XHIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia

Cell

Volumn 153, Issue 6, 2013, Pages 1327-

  Galbraith, Matthew D ^a   Allen, Mary A ^a   Bensard, Claire L ^a   Wang, Xiaoxing ^b,c   Schwinn, Marie K ^d   Qin, Bo ^b,e   Long, Henry W ^b   Daniels, Danette L ^d   Hahn, William C ^b,c   Dowell, Robin D ^a   Espinosa, Joaquín M ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d PROMEGA CORPORATION   (United States)

^e TONGJI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE 8; HYPOXIA INDUCIBLE FACTOR 1ALPHA; RNA POLYMERASE II; TRANSCRIPTION ELONGATION FACTOR;

ARTICLE; CANCER CELL; CANCER CELL CULTURE; CELL PROLIFERATION; CELL STRESS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; COLORECTAL CANCER; CONTROLLED STUDY; GENE ACTIVITY; GENE EXPRESSION; HISTONE ACETYLATION; HUMAN; HUMAN CELL; HYPOXIA; IN VITRO STUDY; ONCOGENE; OSTEOSARCOMA CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN PHOSPHORYLATION; PROTEIN PURIFICATION; TRANSCRIPTION ELONGATION; TRANSCRIPTION INITIATION SITE; WESTERN BLOTTING;

EID: 84878831596     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.04.048     Document Type: Article

References (52)

