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Comprehensive identification of proteins interacting with long non-coding RNA TUG1 in R-loop regulation.

Jingqi Xie1, Miho M Suzuki1, Kenta Iijima2

  • 1Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan.

Journal of Biochemistry
|July 14, 2025
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Summary
This summary is machine-generated.

Taurine Upregulated Gene 1 (TUG1), a long non-coding RNA, interacts with proteins to maintain genomic integrity. This study identifies TUG1

Keywords:
R-loopRNA-binding proteinsTUG1long non-coding RNAproteomics

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Area of Science:

  • Molecular Biology
  • Genomics
  • RNA Biology

Background:

  • Long non-coding RNAs (lncRNAs) are crucial regulators of cellular processes via RNA-binding protein (RBP) interactions.
  • Taurine Upregulated Gene 1 (TUG1) is an overexpressed lncRNA in cancer, involved in R-loop resolution and genomic integrity maintenance.
  • The complete protein interaction landscape and stress response of TUG1 remain largely uncharacterized.

Purpose of the Study:

  • To comprehensively identify TUG1-interacting proteins using CRISPR-assisted RNA-protein interaction detection (CARPID).
  • To investigate the changes in TUG1-protein interactions under R-loop-inducing stress conditions.
  • To elucidate the role of TUG1 in genome maintenance through its protein interactions.

Main Methods:

  • CRISPR-assisted RNA-protein interaction detection (CARPID) coupled with mass spectrometry.
  • Utilized three distinct single-guide RNAs (sgRNAs) targeting TUG1 in HEK293T cells.
  • Analyzed protein interactions under basal and camptothecin (CPT)-induced R-loop stress conditions.

Main Results:

  • Identified 17 TUG1-interacting proteins under basal conditions.
  • Increased to 25 interacting proteins upon CPT treatment, indicating dynamic RBP binding.
  • Observed greater overlap in identified proteins under stress, suggesting a conserved R-loop response network.
  • Confirmed interactions with known R-loop factors like RNA helicases, PARP1, and HNRNPs.

Conclusions:

  • TUG1 interacts with a defined set of proteins to maintain genome integrity.
  • TUG1 actively engages R-loop regulatory machinery under stress.
  • Provides novel insights into lncRNA-mediated R-loop regulation and its contribution to genome stability.