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Updated: Oct 13, 2025

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Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA.

Arpita Ghosh1,2, Satya Prakash Pandey1,2, Asgar Hussain Ansari1,2

  • 1CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India.

Nucleic Acids Research
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Three conserved RNA-G-quadruplexes (rG4s) in MALAT1 regulate alternative splicing by binding proteins to nuclear speckles. Disrupting these rG4s alters gene splicing, revealing their crucial role.

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Area of Science:

  • Molecular Biology
  • Genetics
  • RNA Biology

Background:

  • Long non-coding RNA MALAT1 is abundant and localizes to nuclear speckles.
  • MALAT1 regulates alternative splicing (AS), but its molecular mechanism is unclear.

Purpose of the Study:

  • To elucidate the molecular basis of MALAT1's role in alternative splicing.
  • To investigate the role of RNA structures within MALAT1.

Main Methods:

  • RNA-G-quadruplex (rG4) domain-specific RNA-pull-down coupled with mass spectrometry.
  • RNA-immuno-precipitation and imaging techniques.
  • Site-directed mutagenesis to disrupt rG4 structures.

Main Results:

  • Identified three conserved, stable, parallel rG4s in the 3' region of MALAT1.
  • Demonstrated rG4-dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles.
  • rG4 disruption led to protein delocalization and altered pre-mRNA splicing of endogenous genes, mimicking NCL knockdown.

Conclusions:

  • Conserved rG4 structures in MALAT1's 3' region are critical for its function in regulating alternative splicing.
  • MALAT1 rG4s orchestrate AS by mediating the localization of key proteins like NCL and NPM to nuclear speckles.