Skip to main content
SpringerLink
Log in

MYC promotes global transcription in part by controlling P-TEFb complex formation via DNA-binding independent inhibition of CDK9 SUMOylation

  • Research Paper
  • Published:
Science China Life Sciences Aims and scope Submit manuscript

Abstract

MYC is an oncogenic transcription factor with a novel role in enhancing global transcription when overexpressed. However, how MYC promotes global transcription remains controversial. Here, we used a series of MYC mutants to dissect the molecular basis for MYC-driven global transcription. We found that MYC mutants deficient in DNA binding or known transcriptional activation activities can still promote global transcription and enhance serine 2 phosphorylation (Ser2P) of the RNA polymerase (Pol) II C-terminal domain (CTD), a hallmark of active elongating RNA Pol II. Two distinct regions within MYC can promote global transcription and Ser2P of Pol II CTD. The ability of various MYC mutants to promote global transcription and Ser2P correlates with their ability to suppress CDK9 SUMOylation and enhance positive transcription elongation factor b (P-TEFb) complex formation. We showed that MYC suppresses CDK9 SUMOylation by inhibiting the interaction between CDK9 and SUMO enzymes including UBC9 and PIAS1. Furthermore, MYC’s activity in enhancing global transcription positively contributes to its activity in promoting cell proliferation and transformation. Together, our study demonstrates that MYC promotes global transcription, at least in part, by promoting the formation of the active P-TEFb complex via a sequence-specific DNA-binding activity-independent manner.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  • Adelman, K., and Lis, J.T. (2012). Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet 13, 720–731.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bacon, C.W., and D’Orso, I. (2019). CDK9: a signaling hub for transcriptional control. Transcription 10, 57–75.

    Article  CAS  PubMed  Google Scholar 

  • Baluapuri, A., Wolf, E., and Eilers, M. (2020). Target gene-independent functions of MYC oncoproteins. Nat Rev Mol Cell Biol 21, 255–267.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blackwood, E.M., and Eisenman, R.N. (1991). Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. Science 251, 1211–1217.

    Article  CAS  PubMed  Google Scholar 

  • Chakraborty, A.A., Scuoppo, C., Dey, S., Thomas, L.R., Lorey, S.L., Lowe, S.W., and Tansey, W.P. (2015). A common functional consequence of tumor-derived mutations within c-MYC. Oncogene 34, 2406–2409.

    Article  CAS  PubMed  Google Scholar 

  • Chen, F.X., Smith, E.R., and Shilatifard, A. (2018). Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 19, 464–478.

    Article  CAS  PubMed  Google Scholar 

  • Core, L., and Adelman, K. (2019). Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. Genes Dev 33, 960–982.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cowling, V.H., and Cole, M.D. (2007). The Myc transactivation domain promotes global phosphorylation of the RNA polymerase II carboxyterminal domain independently of direct DNA binding. Mol Cell Biol 27, 2059–2073.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cowling, V.H., and Cole, M.D. (2008). An N-Myc truncation analogous to c-Myc-S induces cell proliferation independently of transactivation but dependent on Myc homology box II. Oncogene 27, 1327–1332.

    Article  CAS  PubMed  Google Scholar 

  • Danecek, P., Bonfield, J.K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S.A., Davies, R.M., et al. (2021). Twelve years of SAMtools and BCFtools. Gigascience 10.

  • Dhanasekaran, R., Deutzmann, A., Mahauad-Fernandez, W.D., Hansen, A. S., Gouw, A.M., and Felsher, D.W. (2022). The MYC oncogene—the grand orchestrator of cancer growth and immune evasion. Nat Rev Clin Oncol 19, 23–36.

    Article  CAS  PubMed  Google Scholar 

  • Duffy, M.J., O’Grady, S., Tang, M., and Crown, J. (2021). MYC as a target for cancer treatment. Cancer Treat Rev 94, 102154.

    Article  CAS  PubMed  Google Scholar 

  • Eilers, M., and Eisenman, R.N. (2008). Myc’s broad reach. Genes Dev 22, 2755–2766.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Faiola, F., Liu, X., Lo, S., Pan, S., Zhang, K., Lymar, E., Farina, A., and Martinez, E. (2005). Dual regulation of c-Myc by p300 via acetylation-dependent control of Myc protein turnover and coactivation of Myc-induced transcription. Mol Cell Biol 25, 10220–10234.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fang, L., Zhang, L., Wei, W., Jin, X., Wang, P., Tong, Y., Li, J., Du, J.X., and Wong, J. (2014). A methylation-phosphorylation switch determines Sox2 stability and function in ESC maintenance or differentiation. Mol Cell 55, 537–551.