1. A.S. Adler, M.L. McCleland, T. Truong, S. Lau, Z. Modrusan, T.M. Soukup, M. Roose-Girma, E.M. Blackwood, and R. Firestein CDK8 maintains tumor dedifferentiation and embryonic stem cell pluripotency Cancer Res. 72 2012 2129 2139
2. A.K. Boehm, A. Saunders, J. Werner, and J.T. Lis Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock Mol. Cell. Biol. 23 2003 7628 7637
3. A.N. Boettiger, and M. Levine Synchronous and stochastic patterns of gene activation in the Drosophila embryo Science 325 2009 471 473
4. H.-M. Bourbon Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex Nucleic Acids Res. 36 2008 3993 4008
5. R.C. Conaway, and J.W. Conaway Function and regulation of the Mediator complex Curr. Opin. Genet. Dev. 21 2011 225 230
6. L.J. Core, and J.T. Lis Transcription regulation through promoter-proximal pausing of RNA polymerase II Science 319 2008 1791 1792
7. L.J. Core, J.J. Waterfall, and J.T. Lis Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science 322 2008 1845 1848
8. A.J. Donner, S. Szostek, J.M. Hoover, and J.M. Espinosa CDK8 is a stimulus-specific positive coregulator of p53 target genes Mol. Cell 27 2007 121 133
9. A.J. Donner, C.C. Ebmeier, D.J. Taatjes, and J.M. Espinosa CDK8 is a positive regulator of transcriptional elongation within the serum response network Nat. Struct. Mol. Biol. 17 2010 194 201
10. R. Firestein, A.J. Bass, S.Y. Kim, I.F. Dunn, S.J. Silver, I. Guney, E. Freed, A.H. Ligon, N. Vena, and S. Ogino CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity Nature 455 2008 547 551
11. M.D. Galbraith, A.J. Donner, and J.M. Espinosa CDK8: a positive regulator of transcription Transcription 1 2010 4 12
12. D.A. Gilchrist, G. Dos Santos, D.C. Fargo, B. Xie, Y. Gao, L. Li, and K. Adelman Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation Cell 143 2010 540 551
13. M.G. Guenther, S.S. Levine, L.A. Boyer, R. Jaenisch, and R.A. Young A chromatin landmark and transcription initiation at most promoters in human cells Cell 130 2007 77 88
14. M. Ivan, K. Kondo, H. Yang, W. Kim, J. Valiando, M. Ohh, A. Salic, J.M. Asara, W.S. Lane, and W.G. Kaelin Jr. HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing Science 292 2001 464 468
15. P. Jaakkola, D.R. Mole, Y.M. Tian, M.I. Wilson, J. Gielbert, S.J. Gaskell, A. von Kriegsheim, H.F. Hebestreit, M. Mukherji, and C.J. Schofield Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation Science 292 2001 468 472
16. M.K. Jang, K. Mochizuki, M. Zhou, H.S. Jeong, J.N. Brady, and K. Ozato The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription Mol. Cell 19 2005 523 534
17. P.J. Kallio, K. Okamoto, S. O'Brien, P. Carrero, Y. Makino, H. Tanaka, and L. Poellinger Signal transduction in hypoxic cells: inducible nuclear translocation and recruitment of the CBP/p300 coactivator by the hypoxia-inducible factor-1alpha EMBO J. 17 1998 6573 6586
18. L.H. Kasper, F. Boussouar, K. Boyd, W. Xu, M. Biesen, J. Rehg, T.A. Baudino, J.L. Cleveland, and P.K. Brindle Two transactivation mechanisms cooperate for the bulk of HIF-1-responsive gene expression EMBO J. 24 2005 3846 3858
19. A.J. Koleske, S. Buratowski, M. Nonet, and R.A. Young A novel transcription factor reveals a functional link between the RNA polymerase II CTD and TFIID Cell 69 1992 883 894
20. M. Levine, and R. Tjian Transcription regulation and animal diversity Nature 424 2003 147 151
21. C. Lin, E.R. Smith, H. Takahashi, K.C. Lai, S. Martin-Brown, L. Florens, M.P. Washburn, J.W. Conaway, R.C. Conaway, and A. Shilatifard AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia Mol. Cell 37 2010 429 437
22. W. Luo, H. Hu, R. Chang, J. Zhong, M. Knabel, R. O'Meally, R.N. Cole, A. Pandey, and G.L. Semenza Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1 Cell 145 2011 732 744
23. S. Malik, and R.G. Roeder The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation Nat. Rev. Genet. 11 2010 761 772
24. I.M. Min, J.J. Waterfall, L.J. Core, R.J. Munroe, J. Schimenti, and J.T. Lis Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells Genes Dev. 25 2011 742 754
25. D.R. Mole, C. Blancher, R.R. Copley, P.J. Pollard, J.M. Gleadle, J. Ragoussis, and P.J. Ratcliffe Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts J. Biol. Chem. 284 2009 16767 16775
