A common set of gene regulatory networks links metabolism and growth inhibition

Molecular Cell

Volumn 16, Issue 3, 2004, Pages 399-411

  Cam, Hugh ^a   Balciunaite, Egle ^a   Blais, Alexandre ^a   Spektor, Alexander ^a   Scarpulla, Richard C ^c   Young, Richard ^b   Kluger, Yuval ^a   Dynlacht, Brian David ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEAR RESPIRATORY FACTOR 1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR E2F; TUMOR SUPPRESSOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING KINETICS; BINDING SITE; CELL CYCLE; CELL GROWTH; CELL METABOLISM; GENE EXPRESSION REGULATION; GENE REPRESSION; GENE TARGETING; GENETIC ALGORITHM; GENOME ANALYSIS; GROWTH INHIBITION; HUMAN; HUMAN CELL; MAMMAL CELL; MITOCHONDRION; PROTEIN BINDING; PROTEIN MOTIF; REGULATORY MECHANISM;

AMINO ACID MOTIFS; APOPTOSIS; BINDING SITES; DNA-BINDING PROTEINS; E2F4 TRANSCRIPTION FACTOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, REGULATOR; HUMANS; NEOPLASMS; NUCLEAR PROTEINS; NUCLEAR RESPIRATORY FACTOR 1; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEINS; RETINOBLASTOMA-LIKE PROTEIN P107; RETINOBLASTOMA-LIKE PROTEIN P130; TRANSCRIPTION FACTORS; TUMOR CELLS, CULTURED;

MAMMALIA;

EID: 8644281106     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2004.09.037     Document Type: Article

References (40)

