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Elife. 2016 Jan 6;5. pii: e10921. doi: 10.7554/eLife.10921.

Tunable protein synthesis by transcript isoforms in human cells.

Floor SN1,2, Doudna JA1,2,3,4,5.

Author information

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.
Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.
Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States.
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.
Department of Chemistry, University of California, Berkeley, Berkeley, California, United States.


Eukaryotic genes generate multiple RNA 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.


RNA processing; RNA-seq; chromosomes; computational biology; deep sequencing; engineered translation; genes; human; systems biology; transcript isoforms; translational control

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