Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A unifying model for mTORC1-mediated regulation of mRNA translation


The mTOR complex 1 (mTORC1) kinase nucleates a pathway that promotes cell growth and proliferation and is the target of rapamycin, a drug with many clinical uses1. mTORC1 regulates messenger RNA translation, but the overall translational program is poorly defined and no unifying model exists to explain how mTORC1 differentially controls the translation of specific mRNAs. Here we use high-resolution transcriptome-scale ribosome profiling to monitor translation in mouse cells acutely treated with the mTOR inhibitor Torin 1, which, unlike rapamycin, fully inhibits mTORC1 (ref. 2). Our data reveal a surprisingly simple model of the mRNA features and mechanisms that confer mTORC1-dependent translation control. The subset of mRNAs that are specifically regulated by mTORC1 consists almost entirely of transcripts with established 5′ terminal oligopyrimidine (TOP) motifs, or, like Hsp90ab1 and Ybx1, with previously unrecognized TOP or related TOP-like motifs that we identified. We find no evidence to support proposals that mTORC1 preferentially regulates mRNAs with increased 5′ untranslated region length or complexity3. mTORC1 phosphorylates a myriad of translational regulators, but how it controls TOP mRNA translation is unknown4. Remarkably, loss of just the 4E-BP family of translational repressors, arguably the best characterized mTORC1 substrates, is sufficient to render TOP and TOP-like mRNA translation resistant to Torin 1. The 4E-BPs inhibit translation initiation by interfering with the interaction between the cap-binding protein eIF4E and eIF4G1. Loss of this interaction diminishes the capacity of eIF4E to bind TOP and TOP-like mRNAs much more than other mRNAs, explaining why mTOR inhibition selectively suppresses their translation. Our results clarify the translational program controlled by mTORC1 and identify 4E-BPs and eIF4G1 as its master effectors.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Profile of mTOR-regulated translation.
Figure 2: Translation of TOP and TOP-like mRNAs is hypersensitive to mTOR inhibition.
Figure 3: mTOR regulates general protein synthesis and TOP mRNA translation through the 4E-BPs.
Figure 4: Destabilization of the eIF4E–eIF4G1 interaction dissociates TOP mRNAs from eIF4E and inhibits their translation.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

Small RNA sequencing data were deposited in the Gene Expression Omnibus ( under accession number GSE36892.


  1. 1

    Zoncu, R., Efeyan, A. & Sabatini, D. M. mTOR: from growth signal integration to cancer, diabetes and ageing. Nature Rev. Mol. Cell Biol. 12, 21–35 (2011)

    CAS  Article  Google Scholar 

  2. 2

    Thoreen, C. C. et al. An ATP-competitive mammalian target of rapamycin inhibitor reveals rapamycin-resistant functions of mTORC1. J. Biol. Chem. 284, 8023–8032 (2009)

    CAS  Article  Google Scholar 

  3. 3

    Hay, N. & Sonenberg, N. Upstream and downstream of mTOR. Genes Dev. 18, 1926–1945 (2004)

    CAS  Article  Google Scholar 

  4. 4

    Patursky-Polischuk, I. et al. The TSC-mTOR pathway mediates translational activation of TOP mRNAs by insulin largely in a raptor- or rictor-independent manner. Mol. Cell. Biol. 29, 640–649 (2009)

    CAS  Article  Google Scholar 

  5. 5

    Bilanges, B. et al. Tuberous sclerosis complex proteins 1 and 2 control serum-dependent translation in a TOP-dependent and -independent manner. Mol. Cell. Biol. 27, 5746–5764 (2007)

    CAS  Article  Google Scholar 

  6. 6

    Gera, J. F. et al. AKT activity determines sensitivity to mammalian target of rapamycin (mTOR) inhibitors by regulating cyclin D1 and c-myc expression. J. Biol. Chem. 279, 2737–2746 (2004)

    CAS  Article  Google Scholar 

  7. 7

    Grolleau, A. et al. Global and specific translational control by rapamycin in T cells uncovered by microarrays and proteomics. J. Biol. Chem. 277, 22175–22184 (2002)

    CAS  Article  Google Scholar 

  8. 8

    Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009)

    CAS  ADS  Article  Google Scholar 

  9. 9

    Redman, K. L. & Rechsteiner, M. Identification of the long ubiquitin extension as ribosomal protein S27a. Nature 338, 438–440 (1989)

    CAS  ADS  Article  Google Scholar 

  10. 10

    Mokrejs, M. et al. IRESite—a tool for the examination of viral and cellular internal ribosome entry sites. Nucleic Acids Res. 38, D131–D136 (2010)

