Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation through mRNA lifespan with most impact on short tails

  1. Sandy Mattijssen
  2. James R Iben
  3. Tianwei Li
  4. Steven L Coon
  5. Richard J Maraia  Is a corresponding author
  1. Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Abstract

La-related protein 4 (LARP4) directly binds both poly(A) and poly(A)-binding protein (PABP). LARP4 was shown to promote poly(A) tail (PAT) lengthening and stabilization of individual mRNAs presumably by protection from deadenylation (Mattijssen et al., 2017). We developed a nucleotide resolution transcriptome-wide, single molecule SM-PAT-seq method. This revealed LARP4 effects on a wide range of PAT lengths for human mRNAs and mouse mRNAs from LARP4 knockout (KO) and control cells. LARP4 effects are clear on long PAT mRNAs but become more prominent at 30-75 nucleotides. We also analyzed time courses of PAT decay transcriptome-wide and for ~200 immune response mRNAs. This demonstrated accelerated deadenylation in KO cells on PATs <75 nucleotides and phasing features consistent with greater PABP dissociation in the absence of LARP4. Thus, LARP4 shapes PAT profiles throughout mRNA lifespan and with impact on mRNA decay at short lengths known to sensitize PABP dissociation in response to deadenylation machinery.

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All data generated or analysed during this study are included in the manuscript and supporting files.

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Author details

  1. Sandy Mattijssen

    Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. James R Iben

    Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Tianwei Li

    Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Steven L Coon

    Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Richard J Maraia

    Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
    For correspondence
    maraiar@dir6.nichd.nih.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5209-0066

Funding

Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD000412-31 PGD)

  • Richard J Maraia

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

Reviewing Editor

  1. Nahum Sonenberg, McGill University, Canada

Version history

  1. Received: June 2, 2020
  2. Accepted: August 2, 2020
  3. Accepted Manuscript published: August 3, 2020 (version 1)
  4. Version of Record published: August 7, 2020 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Sandy Mattijssen
  2. James R Iben
  3. Tianwei Li
  4. Steven L Coon
  5. Richard J Maraia
(2020)
Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation through mRNA lifespan with most impact on short tails
eLife 9:e59186.
https://doi.org/10.7554/eLife.59186

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https://doi.org/10.7554/eLife.59186

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