Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis

Nature

Volumn 511, Issue 7510, 2014, Pages 488-492

  Sabò, Arianna ^a,b   Kress, Theresia R ^a,b   Pelizzola, Mattia ^a   De Pretis, Stefano ^a   Gorski, Marcin M ^b   Tesi, Alessandra ^a   Morelli, Marco J ^a   Bora, Pranami ^a   Doni, Mirko ^b   Verrecchia, Alessandro ^b   Tonelli, Claudia ^b   Fagà, Giovanni ^b   Bianchi, Valerio ^a   Ronchi, Alberto ^a   Low, Diana ^c   Müller, Heiko ^a   Guccione, Ernesto ^c   Campaner, Stefano ^a   Amati, Bruno ^a,c  

^a ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

^b EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

^c INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MYC PROTEIN;

ANIMAL CELL; ANIMAL CELL CULTURE; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; B CELL CULTURE; B CELL LYMPHOMA; B LYMPHOCYTE; CARCINOGENESIS; CELL GROWTH; CELL PROLIFERATION; CHROMATIN IMMUNOPRECIPITATION; COMPARATIVE STUDY; CONTROLLED STUDY; ENHANCER REGION; FIBROBLAST CULTURE; FLUORESCENCE ACTIVATED CELL SORTING; GENE AMPLIFICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE REPRESSION; GENETIC ASSOCIATION; GROWTH REGULATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; TURNOVER TIME; UPREGULATION;

ANIMALS; B-LYMPHOCYTES; CELL PROLIFERATION; CELL TRANSFORMATION, NEOPLASTIC; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DISEASE PROGRESSION; DOWN-REGULATION; FEMALE; FIBROBLASTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME; LYMPHOMA, B-CELL; MALE; MICE; MITOGENS; PROMOTER REGIONS, GENETIC; PROTO-ONCOGENE PROTEINS C-MYC; RNA, MESSENGER; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; UP-REGULATION;

EID: 84904785973     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13537     Document Type: Article

References (56)

