATP-independent manner.
  • ATP hydrolysis induces localized unfolding in a 3'-domain helix, exposing the roX-box motif.
  • MLE interacts with specific nucleotides in R2H1-R2H3, followed by ATP-dependent rearrangement at the 3' end of roX2 RNA.

Conclusions:

  • Provides the first direct evidence of domain-specific MLE-roX2 interaction.
  • Demonstrates ATP-driven lncRNA rearrangement by a helicase.
  • Establishes a framework for understanding helicase-guided lncRNA structural changes in chromatin regulation.