Tunable protein synthesis by transcript isoforms in human cells

  1. Stephen N Floor
  2. Jennifer A Doudna  Is a corresponding author
  1. University of California, Berkeley, United States


Eukaryotic genes generate multiple mRNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profile and reconstructed transcript isoforms from each fraction, which we term Transcript Isoforms in Polysomes sequencing (TrIP-seq). Analysis of these data revealed regulatory features that control ribosome occupancy and translational output of each transcript isoform. We extracted a panel of 5′ and 3′ untranslated regions that control protein production from an unrelated gene in cells over a 100-fold range. Select 5′ untranslated regions exert robust translational control between cell lines, while 3′ untranslated regions can confer cell-type-specific expression. These results expose the large dynamic range of transcript-isoform-specific translational control, identify isoform-specific sequences that control protein output in human cells, and demonstrate that transcript isoform diversity must be considered when relating RNA and protein levels.

Article and author information

Author details

  1. Stephen N Floor

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Jennifer A Doudna

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Rachel Green, Johns Hopkins School of Medicine, United States

Publication history

  1. Received: August 17, 2015
  2. Accepted: January 5, 2016
  3. Accepted Manuscript published: January 6, 2016 (version 1)
  4. Version of Record published: February 10, 2016 (version 2)


© 2016, Floor & Doudna

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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  1. Stephen N Floor
  2. Jennifer A Doudna
Tunable protein synthesis by transcript isoforms in human cells
eLife 5:e10921.

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