Article | Published:

Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix

Nature Structural & Molecular Biology volume 21, pages 633640 (2014) | Download Citation

Abstract

Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a highly abundant nuclear long noncoding RNA that promotes malignancy. A 3′-stem-loop structure is predicted to confer stability by engaging a downstream A-rich tract in a triple helix, similar to the expression and nuclear retention element (ENE) from the KSHV polyadenylated nuclear RNA. The 3.1-Å-resolution crystal structure of the human MALAT1 ENE and A-rich tract reveals a bipartite triple helix containing stacks of five and four U•A-U triples separated by a C+•G-C triplet and C-G doublet, extended by two A-minor interactions. In vivo decay assays indicate that this blunt-ended triple helix, with the 3′ nucleotide in a U•A-U triple, inhibits rapid nuclear RNA decay. Interruption of the triple helix by the C-G doublet induces a 'helical reset' that explains why triple-helical stacks longer than six do not occur in nature.

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Protein Data Bank

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GenBank/EMBL/DDBJ

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Acknowledgements

We are grateful for staff assistance at Advanced Photon Source beamline 24-ID and National Synchrotron Light Source beamline X-25, plasmids from K. Prasanth (University of Illinois, Urbana-Champaign, pSV40-mMALAT1) and A. Alexandrov (Yale University, AVA2136) and iridium (III) hexamine trichloride from S. Strobel (Yale University). We thank P. Moore, K. Tycowski and J. Withers for critical review of the manuscript, A. Miccinello for editorial work and all Steitz-laboratory members for thoughtful discussions. This work was supported by US National Institutes of Health grants GM026154 (J.A.S.) and GM022778 (T.A.S.), a Postdoctoral Fellowship (grant 122267-PF-12-077-01-RMC) from the American Cancer Society (J.A.B.) and the Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Republic of Korea (J.W.). J.A.S. and T.A.S. are supported as investigators of the Howard Hughes Medical Institute.

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Affiliations

  1. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

    • Jessica A Brown
    • , Jimin Wang
    • , Max L Valenstein
    • , Thomas A Steitz
    •  & Joan A Steitz
  2. Department of Chemistry, Yale University, New Haven, Connecticut, USA.

    • David Bulkley
    •  & Thomas A Steitz
  3. Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA.

    • Therese A Yario
    • , Thomas A Steitz
    •  & Joan A Steitz

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Contributions

J.A.B. and J.A.S. designed research; J.A.B., D.B., M.L.V. and T.A.Y. performed research; J.A.B., D.B. and J.W. analyzed data; T.A.S. and J.A.S. oversaw research; J.A.B. and J.A.S. wrote the paper; and all authors discussed the results and commented on the manuscript.

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The authors declare no competing financial interests.

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Correspondence to Joan A Steitz.

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https://doi.org/10.1038/nsmb.2844

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