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Dynamic post-transcriptional regulation during embryonic stem cell differentiation

Patrick R. van den Berg, Bogdan Budnik, View ORCID ProfileNikolai Slavov, Stefan Semrau
doi: https://doi.org/10.1101/123497
Patrick R. van den Berg
1Leiden Institute of Physics, Leiden University, Leiden, Zuid-Holland, 2333 CC, The Netherlands
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Bogdan Budnik
2Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, MA 02138, USA
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Nikolai Slavov
3Department of Bioengineering, Northeastern University, Boston, Massachusetts, MA 02115
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Stefan Semrau
1Leiden Institute of Physics, Leiden University, Leiden, Zuid-Holland, 2333 CC, The Netherlands
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Summary

During in vitro differentiation, pluripotent stem cells undergo extensive remodeling of their gene expression profile. While studied extensively at the transcriptome level, much less is known about protein dynamics. Here, we measured mRNA and protein levels of 7459 genes during differentiation of embryonic stem cells (ESCs). This comprehensive data set revealed pervasive discordance between mRNA and protein. The high temporal resolution of the data made it possible to determine protein turnover rates genome-wide by fitting a kinetic model. This model further enabled us to systematically identify dynamic post-transcriptional regulation. Moreover, we linked different modes of regulation to the function of specific gene sets. Finally, we showed that the kinetic model can be applied to singlecell transcriptomics data to predict protein levels in differentiated cell types. In conclusion, our comprehensive data set, easily accessible through a web application, is a valuable resource for the discovery of post-transcriptional regulation in ESC differentiation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 17, 2017.
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Dynamic post-transcriptional regulation during embryonic stem cell differentiation
Patrick R. van den Berg, Bogdan Budnik, Nikolai Slavov, Stefan Semrau
bioRxiv 123497; doi: https://doi.org/10.1101/123497
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Dynamic post-transcriptional regulation during embryonic stem cell differentiation
Patrick R. van den Berg, Bogdan Budnik, Nikolai Slavov, Stefan Semrau
bioRxiv 123497; doi: https://doi.org/10.1101/123497

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