    Article  CAS  PubMed  Google Scholar 

  • Gargano, B., Amente, S., Majello, B., and Lania, L. (2007). P-TEFb is a crucial co-factor for Myc transactivation. Cell Cycle 6, 2031–2037.

    Article  CAS  PubMed  Google Scholar 

  • Gressel, S., Schwalb, B., Decker, T.M., Qin, W., Leonhardt, H., Eick, D., and Cramer, P. (2017). CDK9-dependent RNA polymerase II pausing controls transcription initiation. eLife 6, e29736.

    Article  PubMed  PubMed Central  Google Scholar 

  • Haukenes, G., Szilvay, A.M., Brokstad, K.A., Kanestrøm, A., and Kalland, K.H. (1997). Labeling of RNA transcripts of eukaryotic cells in culture with BrUTP using a liposome transfection reagent (DOTAP). Biotechniques 22, 308–312.

    Article  CAS  PubMed  Google Scholar 

  • Herbst, A., Hemann, M.T., Tworkowski, K.A., Salghetti, S.E., Lowe, S.W., and Tansey, W.P. (2005). A conserved element in Myc that negatively regulates its proapoptotic activity. EMBO Rep 6, 177–183.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kalkat, M., Resetca, D., Lourenco, C., Chan, P.K., Wei, Y., Shiah, Y.J., Vitkin, N., Tong, Y., Sunnerhagen, M., Done, S.J., et al. (2018). MYC protein interactome profiling reveals functionally distinct regions that cooperate to drive tumorigenesis. Mol Cell 72, 836–848.e7.

    Article  CAS  PubMed  Google Scholar 

  • Kanazawa, S., Soucek, L., Evan, G., Okamoto, T., and Peterlin, B.M. (2003). c-Myc recruits P-TEFb for transcription, cellular proliferation and apoptosis. Oncogene 22, 5707–5711.

    Article  CAS  PubMed  Google Scholar 

  • Kim, D., Paggi, J.M., Park, C., Bennett, C., and Salzberg, S.L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kress, T.R., Sabò, A., and Amati, B. (2015). MYC: connecting selective transcriptional control to global RNA production. Nat Rev Cancer 15, 593–607.

    Article  CAS  PubMed  Google Scholar 

  • Kurland, J.F., and Tansey, W.P. (2008). Myc-mediated transcriptional repression by recruitment of histone deacetylase. Cancer Res 68, 3624–3629.

    Article  CAS  PubMed  Google Scholar 

  • Kwak, H., and Lis, J.T. (2013). Control of transcriptional elongation. Annu Rev Genet 47, 483–508.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, J., Wang, R., Jin, J., Han, M., Chen, Z., Gao, Y., Hu, X., Zhu, H., Gao, H., Lu, K., et al. (2020). USP7 negatively controls global DNA methylation by attenuating ubiquitinated histone-dependent DNMT1 recruitment. Cell Discov 6, 58.

    Article  PubMed  PubMed Central  Google Scholar 

  • Li, Q., Price, J.P., Byers, S.A., Cheng, D., Peng, J., and Price, D.H. (2005). Analysis of the large inactive P-TEFb complex indicates that it contains one 7SK molecule, a dimer of HEXIM1 or HEXIM2, and two P-TEFb molecules containing Cdk9 phosphorylated at threonine 186. J Biol Chem 280, 28819–28826.

    Article  CAS  PubMed  Google Scholar 

  • Liao, Y., Smyth, G.K., and Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930.

    Article  CAS  PubMed  Google Scholar 

  • Lin, C.Y., Lovén, J., Rahl, P.B., Paranal, R.M., Burge, C.B., Bradner, J.E., Lee, T.I., and Young, R.A. (2012). Transcriptional amplification in tumor cells with elevated c-Myc. Cell 151, 56–67.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu, X., Tesfai, J., Evrard, Y.A., Dent, S.Y.R., and Martinez, E. (2003). c-Myc transformation domain recruits the human STAGA complex and requires TRRAP and GCN5 acetylase activity for transcription activation. J Biol Chem 278, 20405–20412.

    Article  CAS  PubMed  Google Scholar 

  • Lourenco, C., Resetca, D., Redel, C., Lin, P., MacDonald, A.S., Ciaccio, R., Kenney, T.M.G., Wei, Y., Andrews, D.W., Sunnerhagen, M., et al. (2021). MYC protein interactors in gene transcription and cancer. Nat Rev Cancer 21, 579–591.