    CAS  Article  Google Scholar 

  11. 11

    Kozak, M. A second look at cellular mRNA sequences said to function as internal ribosome entry sites. Nucleic Acids Res. 33, 6593–6602 (2005)

    CAS  Article  Google Scholar 

  12. 12

    Martin, F. et al. Cap-assisted internal initiation of translation of histone H4. Mol. Cell 41, 197–209 (2011)

    CAS  Article  Google Scholar 

  13. 13

    Meyuhas, O. Synthesis of the translational apparatus is regulated at the translational level. Eur. J. Biochem. 267, 6321–6330 (2000)

    CAS  Article  Google Scholar 

  14. 14

    De Benedetti, A. & Graff, J. R. eIF-4E expression and its role in malignancies and metastases. Oncogene 23, 3189–3199 (2004)

    CAS  Article  Google Scholar 

  15. 15

    Shi, Y., Sharma, A., Wu, H., Lichtenstein, A. & Gera, J. Cyclin D1 and c-myc internal ribosome entry site (IRES)-dependent translation is regulated by AKT activity and enhanced by rapamycin through a p38 MAPK- and ERK-dependent pathway. J. Biol. Chem. 280, 10964–10973 (2005)

    CAS  Article  Google Scholar 

  16. 16

    Dowling, R. J. et al. mTORC1-mediated cell proliferation, but not cell growth, controlled by the 4E-BPs. Science 328, 1172–1176 (2010)

    CAS  ADS  Article  Google Scholar 

  17. 17

    Jefferies, H. B., Reinhard, C., Kozma, S. C. & Thomas, G. Rapamycin selectively represses translation of the “polypyrimidine tract” mRNA family. Proc. Natl Acad. Sci. USA 91, 4441–4445 (1994)

    CAS  ADS  Article  Google Scholar 

  18. 18

    Iadevaia, V., Caldarola, S., Tino, E., Amaldi, F. & Loreni, F. All translation elongation factors and the e, f, and h subunits of translation initiation factor 3 are encoded by 5′-terminal oligopyrimidine (TOP) mRNAs. RNA 14, 1730–1736 (2008)

    CAS  Article  Google Scholar 

  19. 19

    Yamashita, R., Wakaguri, H., Sugano, S., Suzuki, Y. & Nakai, K. DBTSS provides a tissue specific dynamic view of transcription start sites. Nucleic Acids Res. 38, D98–D104 (2010)

    CAS  Article  Google Scholar 

  20. 20

    Lamouille, S. & Derynck, R. Cell size and invasion in TGF-β-induced epithelial to mesenchymal transition is regulated by activation of the mTOR pathway. J. Cell Biol. 178, 437–451 (2007)

    CAS  Article  Google Scholar 

  21. 21

    Thiery, J. P., Acloque, H., Huang, R. Y. & Nieto, M. A. Epithelial-mesenchymal transitions in development and disease. Cell 139, 871–890 (2009)

    CAS  Article  Google Scholar 

  22. 22

    Jefferies, H. B. et al. Rapamycin suppresses 5′TOP mRNA translation through inhibition of p70s6k. EMBO J. 16, 3693–3704 (1997)

    CAS  Article  Google Scholar 

  23. 23

    Pende, M. et al. S6K1−/−/S6K2−/− mice exhibit perinatal lethality and rapamycin-sensitive 5′-terminal oligopyrimidine mRNA translation and reveal a mitogen-activated protein kinase-dependent S6 kinase pathway. Mol. Cell. Biol. 24, 3112–3124 (2004)

    CAS  Article  Google Scholar 

  24. 24

    Choo, A. Y., Yoon, S. O., Kim, S. G., Roux, P. P. & Blenis, J. Rapamycin differentially inhibits S6Ks and 4E-BP1 to mediate cell-type-specific repression of mRNA translation. Proc. Natl Acad. Sci. USA 105, 17414–17419 (2008)

    CAS  ADS  Article  Google Scholar 

  25. 25

    Feldman, M. E. et al. Active-site inhibitors of mTOR target rapamycin-resistant outputs of mTORC1 and mTORC2. PLoS Biol. 7, e38 (2009)

    Article  Google Scholar 

  26. 26

    Ptushkina, M. et al. Cooperative modulation by eIF4G of eIF4E-binding to the mRNA 5′ cap in yeast involves a site partially shared by p20. EMBO J. 17, 4798–4808 (1998)

    CAS  Article  Google Scholar 

  27. 27

    Harris, T. E. et al. mTOR-dependent stimulation of the association of elF4G and elF3 by insulin. EMBO J 25, 1659–1668 (2006)

