Embryonic Stem Cells Exhibit mRNA Isoform Specific Translational Regulation

PloS One
Queenie Wing-Lei WongLeah A Vardy

Abstract

The presence of multiple variants for many mRNAs is a major contributor to protein diversity. The processing of these variants is tightly controlled in a cell-type specific manner and has a significant impact on gene expression control. Here we investigate the differential translation rates of individual mRNA variants in embryonic stem cells (ESCs) and in ESC derived Neural Precursor Cells (NPCs) using polysome profiling coupled to RNA sequencing. We show that there are a significant number of detectable mRNA variants in ESCs and NPCs and that many of them show variant specific translation rates. This is correlated with differences in the UTRs of the variants with the 5'UTR playing a predominant role. We suggest that mRNA variants that contain alternate UTRs are under different post-transcriptional controls. This is likely due to the presence or absence of miRNA and protein binding sites that regulate translation rate. This highlights the importance of addressing translation rate when using mRNA levels as a read out of protein abundance. Additional analysis shows that many annotated non-coding mRNAs are present on the polysome fractions in ESCs and NPCs. We believe that the use of polysome fractionation coupled to RNA sequencin...Continue Reading

References

Jan 14, 2003·Nature Biotechnology·Qi-Long YingAustin Smith
Aug 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jerome AubertAustin Smith
Dec 5, 2006·Methods in Enzymology·Steven M PollardSally Lowell
Feb 8, 2008·The EMBO Journal·Sven DanckwardtAndreas E Kulozik
Apr 18, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sarah E CalvoVamsi K Mootha
Apr 18, 2009·Proceedings of the National Academy of Sciences of the United States of America·Zhe JiBin Tian
Jun 23, 2009·Development·Ian Chambers, Simon R Tomlinson
Dec 19, 2009·Nature Reviews. Genetics·Donny D Licatalosi, Robert B Darnell
May 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Nathan SalomonisBruce R Conklin
Jun 11, 2010·Annual Review of Biochemistry·Marc Robert FabianWitold Filipowicz
Feb 18, 2011·Journal of Cell Science·Miho IbiMasaki Inagaki
Jul 1, 2010·Wiley Interdisciplinary Reviews. RNA·Sandy MattijssenGer J M Pruijn
Apr 25, 2012·The Journal of Cell Biology·Akihito InokoMasaki Inagaki
Jun 8, 2012·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Meng Amy Li, Lin He
Jul 10, 2012·Nucleic Acids Research·Eleonora de KlerkPeter A C 't Hoen
Sep 8, 2012·Nature·Sarah DjebaliThomas R Gingeras
Sep 27, 2012·IUBMB Life·Carly J HynesThomas Preiss
Dec 12, 2012·Cell Research·Jia-Chi Yeo, Huck-Hui Ng
Jun 21, 2013·Genome Research·Timothy Sterne-WeilerJeremy R Sanford
Aug 21, 2013·PLoS Genetics·Cristina BarbosaLuísa Romão
Nov 28, 2013·Proceedings of the National Academy of Sciences of the United States of America·Kin Fai AuWing Hung Wong
Mar 29, 2014·Nature·Alistair R R ForrestYoshihide Hayashizaki
Jun 7, 2014·Cell Stem Cell·Thorold W Theunissen, Rudolf Jaenisch
Sep 6, 2014·Cell Stem Cell·Julia Ye, Robert Blelloch
Sep 19, 2014·ELife·Jorge Ruiz-OreraM Mar Alba
Jan 27, 2015·World Journal of Stem Cells·Kenian ChenJiaqian Wu
Feb 5, 2015·Trends in Genetics : TIG·Eleonora de Klerk, Peter A C 't Hoen

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Citations

Nov 21, 2017·The Journal of Reproduction and Development·Kohta KikuchiManabu Kawahara
Jan 8, 2021·Frontiers in Genetics·Shuxia ZhangYoufa Zhou
Jul 18, 2021·Nature Reviews. Molecular Cell Biology·James A SabaFiona M Watt

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Datasets Mentioned

BETA
GSE73467

Methods Mentioned

BETA
RNAseq
RNA seq
PCR
transfection
footprinting
flow cytometry
Assay

Software Mentioned

Partek Genomics Suite
LifeScope
UCSC browser
Partek

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