1. Eilers, M.&Eisenman, R. N.Myc's broad reach. GenesDev. 22, 2755-2766 (2008).
2. Herkert, B. & Eilers, M. Transcriptional repression: The dark side of Myc. Genes Cancer 1, 580-586 (2010).
3. Dang, C. V. MYC, metabolism, cell growth, and tumorigenesis. Cold Spring Harbor Perspect. Med. 3, http://dx.doi.org/10.1101/cshperspect.a014217 (2013).
4. Lin, C. Y. et al. Transcriptionalamplification in tumor cells with elevated c-Myc. Cell 151, 56-67 (2012).
5. Nie, Z. et al. c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell 151, 68-79 (2012).
6. Darzynkiewicz, Z., Traganos, F. & Melamed, M. R. New cell cycle compartments identified by multiparameter flow cytometry. Cytometry 1, 98-108 (1980).
7. de Alboran, I. M. et al. Analysis of C-MYC function in normal cells via conditional gene-targeted mutation. Immunity 14, 45-55 (2001).
8. Perna, D. et al. Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts. Oncogene 31, 1695-1709 (2012).
9. Guccione, E. et al. Myc-binding-site recognition in the human genome is determined by chromatin context. Nature Cell Biol. 8, 764-770 (2006).
10. Soufi, A., Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151, 994-1004 (2012).
11. Sabo, A.&Amati, B.Genomerecognition byMYC.Cold SpringHarbor Perspect.Med. 4, http://dx.doi.org/10.1101/cshperspect.a014191 (2014).
12. Zhou, V. W., Goren, A. & Bernstein, B. E. Charting histone modifications and the functional organization of mammalian genomes. Nature Rev. Genet. 12, 7-18 (2011).
13. Calo, E. & Wysocka, J. Modification of enhancer chromatin: what, how, and why? Mol. Cell 49, 825-837 (2013).
14. Lin, Y. C. et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nature Immunol. 11, 635-643 (2010).
15. Lovén, J. et al. Revisiting global gene expression analysis. Cell 151, 476-482 (2012).
16. Iritani, B. M. & Eisenman, R. N. c-Myc enhances protein synthesis and cell size during B lymphocyte development. Proc. Natl Acad. Sci. USA 96, 13180-13185 (1999).
17. Schuhmacher, M. et al. Control of cell growth by c-Myc in the absence of cell division. Curr. Biol. 9, 1255-1258 (1999).
18. Yustein, J. T. et al. Induction of ectopic Myc target gene JAG2 augments hypoxic growth and tumorigenesis in a human B-cell model. Proc. Natl Acad. Sci. USA 107, 3534-3539 (2010).
19. Kouzine, F. et al. Global regulation of promoter melting in naive lymphocytes. Cell 153, 988-999 (2013).
20. Murn, J. et al. A Myc-regulated transcriptional network controls B-cell fate in response to BCR triggering. BMC Genomics 10, 323 (2009).
21. Fan, J. et al. Time-dependent c-Myc transactomesmapped by array-based nuclear run-onreveal transcriptionalmodules inhumanBcells.PLoSONE 5, e9691 (2010).
22. Fernandez, P. C. et al. Genomic targets of the humanc-Myc protein. Genes Dev. 17, 1115-1129 (2003).
23. Guertin, M. J. & Lis, J. T. Mechanisms by which transcription factors gain access to target sequence elements in chromatin.Curr.Opin. Genet. Dev. 23, 116-123 (2013).
24. Rounbehler, R. J. et al. Tristetraprolin impairs Myc-induced lymphoma and abolishes the malignant state. Cell 150, 563-574 (2012).
25. Graves, J. A. et al. Mitochondrial structure, function and dynamics are temporally controlled by c-Myc. PLoS ONE 7, e37699 (2012).
26. Wang, R. et al. The transcription factor Myc controls metabolic reprogramming upon T lymphocyte activation. Immunity 35, 871-882 (2011).
27. Liu, Y. C. et al. Global regulation of nucleotide biosynthetic genes by c-Myc. PLoS ONE 3, e2722 (2008).
28. Marguerat, S. & Bahler, J. Coordinating genome expression with cell size. Trends Genet. 28, 560-565 (2012).
29. das Neves, R. P. et al. Connecting variability in global transcription rate to mitochondrial variability. PLoS Biol. 8, e1000560 (2010).
30. Rahl, P. B. et al. c-Myc regulates transcriptional pause release. Cell 141, 432-445 (2010).
31. Adams, J. M. et al. The c-myc oncogene driven by immunoglobulin enhancers induces lymphoid malignancy in transgenic mice. Nature 318, 533-538 (1985).
32. Schmitt, C. A. et al. Dissecting p53 tumor suppressor functions in vivo. Cancer Cell 1, 289-298 (2002).
33. Gorrini, C. et al. Tip60 is a haplo-insufficient tumour suppressor required for an oncogene-induced DNA damage response. Nature 448, 1063-1067 (2007).
34. Pajic, A. et al. Cell cycle activation by c-myc in a Burkitt lymphoma model cell line. Int. J. Cancer 87, 787-793 (2000).
35. Trumpp, A. et al. c-Myc regulatesmammalian body size by controlling cell number but not cell size. Nature 414, 768-773 (2001).
36. Peitz, M., Pfannkuche, K., Rajewsky, K. & Edenhofer, F. Ability of the hydrophobic FGF and basic TAT peptides to promote cellular uptake of recombinant Cre recombinase: A tool for efficient genetic engineering of mammalian genomes. Proc. Natl Acad. Sci. USA 99, 4489-4494 (2002).
37. Gerondakis, S., Grumont, R. J. & Banerjee, A. Regulating B-cell activation and survival in response to TLR signals. Immunol. Cell Biol. 85, 471-475 (2007).
38. Morgenstern, J. P. & Land, H. Advanced mammalian gene transfer: high titre retroviral vectors with multiple drug selection markers and a complementary helper-free packaging cell line. Nucleic Acids Res. 18, 3587-3596 (1990).
39. Littlewood, T. D., Hancock, D. C., Danielian, P. S., Parker, M. G. & Evan, G. I. A modified oestrogen receptor ligand-binding domain as an improved switch for the regulation of heterologous proteins. Nucleic Acids Res. 23, 1686-1690 (1995).
40. Frank, S. R., Schroeder, M., Fernandez, P., Taubert, S. & Amati, B. Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation. Genes Dev. 15, 2069-2082 (2001).
41. Blecher-Gonen, R. et al. High-throughput chromatin immunoprecipitation for genome-widemapping of in vivo protein-DNAinteractions and epigenomic states. Nature Protocols 8, 539-554 (2013).
42. Rabani, M. et al.Metabolic labeling ofRNAuncovers principles ofRNAproduction and degradation dynamics inmammalian cells. Nature Biotechnol. 29, 436-442 (2011).
43. He, H. H. et al. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 22, 1015-1025 (2012).
44. Sabo, P. J. et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods 3, 511-518 (2006).
45. Campaner, S. et al. Cdk2 suppresses cellular senescence induced by the c-myc oncogene. Nature Cell Biol. 12, 54-59 (2010).
46. Geiss, G. K. et al. Direct multiplexed measurement of gene expression with colorcoded probe pairs. Nature Biotechnol. 26, 317-325 (2008).
47. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
48. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
49. Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39, 1512-1516 (2007).
50. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
51. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifyingmammalian transcriptomesbyRNA-Seq. NatureMethods 5, 621-628 (2008).
52. Gentleman, R. C. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
53. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
54. Shaffer, A. L. et al. XBP1, downstreamof Blimp-1, expands the secretory apparatus and other organelles, and increases protein synthesis in plasma cell differentiation. Immunity 21, 81-93 (2004).
55. Ehrensberger, A. H., Kelly, G. P. & Svejstrup, J. Q. Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps. Cell 154, 713-715 (2013).
56. Bouchard, C., Marquardt, J., Bras, A., Medema, R. H. & Eilers, M. Myc-induced proliferation and transformation require Akt-mediated phosphorylation of FoxO proteins. EMBO J. 23, 2830-2840 (2004).