    Article  CAS  PubMed  Google Scholar 

  • Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq 2. Genome Biol 15, 550.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ma, X., Yang, T., Luo, Y., Wu, L., Jiang, Y., Song, Z., Pan, T., Liu, B., Liu, G., Liu, J., et al. (2019). TRIM28 promotes HIV-1 latency by SUMOylating CDK9 and inhibiting P-TEFb. eLife 8, e42426.

    Article  PubMed  PubMed Central  Google Scholar 

  • Marshall, N.F., Peng, J., Xie, Z., and Price, D.H. (1996). Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J Biol Chem 271, 27176–27183.

    Article  CAS  PubMed  Google Scholar 

  • McMahon, S.B., Van Buskirk, H.A., Dugan, K.A., Copeland, T.D., and Cole, M.D. (1998). The novel ATM-related protein TRRAP is an essential cofactor for the c-Myc and E2F oncoproteins. Cell 94, 363–374.

    Article  CAS  PubMed  Google Scholar 

  • Michels, A.A., Fraldi, A., Li, Q., Adamson, T.E., Bonnet, F., Nguyen, V.T., Sedore, S.C., Price, J.P., Price, D.H., Lania, L., et al. (2004). Binding of the 7SK snRNA turns the HEXIM1 protein into a P-TEFb (CDK9/cyclin T) inhibitor. EMBO J 23, 2608–2619.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nie, Z., Guo, C., Das, S.K., Chow, C.C., Batchelor, E., Simons Jnr, S.S., and Levens, D. (2020). Dissecting transcriptional amplification by MYC. eLife 9, e52483.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nie, Z., Hu, G., Wei, G., Cui, K., Yamane, A., Resch, W., Wang, R., Green, D.R., Tessarollo, L., Casellas, R., et al. (2012). c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell 151, 68–79.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osman, S., and Cramer, P. (2020). Structural biology of RNA polymerase II transcription: 20 years on. Annu Rev Cell Dev Biol 36, 1–34.

    Article  CAS  PubMed  Google Scholar 

  • Parua, P.K., Booth, G.T., Sansó, M., Benjamin, B., Tanny, J.C., Lis, J.T., and Fisher, R.P. (2018). A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II. Nature 558, 460–464.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peng, Y., Wang, Z., Wang, Z., Yu, F., Li, J., and Wong, J. (2019). SUMOylation down-regulates rDNA transcription by repressing expression of upstream-binding factor and proto-oncogene c-Myc. J Biol Chem 294, 19155–19166.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peterlin, B.M., and Price, D.H. (2006). Controlling the elongation phase of transcription with P-TEFb. Mol Cell 23, 297–305.

    Article  CAS  PubMed  Google Scholar 

  • Rahl, P.B., Lin, C.Y., Seila, A.C., Flynn, R.A., McCuine, S., Burge, C.B., Sharp, P.A., and Young, R.A. (2010). c-Myc regulates transcriptional pause release. Cell 141, 432–445.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roeder, R.G. (2019). 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 26, 783–791.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sabò, A., Kress, T.R., Pelizzola, M., de Pretis, S., Gorski, M.M., Tesi, A., Morelli, M.J., Bora, P., Doni, M., Verrecchia, A., et al. (2014). Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature 511, 488–492.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sansó, M., Levin, R.S., Lipp, J.J., Wang, V.Y.F., Greifenberg, A.K., Quezada, E.M., Ali, A., Ghosh, A., Larochelle, S., Rana, T.M., et al. (2016). P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates. Genes Dev 30, 117–131.

    Article  PubMed  PubMed Central  Google Scholar 

  • Shi, G., Wu, M., Fang, L., Yu, F., Cheng, S., Li, J., Du, J.X., and Wong, J. (2014). PHD finger protein 2 (PHF2) represses ribosomal RNA gene transcription by antagonizing PHF finger protein 8 (PHF8) and recruiting methyltransferase SUV39H1. J Biol Chem 289, 29691–29700.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas, L.R., Foshage, A.M., Weissmiller, A.M., Popay, T.M., Grieb, B. C., Qualls, S.J., Ng, V., Carboneau, B., Lorey, S., Eischen, C.M., et al. (2016). Interaction of MYC with host cell factor-1 is mediated by the evolutionarily conserved Myc box IV motif. Oncogene 35, 3613–3618.