26. A. Mukhopadhyay, J.M. Kramer, G. Merkx, D. Lugtenberg, D.F. Smeets, M.A. Oortveld, E.A. Blokland, J. Agrawal, A. Schenck, and H. van Bokhoven CDK19 is disrupted in a female patient with bilateral congenital retinal folds, microcephaly and mild mental retardation Hum. Genet. 128 2010 281 291
27. G.W. Muse, D.A. Gilchrist, S. Nechaev, R. Shah, J.S. Parker, S.F. Grissom, J. Zeitlinger, and K. Adelman RNA polymerase is poised for activation across the genome Nat. Genet. 39 2007 1507 1511
28. B.M. Peterlin, and D.H. Price Controlling the elongation phase of transcription with P-TEFb Mol. Cell 23 2006 297 305
29. P.B. Rahl, C.Y. Lin, A.C. Seila, R.A. Flynn, S. McCuine, C.B. Burge, P.A. Sharp, and R.A. Young c-Myc regulates transcriptional pause release Cell 141 2010 432 445
30. H.E. Ryan, J. Lo, and R.S. Johnson HIF-1 alpha is required for solid tumor formation and embryonic vascularization EMBO J. 17 1998 3005 3015
31. S. Sato, C. Tomomori-Sato, T.J. Parmely, L. Florens, B. Zybailov, S.K. Swanson, C.A. Banks, J. Jin, Y. Cai, and M.P. Washburn A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology Mol. Cell 14 2004 685 691
32. G.L. Semenza Hypoxia-inducible factors in physiology and medicine Cell 148 2012 399 408
33. H. Takahashi, T.J. Parmely, S. Sato, C. Tomomori-Sato, C.A.S. Banks, S.E. Kong, H. Szutorisz, S.K. Swanson, S. Martin-Brown, and M.P. Washburn Human mediator subunit MED26 functions as a docking site for transcription elongation factors Cell 146 2011 92 104
34. C.M. Thompson, A.J. Koleske, D.M. Chao, and R.A. Young A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast Cell 73 1993 1361 1375
35. G.L. Wang, B.H. Jiang, E.A. Rue, and G.L. Semenza Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension Proc. Natl. Acad. Sci. USA 92 1995 5510 5514
36. G. Wang, M.A. Balamotis, J.L. Stevens, Y. Yamaguchi, H. Handa, and A.J. Berk Mediator requirement for both recruitment and postrecruitment steps in transcription initiation Mol. Cell 17 2005 683 694
37. T. Westerling, E. Kuuluvainen, and T.P. Mäkelä Cdk8 is essential for preimplantation mouse development Mol. Cell. Biol. 27 2007 6177 6182
38. X. Xia, and A.L. Kung Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia Genome Biol. 10 2009 R113
39. Z. Yang, J.H. Yik, R. Chen, N. He, M.K. Jang, K. Ozato, and Q. Zhou Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4 Mol. Cell 19 2005 535 545
40. J. Zeitlinger, A. Stark, M. Kellis, J.W. Hong, S. Nechaev, K. Adelman, M. Levine, and R.A. Young RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo Nat. Genet. 39 2007 1512 1516
41. J. Goecks, A. Nekrutenko, J. Taylor Galaxy Team Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol. 11 2010 R86
42. R.E. Henry, Z. Andrysik, R. París, M.D. Galbraith, and J.M. Espinosa A DR4:tBID axis drives the p53 apoptotic response by promoting oligomerization of poised BAX EMBO J. 31 2012 1266 1278
43. M.T. Knuesel, K.D. Meyer, A.J. Donner, J.M. Espinosa, and D.J. Taatjes The human CDK8 subcomplex is a histone kinase that requires Med12 for activity and can function independently of mediator Mol. Cell. Biol. 29 2009 650 661
44. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
45. C. Lin, A.S. Garrett, B. De Kumar, E.R. Smith, M. Gogol, C. Seidel, R. Krumlauf, and A. Shilatifard Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC) Genes Dev. 25 2011 1486 1498
46. C.Y. McLean, D. Bristor, M. Hiller, S.L. Clarke, B.T. Schaar, C.B. Lowe, A.M. Wenger, and G. Bejerano GREAT improves functional interpretation of cis-regulatory regions Nat. Biotechnol. 28 2010 495 501
47. K.D. Meyer, A.J. Donner, M.T. Knuesel, A.G. York, J.M. Espinosa, and D.J. Taatjes Cooperative activity of cdk8 and GCN5L within Mediator directs tandem phosphoacetylation of histone H3 EMBO J. 27 2008 1447 1457
48. A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
49. D.J. Taatjes, and R. Tjian Structure and function of CRSP/Med2; a promoter-selective transcriptional coactivator complex Mol. Cell 14 2004 675 683
50. H. Thorvaldsdottir, J.T. Robinson, and J.P. Mesirov Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration Brief. Bioinform. 14 2012 178 192
51. D. Wang, I. Garcia-Bassets, C. Benner, W. Li, X. Su, Y. Zhou, J. Qiu, W. Liu, M.U. Kaikkonen, and K.A. Ohgi Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA Nature 474 2011 390 394
52. Y. Zhang, T. Liu, C.A. Meyer, J. Eeckhoute, D.S. Johnson, B.E. Bernstein, C. Nusbaum, R.M. Myers, M. Brown, W. Li, and X.S. Liu Model-based analysis of ChIP-Seq (MACS) Genome Biol. 9 2008 R137