Mechanism of efficient double-strand break repair by a long non-coding RNA

Abstract Mechanistic studies in DNA repair have focused on roles of multi-protein DNA complexes, so how long non-coding RNAs (lncRNAs) regulate DNA repair is less well understood. Yet, lncRNA LINP1 is over-expressed in multiple cancers and confers resistance to ionizing radiation and chemotherapeutic drugs. Here, we unveil structural and mechanistic insights into LINP1’s ability to facilitate non-homologous end joining (NHEJ). We characterized LINP1 structure and flexibility and analyzed interactions with the NHEJ factor Ku70/Ku80 (Ku) and Ku complexes that direct NHEJ. LINP1 self-assembles into phase-separated condensates via RNA–RNA interactions that reorganize to form filamentous Ku-containing aggregates. Structured motifs in LINP1 bind Ku, promoting Ku multimerization and stabilization of the initial synaptic event for NHEJ. Significantly, LINP1 acts as an effective proxy for PAXX. Collective results reveal how lncRNA effectively replaces a DNA repair protein for efficient NHEJ with implications for development of resistance to cancer therapy.

• Publication year

  2020

• Venue

  Nucleic Acids Research

• Publication date

  2020-10-12

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/nar/gkaa784PMID 33045735PMCID 7641761
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2018influential reference
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  2018influential reference
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• Detection and repair of ionizing radiation-induced DNA double strand breaks: new developments in nonhomologous end joining.

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• Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

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