    Article  CAS  PubMed  Google Scholar 

  • Thomas, L.R., Wang, Q., Grieb, B.C., Phan, J., Foshage, A.M., Sun, Q., Olejniczak, E.T., Clark, T., Dey, S., Lorey, S., et al. (2015). Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC. Mol Cell 58, 440–452.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vervoorts, J., Lüscher-Firzlaff, J.M., Rottmann, S., Lilischkis, R., Walsemann, G., Dohmann, K., Austen, M., and Lüscher, B. (2003). Stimulation of c-MYC transcriptional activity and acetylation by recruitment of the cofactor CBP. EMBO Rep 4, 484–490.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vos, S.M., Farnung, L., Urlaub, H., and Cramer, P. (2018). Structure of paused transcription complex Pol II-DSIF-NELF. Nature 560, 601–606.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Walz, S., Lorenzin, F., Morton, J., Wiese, K.E., von Eyss, B., Herold, S., Rycak, L., Dumay-Odelot, H., Karim, S., Bartkuhn, M., et al. (2014). Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles. Nature 511, 483–487.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wolf, E., Lin, C.Y., Eilers, M., and Levens, D.L. (2015). Taming of the beast: shaping Myc-dependent amplification. Trends Cell Biol 25, 241–248.

    Article  CAS  PubMed  Google Scholar 

  • Yamaguchi, Y., Shibata, H., and Handa, H. (2013). Transcription elongation factors DSIF and NELF: promoter-proximal pausing and beyond. Biochim Biophys Acta 1829, 98–104.

    Article  CAS  PubMed  Google Scholar 

  • Yik, J.H.N., Chen, R., Nishimura, R., Jennings, J.L., Link, A.J., and Zhou, Q. (2003). Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Mol Cell 12, 971–982.

    Article  CAS  PubMed  Google Scholar 

  • Yu, F., Shi, G., Cheng, S., Chen, J., Wu, S.Y., Wang, Z., Xia, N., Zhai, Y., Wang, Z., Peng, Y., et al. (2018). SUMO suppresses and MYC amplifies transcription globally by regulating CDK9 sumoylation. Cell Res 28, 670–685.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, N., Ichikawa, W., Faiola, F., Lo, S.Y., Liu, X., and Martinez, E. (2014). MYC interacts with the human STAGA coactivator complex via multivalent contacts with the GCN5 and TRRAP subunits. Biochim Biophys Acta 1839, 395–405.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, Q., West-Osterfield, K., Spears, E., Li, Z., Panaccione, A., and Hann, S. (2017). MB0 and MBI are independent and distinct transactivation domains in MYC that are essential for transformation. Genes 8, 134.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhou, Q., Li, T., and Price, D.H. (2012). RNA polymerase II elongation control. Annu Rev Biochem 81, 119–143.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (32070643, 32130051, 31961133009), Science and Technology Commission of Shanghai Municipality (20JC1411500), the ECNU Public Platform for Innovation (011) and the Instruments Sharing Platform of the School of Life Sciences, East China Normal University. C.-M.C.’s research is currently supported by the US National Institutes of Health (NIH) grant 1RO1CA251698-01 and Cancer Prevention and Research Institute of Texas (CPRIT) grant RP190077. We thank Professor Bing Li (Shanghai Jiao Tong University School of Medicine) for providing FLAG-CDK9 stable HEK293T cell line. We thank all the other members of Wong’s laboratory for their valuable discussions and technical supports.

Author information

Author notes

  1. Contributed equally to this work

Authors and Affiliations

  1. Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China

    Qingqing Guan, Zhaosu Chen, Yuanyong Huang, Jiemin Wong & Jiwen Li

  2. Department of Medicine, UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA

    Fang Yu

  3. CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Lingling Liu & Gang Wei

  4. Simmons Comprehensive Cancer Center, Department of Pharmacology, and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA

    Cheng-Ming Chiang

Authors
  1. Qingqing Guan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhaosu Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fang Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lingling Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yuanyong Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Gang Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Cheng-Ming Chiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jiemin Wong
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jiwen Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Jiemin Wong or Jiwen Li.

Ethics declarations

Compliance and ethics The author(s) declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Guan, Q., Chen, Z., Yu, F. et al. MYC promotes global transcription in part by controlling P-TEFb complex formation via DNA-binding independent inhibition of CDK9 SUMOylation. Sci. China Life Sci. 66, 2167–2184 (2023). https://doi.org/10.1007/s11427-022-2281-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-022-2281-6

Search

Navigation