    CAS  Article  Google Scholar 

  28. 28

    Lee, S. H. & McCormick, F. p97/DAP5 is a ribosome-associated factor that facilitates protein synthesis and cell proliferation by modulating the synthesis of cell cycle proteins. EMBO J. 25, 4008–4019 (2006)

    CAS  Article  Google Scholar 

  29. 29

    Ramirez-Valle, F., Braunstein, S., Zavadil, J., Formenti, S. C. & Schneider, R. J. eIF4GI links nutrient sensing by mTOR to cell proliferation and inhibition of autophagy. J. Cell Biol. 181, 293–307 (2008)

    CAS  Article  Google Scholar 

  30. 30

    Liu, Q. et al. Discovery of 1-(4-(4-propionylpiperazin-1-yl)-3-(trifluoromethyl)phenyl)-9-(quinolin-3- yl)benzo[h][1,6]naphthyridin-2(1H)-one as a highly potent, selective mammalian target of rapamycin (mTOR) inhibitor for the treatment of cancer. J. Med. Chem. 53, 7146–7155 (2010)

    CAS  ADS  Article  Google Scholar 

  31. 31

    Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006)

    CAS  Article  Google Scholar 

  32. 32

    Ali, S. M. & Sabatini, D. M. Structure of S6 kinase 1 determines whether raptor-mTOR or rictor-mTOR phosphorylates its hydrophobic motif site. J. Biol. Chem. 280, 19445–19448 (2005)

    CAS  Article  Google Scholar 

  33. 33

    Levine, E. M., Becker, Y., Boone, C. W. & Eagle, H. Contact inhibition, macromolecular synthesis, and polyribosomes in cultured human diploid fibroblasts. Proc. Natl Acad. Sci. USA 53, 350–356 (1965)

    CAS  ADS  Article  Google Scholar 

  34. 34

    Langmead, B. Aligning short sequencing reads with Bowtie. Curr. Protoc. Bioinformatics Chapter 11, Unit 11.7. (2010)

  35. 35

    Guo, H., Ingolia, N. T., Weissman, J. S. & Bartel, D. P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466, 835–840 (2010)

    CAS  ADS  Article  Google Scholar 

  36. 36

    Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621–628 (2008)

    CAS  Article  Google Scholar 

  37. 37

    Markham, N. R. & Zuker, M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 33, W577–W581 (2005)

    CAS  Article  Google Scholar 

  38. 38

    Huang, D. W., Sherman, B. T., Lempicki R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57 (2009)

    CAS  Article  Google Scholar 

  39. 39

    Huang, D. W. Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1–13 (2009)

    Article  Google Scholar 

Download references


We thank members of the Gray and Sabatini laboratories for helpful discussions, H. Guo, S. Hawthorne, G. Brar, J. Damon, C. Miller and W. Gilbert for advice and N. Sonenberg for providing 4EBP1/2 wild-type and double-knockout MEFs. This work was supported by the National Institutes of Health (CA103866 and CA129105 to D.M.S.), Department of Defense (W81XWH-07-0448 to D.M.S.), the W.M. Keck Foundation (D.M.S.), LAM Foundation (D.M.S.), Dana Farber Cancer Institute (N.S.G., C.C.T.), and fellowship support from the American Cancer Society (C.C.T.), and the National Science Foundation (L.C. and T.W.). D.M.S. is an investigator of the Howard Hughes Medical Institute.

Author information




C.C.T. and D.M.S. conceived the project. C.C.T. designed and performed most experiments and data analyses with input from D.M.S. and N.S.G. L.C. and H.R.K. assisted with experiments and T.W. with sequence analysis. C.C.T. and D.M.S. wrote and edited the manuscript with input from N.S.G.

Corresponding authors

Correspondence to Nathanael S. Gray or David M. Sabatini.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-9. (PDF 1636 kb)

Supplementary Table 1

In this table we see changes in translational efficiency, ribosome density (RD) and total transcript levels of 4840 robustly detected mRNAs for WT and DKO cells treated with Torin1 for 2 h. (XLS 871 kb)

Supplementary Table 2

In this table we see Torin1-dependent translational regulation of selected functional classes of mRNAs. (XLS 78 kb)

Supplementary Table 3

In this table we see TOP and TOP-like annotations for 43 mRNAs not previously known to encode a TOP motif and which are amongst the 100 transcripts whose translation is most suppressed by mTOR inhibition. (XLS 24 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Thoreen, C., Chantranupong, L., Keys, H. et al. A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 485, 109–113 (2012).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing