1. Biochemistry and Chemical Biology
  2. Computational and Systems Biology
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Dissection of affinity captured LINE-1 macromolecular complexes

  1. Martin S Taylor
  2. Ilya Altukhov
  3. Kelly R Molloy
  4. Paolo Mita
  5. Hua Jiang
  6. Emily M Adney
  7. Aleksandra Wudzinska
  8. Sana Badri
  9. Dmitry Ischenko
  10. George Eng
  11. Kathleen H Burns
  12. David Fenyö
  13. Brian T Chait
  14. Dmitry Alexeev
  15. Michael P Rout
  16. Jef D Boeke
  17. John LaCava  Is a corresponding author
  1. Massachusetts General Hospital, United States
  2. Moscow Institute of Physics and Technology, Russian Federation
  3. The Rockefeller University, United States
  4. NYU Langone Medical Center, United States
  5. Johns Hopkins University School of Medicine, United States
  6. Novosibirsk State University, Russian Federation
Research Article
  • Cited 27
  • Views 3,520
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Cite this article as: eLife 2018;7:e30094 doi: 10.7554/eLife.30094

Abstract

Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications, quantitative mass spectrometry, and next generation RNA sequencing, we have characterized the proteins and nucleic acids associated with distinctive, enzymatically active L1 macromolecular complexes. Among them, we describe a cytoplasmic intermediate that we hypothesize to be the canonical ORF1p/ORF2p/L1-RNA-containing RNP, and we describe a nuclear population containing ORF2p, but lacking ORF1p, which likely contains host factors participating in target-primed reverse transcription.

Data availability

The following data sets were generated
    1. LaCava J
    (2017) RNA-seq FASTAQ files
    Publicly available at ProteomeXchange (accession no: PXD008542).
    http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD008542
    1. LaCava J
    (2017) RNAs associated with affinity captured LINE-1 ribonucleoproteins
    Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE108270).
    https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108270

Article and author information

Author details

  1. Martin S Taylor

    Department of Pathology, Massachusetts General Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Ilya Altukhov

    Department of Molecular and Bio Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9821-1890

  3. Kelly R Molloy

    Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Paolo Mita

    Institute for Systems Genetics, Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2093-4906

  5. Hua Jiang

    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Emily M Adney

    Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Aleksandra Wudzinska

    Institute for Systems Genetics, Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Sana Badri

    Department of Pathology, NYU Langone Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Dmitry Ischenko

    Department of Molecular and Bio Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.

  10. George Eng

    Department of Pathology, Massachusetts General Hospital, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.

  11. Kathleen H Burns

    McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1620-3761

  12. David Fenyö

    Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5049-3825

  13. Brian T Chait

    Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  14. Dmitry Alexeev

    Novosibirsk State University, Novosibirsk, Russian Federation
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0783-1176

  15. Michael P Rout

    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  16. Jef D Boeke

    Institute for Systems Genetics, Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5322-4946

  17. John LaCava

    Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
    For correspondence
    jlacava@rockefeller.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6307-7713

Funding

National Institutes of Health (P41GM109824)

  • Michael P Rout

National Institutes of Health (P41GM103314)

  • Brian T Chait

National Institutes of Health (P50GM107632)

  • Jef D Boeke

National Institutes of Health (R01GM654321)

  • Jef D Boeke

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Stephen P Goff, Howard Hughes Medical Institute, Columbia University, United States

Publication history

  1. Received: July 1, 2017
  2. Accepted: December 18, 2017
  3. Accepted Manuscript published: January 8, 2018 (version 1)
  4. Accepted Manuscript updated: January 10, 2018 (version 2)
  5. Version of Record published: February 21, 2018 (version 3)
  6. Version of Record updated: May 15, 2018 (version 4)
  7. Version of Record updated: September 11, 2018 (version 5)
  8. Version of Record updated: January 8, 2019 (version 6)

Copyright

© 2018, Taylor et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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Further reading

    1. Cell Biology

    LINE-1 protein localization and functional dynamics during the cell cycle

    Paolo Mita et al.
    Research Article Updated

    LINE-1/L1 retrotransposon sequences comprise 17% of the human genome. Among the many classes of mobile genetic elements, L1 is the only autonomous retrotransposon that still drives human genomic plasticity today. Through its co-evolution with the human genome, L1 has intertwined itself with host cell biology. However, a clear understanding of L1’s lifecycle and the processes involved in restricting its insertion and intragenomic spread remains elusive. Here we identify modes of L1 proteins’ entrance into the nucleus, a necessary step for L1 proliferation. Using functional, biochemical, and imaging approaches, we also show a clear cell cycle bias for L1 retrotransposition that peaks during the S phase. Our observations provide a basis for novel interpretations about the nature of nuclear and cytoplasmic L1 ribonucleoproteins (RNPs) and the potential role of DNA replication in L1 retrotransposition.

    1. Cell Biology
    2. Genetics and Genomics

    Retrotransposons: On the move

    Sandra L Martin
    Insight

    The mechanisms by which a retrotransposon called LINE-1 duplicates itself and spreads through the human genome are becoming clearer.

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    Myopalladin (MYPN) is a striated muscle-specific immunoglobulin domain-containing protein located in the sarcomeric Z-line and I-band. MYPN gene mutations are causative for dilated (DCM), hypertrophic and restrictive cardiomyopathy. In a yeast two-hybrid screening, MYPN was found to bind to titin in the Z-line, which was confirmed by microscale thermophoresis. Cardiac analyses of MYPN knockout (MKO) mice showed the development of mild cardiac dilation and systolic dysfunction, associated with decreased myofibrillar isometric tension generation and increased resting tension at longer sarcomere lengths. MKO mice exhibited a normal hypertrophic response to transaortic constriction (TAC), but rapidly developed severe cardiac dilation and systolic dysfunction, associated with fibrosis, increased fetal gene expression, higher intercalated disc fold amplitude, decreased calsequestrin-2 protein levels, and increased desmoplakin and SORBS2 protein levels. Cardiomyocyte analyses showed delayed Ca2+ release and reuptake in unstressed MKO mice as well as reduced Ca2+ spark amplitude post-TAC, suggesting that altered Ca2+ handling may contribute to the development of DCM in MKO mice.