1. Avni D., Yang H., Martelli F., Hofmann F., ElShamy W.M., Ganesan S., Scully R., Livingston D.M. Active localization of the retinoblastoma protein in chromatin and its response to S phase DNA damage. Mol. Cell. 12:2003;735-746
2. Bruce J.L., Hurford R.K. Jr., Classon M., Koh J., Dyson N. Requirements for cell cycle arrest by p16INK4a. Mol. Cell. 6:2000;737-742
3. Cam H., Dynlacht B.D. Emerging roles for E2F. beyond the G1/S transition and DNA replication Cancer Cell. 3:2003;311-316
4. Dannenberg J.H., van Rossum A., Schuijff L., te Riele H. Ablation of the retinoblastoma gene family deregulates G(1) control causing immortalization and increased cell turnover under growth-restricting conditions. Genes Dev. 14:2000;3051-3064
5. Dimova D.K., Stevaux O., Frolov M.V., Dyson N.J. Cell cycle-dependent and cell cycle-independent control of transcription by the Drosophila E2F/RB pathway. Genes Dev. 17:2003;2308-2320
6. Gaubatz S., Lindeman G.J., Ishida S., Jakoi L., Nevins J.R., Livingston D.M., Rempel R.E. E2F4 and E2F5 play an essential role in pocket protein-mediated G1 control. Mol. Cell. 6:2000;729-735
7. Giangrande P.H., Hallstrom T.C., Tunyaplin C., Calame K., Nevins J.R. Identification of E-box factor TFE3 as a functional partner for the E2F3 transcription factor. Mol. Cell. Biol. 23:2003;3707-3720
8. Giangrande P.H., Zhu W., Rempel R.E., Laakso N., Nevins J.R. Combinatorial gene control involving E2F and E Box family members. EMBO J. 23:2004;1336-1347
9. Gugneja S., Scarpulla R.C. Serine phosphorylation within a concise amino-terminal domain in nuclear respiratory factor 1 enhances DNA binding. J. Biol. Chem. 272:1997;18732-18739
10. Herzig R.P., Scacco S., Scarpulla R.C. Sequential serum-dependent activation of CREB and NRF-1 leads to enhanced mitochondrial respiration through the induction of cytochrome c. J. Biol. Chem. 275:2000;13134-13141
11. Huo L., Scarpulla R.C. Mitochondrial DNA instability and peri-implantation lethality associated with targeted disruption of nuclear respiratory factor 1 in mice. Mol. Cell. Biol. 21:2001;644-654
12. Hurford R.K. Jr., Cobrinik D., Lee M.H., Dyson N. pRB and p107/p130 are required for the regulated expression of different sets of E2F responsive genes. Genes Dev. 11:1997;1447-1463
13. Ishida S., Huang E., Zuzan H., Spang R., Leone G., West M., Nevins J.R. Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol. Cell. Biol. 21:2001;4684-4699
14. Jiang H., Chou H.S., Zhu L. Requirement of cyclin E-Cdk2 inhibition in p16(INK4a)-mediated growth suppression. Mol. Cell. Biol. 18:1998;5284-5290
15. Kelly D.P., Scarpulla R.C. Transcriptional regulatory circuits controlling mitochondrial biogenesis and function. Genes Dev. 18:2004;357-368
16. Lee E.Y., Cam H., Ziebold U., Rayman J.B., Lees J.A., Dynlacht B.D. E2F4 loss suppresses tumorigenesis in RB mutant mice through a novel mechanism. Cancer Cell. 2:2002;463-472
17. Liu X.S., Brutlag D.L., Liu J.S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20:2002;835-839
18. Muller H., Bracken A.P., Vernell R., Moroni M.C., Christians F., Grassilli E., Prosperini E., Vigo E., Oliner J.D., Helin K. E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes Dev. 15:2001;267-285
19. Narita M., Nunez S., Heard E., Lin A.W., Hearn S.A., Spector D.L., Hannon G.J., Lowe S.W. Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell. 113:2003;703-716
20. Odom D.T., Zizlsperger N., Gordon D.B., Bell G.W., Rinaldi N.J., Murray H.L., Volkert T.L., Schreiber J., Rolfe P.A., Gifford D.K., et al. Control of pancreas and liver gene expression by HNF transcription factors. Science. 303:2004;1378-1381
21. Polager S., Kalma Y., Berkovich E., Ginsberg D. E2Fs up-regulate expression of genes involved in DNA replication, DNA repair and mitosis. Oncogene. 21:2002;437-446
22. Pomeroy S.L., Tamayo P., Gaasenbeek M., Sturla L.M., Angelo M., McLaughlin M.E., Kim J.Y., Goumnerova L.C., Black P.M., Lau C., et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 415:2002;436-442
23. Rayman J.B., Takahashi Y., Indjeian V.B., Dannenberg J.H., Catchpole S., Watson R.J., te Riele H., Dynlacht B.D. E2F mediates cell cycle-dependent transcriptional repression in vivo by recruitment of an HDAC1/mSin3B corepressor complex. Genes Dev. 16:2002;933-947
24. Ren B., Dynlacht B.D. Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol. 376:2004;304-315
25. Ren B., Cam H., Takahashi Y., Volkert T., Terragni J., Young R.A., Dynlacht B.D. E2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpoints. Genes Dev. 16:2002;245-256
26. Ross J.F., Liu X., Dynlacht B.D. Mechanism of transcriptional repression of E2F by the retinoblastoma tumor suppressor protein. Mol. Cell. 3:1999;195-205
27. Sage J., Mulligan G.J., Attardi L.D., Miller A., Chen S., Williams B., Theodorou E., Jacks T. Targeted disruption of the three Rb-related genes leads to loss of G(1) control and immortalization. Genes Dev. 14:2000;3037-3050
28. Sage J., Miller A.L., Perez-Mancera P.A., Wysocki J.M., Jacks T. Acute mutation of retinoblastoma gene function is sufficient for cell cycle re-entry. Nature. 424:2003;223-228
29. Scarpulla R.C. Nuclear activators and coactivators in mammalian mitochondrial biogenesis. Biochim. Biophys. Acta. 1576:2002;1-14
30. Serrano M., Lee H., Chin L., Cordon-Cardo C., Beach D., DePinho R.A. Role of the INK4a locus in tumor suppression and cell mortality. Cell. 85:1996;27-37
31. Sherr C.J. Principles of tumor suppression. Cell. 116:2004;235-246
32. Stevaux O., Dimova D., Frolov M.V., Taylor-Harding B., Morris E., Dyson N. Distinct mechanisms of E2F regulation by Drosophila RBF1 and RBF2. EMBO J. 21:2002;4927-4937
33. Takahashi Y., Rayman J.B., Dynlacht B.D. Analysis of promoter binding by the E2F and pRB families in vivo. distinct E2F proteins mediate activation and repression Genes Dev. 14:2000;804-816
34. Thomas D.M., Carty S.A., Piscopo D.M., Lee J.S., Wang W.F., Forrester W.C., Hinds P.W. The retinoblastoma protein acts as a transcriptional coactivator required for osteogenic differentiation. Mol. Cell. 8:2001;303-316
35. Trimarchi J.M., Lees J.A. Sibling rivalry in the E2F family. Nat. Rev. Mol. Cell Biol. 3:2002;11-20
36. Virbasius J.V., Scarpulla R.C. Activation of the human mitochondrial transcription factor A gene by nuclear respiratory factors. a potential regulatory link between nuclear and mitochondrial gene expression in organelle biogenesis Proc. Natl. Acad. Sci. USA. 91:1994;1309-1313
37. Virbasius C.A., Virbasius J.V., Scarpulla R.C. NRF-1, an activator involved in nuclear-mitochondrial interactions, utilizes a new DNA-binding domain conserved in a family of developmental regulators. Genes Dev. 7:1993;2431-2445
38. Weinmann A.S., Yan P.S., Oberley M.J., Huang T.H., Farnham P.J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 16:2002;235-244
39. Whitfield M.L., Sherlock G., Saldanha A.J., Murray J.I., Ball C.A., Alexander K.E., Matese J.C., Perou C.M., Hurt M.M., Brown P.O., et al. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell. 13:2002;1977-2000
40. Wu L., Timmers C., Maiti B., Saavedra H.I., Sang L., Chong G.T., Nuckolls F., Giangrande P., Wright F.A., Field S.J., et al. The E2F1-3 transcription factors are essential for cellular proliferation. Nature. 414:2001;457-462