Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation

Genome Research

Volumn 27, Issue 10, 2017, Pages 1658-1664

  De Pretis, Stefano ^a   Kress, Theresia R ^a,b,c   Morelli, Marco J ^a   Sabò, Arianna ^a   Locarno, Chiara ^a   Verrecchia, Alessandro ^b   Doni, Mirko ^b   Campaner, Stefano ^a   Amati, Bruno ^a,b   Pelizzola, Mattia ^a  

^a ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

^b EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

^c BOEHRINGER INGELHEIM PHARMA GMBH AND CO KG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COREPRESSOR PROTEIN; MYC PROTEIN; RNA POLYMERASE II; UNCLASSIFIED DRUG; ZBTB17 PROTEIN; MIZ1 PROTEIN, MOUSE; MYC PROTEIN, MOUSE; NUCLEAR PROTEIN; PROTEIN INHIBITOR OF ACTIVATED STAT; RNA PRECURSOR;

ANIMAL CELL; ARTICLE; CELL LABELING; CELL PROLIFERATION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; ENZYME ANALYSIS; FIBROBLAST; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENE REPRESSION; HUMAN; HUMAN CELL; MATHEMATICAL MODEL; MESSENGER RNA SYNTHESIS; MOLECULAR DYNAMICS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; RNA ANALYSIS; RNA DEGRADATION; RNA PROCESSING; RNA SEQUENCE; RNA TRANSCRIPTION; TRANSCRIPTION ELONGATION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; U2OS CELL LINE; ANIMAL; BIOSYNTHESIS; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PHYSIOLOGY; TRANSFORMED CELL LINE;

ANIMALS; CELL LINE, TRANSFORMED; MICE; NUCLEAR PROTEINS; PROMOTER REGIONS, GENETIC; PROTEIN INHIBITORS OF ACTIVATED STAT; PROTO-ONCOGENE PROTEINS C-MYC; RNA POLYMERASE II; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; TRANSCRIPTION, GENETIC;

EID: 85030627973     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.226035.117     Document Type: Article

References (23)

1. Bouchard C, Marquardt J, Brás A, Medema RH, Eilers M. 2004. Myc-induced proliferation and transformation require Akt-mediated phosphorylation of FoxO proteins. EMBO J 23: 2830-2840.
2. Braun KA, Young ET 2014. Coupling mRNA synthesis and decay. Mol Cell Biol 34: 4078-4087.
3. Cole MD. 2014. MYC association with cancer risk and a new model of MYC-mediated repression. Cold Spring Harb Perspect Med 4: a014316.
4. Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL 2013. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell 50: 212-222.
5. de Pretis S, Kress T, Morelli MJ, Melloni GEM, Riva L, Amati B, Pelizzola M. 2015. INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. Bioinformatics 31: 2829-2835.
6. Dujardin G, Lafaille C, la Mata de M, Marasco LE, Muñoz MJ, Le Jossic-Corcos C, Corcos L, Kornblihtt AR. 2014. How slow RNA polymerase II elongation favors alternative exon skipping. Mol Cell 54: 683-690.
7. Eberhardy SR, Farnham PJ 2002. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J Biol Chem 277: 40156-40162.
8. Ehrensberger AH, Kelly GP, Svejstrup JQ 2013. Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps. Cell 154: 713-715.
9. Hsu TYT, Simon LM, Neill NJ, Marcotte R, Sayad A, Bland CS, Echeverria GV, Sun T, Kurley SJ, Tyagi S, et al 2015. The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature 525: 384-388.
10. Jonkers I, Lis JT 2015. Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 16: 167-177.
11. Kaur M, Cole MD 2013. MYC acts via the PTEN tumor suppressor to elicit autoregulation and genome-wide gene repression by activation of the Ezh2 methyltransferase. Cancer Res 73: 695-705.
12. Koh CM, Bezzi M, Low DHP, Ang WX, Teo SX, Gay FPH, Al-Haddawi M, Tan SY, Osato M, Sabò A, et al. 2015. MYC regulates the core pre-mRNA splicing machinery as an essential step in lymphomagenesis. Nature 523: 96-100.
13. Kress TR, Sabò A, Amati B. 2015. MYC: connecting selective transcriptional control to global RNA production. Nat Rev Cancer 15: 593-607.
14. Kress TR, Pellanda P, Pellegrinet L, Bianchi V, Nicoli P, Doni M, Recordati C, Bianchi S, Rotta L, Capra T, et al 2016. Identification of MYC-dependent transcriptional programs in oncogene-addicted liver tumors. Cancer Res 76: 3463-3472.
15. Lin CY, Lovén J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA 2012. Transcriptional amplification in tumor cells with elevated c-Myc. Cell 151: 56-67.
16. Lorenzin F, Benary U, Baluapuri A, Walz S, Jung LA, Eyss von B, Kisker C, Wolf J, Eilers M, Wolf E. 2016. Different promoter affinities account for specificity in MYC-dependent gene regulation. eLife 5: 1009.
17. Melvin WT, Milne HB, Slater AA, Allen HJ, Keir HM 1978. Incorporation of 6-thioguanosine and 4-thiouridineinto RNA. Applicationtoisolation of newly synthesised RNA by affinity chromatography. Eur J Biochem 92: 373-379.
18. Nie Z, Hu G, Wei G, Cui K, Yamane A, Resch W, Wang R, Green DR, 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.
19. Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, et al 2011. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 29: 436-442.
20. Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA 2010. c-Myc regulates transcriptional pause release. Cell 141: 432-445.
21. Sabò A, Kress TR, Pelizzola M, de Pretis S, Gorski MM, Tesi A, Morelli MJ, Bora P, Doni M, Verrecchia A, et al. 2014. Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature 511: 488-492.
22. Trumpp A, Refaeli Y, Oskarsson T, Gasser S, Murphy M, Martin GR, Bishop JM 2001. c-Myc regulates mammalian body size by controlling cell number but not cell size. Nature 414: 768-773.
23. Walz S, Lorenzin F, Morton J, Wiese KE, Eyss von B, Herold S, Rycak L, Dumay-Odelot H, Karim S, Bartkuhn M, et al 2014. Activation and repressionby oncogenic MYC shape tumour-specific gene expression profiles. Nature 511: 483-487.