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Tunable protein synthesis by transcript isoforms in human cells.

Floor SN, Doudna JA - Elife (2016)

Bottom Line: 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).Select 5' untranslated regions exert robust translational control between cell lines, while 3' untranslated regions can confer cell type-specific expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.

ABSTRACT
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.

No MeSH data available.


Additional examples of transcript isoforms that exhibit differential expression in human embryos and differential translation in TrIP-seq data.DOI:http://dx.doi.org/10.7554/eLife.10921.016
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fig4s2: Additional examples of transcript isoforms that exhibit differential expression in human embryos and differential translation in TrIP-seq data.DOI:http://dx.doi.org/10.7554/eLife.10921.016

Mentions: We then collected genes with isoforms that change between early and late embryonic stages. Clustering of abundances for 45,895 isoforms across embryogenesis yielded seven clusters with varying profiles, which we then analyzed by comparing transcripts of the same gene located in different embryonic clusters as before (Figure 4—figure supplement 1A). These isoforms were filtered by those that move between low- and high-polysome clusters in the TrIP-seq data, yielding 366 isoform pairs belonging to 270 genes that are developmentally regulated and exhibit differential translation in HEK 293T cells. For example, the CSDE1 gene expresses one isoform in oocytes, early development and in human ES cells, which is poorly translated (CSDE1-002), but a second appears following fertilization that is well-translated (CSDE1-007; Figure 4B,C). As global zygotic transcription begins in the two-cell stage (Vassena et al., 2011; Yan et al., 2013), it is possible that the alternative CSDE1 isoform is supplied by the spermatid (Fischer et al., 2012; Soumillon et al., 2013) or that it may be precociously transcribed. We also present three other genes (EIF4A2, RNF170, and TBC1D15) that show stage-specific expression in the embryo data and differential polysome association in HEK 293T cells (Figure 4—figure supplement 2). Therefore, widespread changes at the transcriptome level during human embryogenesis may produce concomitant changes in protein production, which can now be predicted using TrIP-seq data.


Tunable protein synthesis by transcript isoforms in human cells.

Floor SN, Doudna JA - Elife (2016)

Additional examples of transcript isoforms that exhibit differential expression in human embryos and differential translation in TrIP-seq data.DOI:http://dx.doi.org/10.7554/eLife.10921.016
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4764583&req=5

fig4s2: Additional examples of transcript isoforms that exhibit differential expression in human embryos and differential translation in TrIP-seq data.DOI:http://dx.doi.org/10.7554/eLife.10921.016
Mentions: We then collected genes with isoforms that change between early and late embryonic stages. Clustering of abundances for 45,895 isoforms across embryogenesis yielded seven clusters with varying profiles, which we then analyzed by comparing transcripts of the same gene located in different embryonic clusters as before (Figure 4—figure supplement 1A). These isoforms were filtered by those that move between low- and high-polysome clusters in the TrIP-seq data, yielding 366 isoform pairs belonging to 270 genes that are developmentally regulated and exhibit differential translation in HEK 293T cells. For example, the CSDE1 gene expresses one isoform in oocytes, early development and in human ES cells, which is poorly translated (CSDE1-002), but a second appears following fertilization that is well-translated (CSDE1-007; Figure 4B,C). As global zygotic transcription begins in the two-cell stage (Vassena et al., 2011; Yan et al., 2013), it is possible that the alternative CSDE1 isoform is supplied by the spermatid (Fischer et al., 2012; Soumillon et al., 2013) or that it may be precociously transcribed. We also present three other genes (EIF4A2, RNF170, and TBC1D15) that show stage-specific expression in the embryo data and differential polysome association in HEK 293T cells (Figure 4—figure supplement 2). Therefore, widespread changes at the transcriptome level during human embryogenesis may produce concomitant changes in protein production, which can now be predicted using TrIP-seq data.

Bottom Line: 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).Select 5' untranslated regions exert robust translational control between cell lines, while 3' untranslated regions can confer cell type-specific expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.

ABSTRACT
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.

No MeSH data available.