The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

Mathias Munschauer (), Celina T. Nguyen, Klara Sirokman, Christina R. Hartigan, Larson Hogstrom, Jesse M. Engreitz, Jacob C. Ulirsch, Charles P. Fulco, Vidya Subramanian, Jenny Chen, Monica Schenone, Mitchell Guttman, Steven A. Carr and Eric S. Lander ()
Additional contact information
Mathias Munschauer: Broad Institute of MIT and Harvard
Celina T. Nguyen: Broad Institute of MIT and Harvard
Klara Sirokman: Broad Institute of MIT and Harvard
Christina R. Hartigan: Broad Institute of MIT and Harvard
Larson Hogstrom: Broad Institute of MIT and Harvard
Jesse M. Engreitz: Broad Institute of MIT and Harvard
Jacob C. Ulirsch: Broad Institute of MIT and Harvard
Charles P. Fulco: Broad Institute of MIT and Harvard
Vidya Subramanian: Broad Institute of MIT and Harvard
Jenny Chen: Broad Institute of MIT and Harvard
Monica Schenone: Broad Institute of MIT and Harvard
Mitchell Guttman: California Institute of Technology
Steven A. Carr: Broad Institute of MIT and Harvard
Eric S. Lander: Broad Institute of MIT and Harvard

Nature, 2018, vol. 561, issue 7721, 132-136

Abstract: Abstract The human genome contains thousands of long non-coding RNAs1, but specific biological functions and biochemical mechanisms have been discovered for only about a dozen2–7. A specific long non-coding RNA—non-coding RNA activated by DNA damage (NORAD)—has recently been shown to be required for maintaining genomic stability8, but its molecular mechanism is unknown. Here we combine RNA antisense purification and quantitative mass spectrometry to identify proteins that directly interact with NORAD in living cells. We show that NORAD interacts with proteins involved in DNA replication and repair in steady-state cells and localizes to the nucleus upon stimulation with replication stress or DNA damage. In particular, NORAD interacts with RBMX, a component of the DNA-damage response, and contains the strongest RBMX-binding site in the transcriptome. We demonstrate that NORAD controls the ability of RBMX to assemble a ribonucleoprotein complex—which we term NORAD-activated ribonucleoprotein complex 1 (NARC1)—that contains the known suppressors of genomic instability topoisomerase I (TOP1), ALYREF and the PRPF19–CDC5L complex. Cells depleted for NORAD or RBMX display an increased frequency of chromosome segregation defects, reduced replication-fork velocity and altered cell-cycle progression—which represent phenotypes that are mechanistically linked to TOP1 and PRPF19–CDC5L function. Expression of NORAD in trans can rescue defects caused by NORAD depletion, but rescue is significantly impaired when the RBMX-binding site in NORAD is deleted. Our results demonstrate that the interaction between NORAD and RBMX is important for NORAD function, and that NORAD is required for the assembly of the previously unknown topoisomerase complex NARC1, which contributes to maintaining genomic stability. In addition, we uncover a previously unknown function for long non-coding RNAs in modulating the ability of an RNA-binding protein to assemble a higher-order ribonucleoprotein complex.

Keywords: Antisense Purification; Replication Fork Velocity; Crosslinking And Immunoprecipitation (CLIP); Supplemented Cell Culture Medium; Pumilio Proteins (PUM2) (search for similar items in EconPapers)
Date: 2018
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DOI: 10.1038/s41586-018-0453-z

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