The dynamics of E1A in regulating networks and canonical pathways in quiescent cells

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Dazard, Jean Eudes ^a   Zhang, Keman ^a   Sha, Jingfeng ^a   Yasin, Omar ^a   Cai, Linda ^a   Nguyen, Chien ^a   Ghosh, Mrinal ^b   Bongorno, Jennifer ^c   Harter, Marian L ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

^c CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOVIRIDAE;

EID: 79957461749     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-160     Document Type: Article

References (37)

1. Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival. DL Miller CL Myers B Rickards HA Coller SJ Flint, Genome Biol 2007 8 58 10.1186/gb-2007-8-4-r58 17430596
2. Recent lessons in gene expression, cell cycle control, and cell biology from adenovirus. AJ Berk, Oncogene 2005 24 7673 7685 10.1038/sj.onc.1209040 16299528 (Pubitemid 41670670)
3. An adenovirus early region 1A protein is required for maximal viral DNA replication in growth-arrested human cells. KR Spindler CY Eng AJ Berk, Journal of Virology 1985 53 742 750 3973965 (Pubitemid 15173276)
4. A viral mechanism for remodeling chromatin structure in G0 cells. MK Ghosh ML Harter, Mol Cell 2003 12 255 260 10.1016/S1097-2765(03)00225-9 12887910 (Pubitemid 36945049)
5. E1A interacts with two opposing transcriptional pathways to induce quiescent cells into S phase. J Sha MK Ghosh K Zhang ML Harter, J Virol 2010 84 4050 4059 10.1128/JVI.02131-09 20089639
6. Inactivation of p21 by E1A leads to the induction of apoptosis in DNA-damaged cells. D Chattopadhyay MK Ghosh A Mal ML Harter, J Virol 2001 75 9844 9856 10.1128/JVI.75.20.9844-9856.2001 11559818 (Pubitemid 32900120)
7. The E1A oncoprotein disables the CDK inhibitor p27 Kip1 in TGF-á treated cells. A Mal RYC Poon PH Howe H Toyoshima T Hunter ML Harter, Nature 1996 380 262 265 10.1038/380262a0 8637577
8. Molecular mechanisms of E2F-dependent activation and pRB-mediated repression. MV Frolov NJ Dyson, J Cell Sci 2004 117 2173 2181 10.1242/jcs.01227 15126619 (Pubitemid 38807486)
9. E2F meditates cell cycle-dependent transrciptional repression in vivo by recruitment of an HDAC1/mSin3B corepressor complex. JB Rayman Y Takahashi VB Indjeian JH Dannenberg S Catchpole RJ Watson H te Riele BD Dynlacht, Genes & Dev 2002 16 933 947 10.1101/gad.969202 21618648 (Pubitemid 34408543)
10. Analysis of promoter binding by the E2F and pRB families in vivo: distinct E2F proteins mediate activation and repression. Y Takahashi JB Rayman BD Dynlacht, Genes Dev 2000 14 804 816 10766737 (Pubitemid 30215000)
11. A common set of gene regulatory networks links metabolism and growth inhibition. H Cam E Balciunaite A Blais A Spektor RC Scarpulla R Young Y Kluger BD Dynlacht, Mol Cell 2004 16 399 411 10.1016/j.molcel.2004.09.037 15525513 (Pubitemid 39504794)
12. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. X Xu M Bieda VX Jin A Rabinovich MJ Oberley R Green PJ Farnham, Genome Res 2007 17 1550 1561 10.1101/gr.6783507 17908821 (Pubitemid 350074851)
13. The adenovirus E1A protein overrides the requirement for cellular ras in initiating DNA synthesis. DW Stacey SF Dobrowolski A Piotrkowski ML Harter, EMBO J 1994 13 6107 6114 7813447
14. Operating characteristics and extensions of the false discovery rate procedure. C Genovese L Wasserman, J R Statist Soc 2002 64 499 517 10.1111/1467-9868.00347
15. Spike and slab gene selection for multigroup microarray data. H Ishwaran JS Rao, J Amer Stat Assoc 2005 100 764 780 10.1198/016214505000000051 (Pubitemid 41276327)
16. Spike and slab variable selection: frequentist and Bayesian strategies. H Ishwaran JS Rao, The Annals of Statistics 2005 33 730 773 10.1214/ 009053604000001147 (Pubitemid 41053721)
17. Detecting differentially expressed genes in microarrays using Bayesian model selection. H Ishwaran JS Rao, J Amer Stat Assoc 2003 98 438 455 10.1198/016214503000224 (Pubitemid 36931567)
18. Epigenetic reprogramming by adenovirus e1a. R Ferrari M Pellegrini GA Horwitz W Xie AJ Berk SK Kurdistani, Science 2008 321 1086 1088 10.1126/science.1155546 18719284
19. Maintaining genome stability at the replication fork. D Branzei M Foiani, Nat Rev Mol Cell Biol 2010 11 208 219 10.1038/nrm2852 20177396
20. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. B Ren H Cam Y Takahashi T Volkert J Terragni RA Young BD Dynlacht, Genes Dev 2002 16 245 256 10.1101/gad.949802 11799067 (Pubitemid 34075816)
21. Quiescent murine cells lack global genomic repair but are proficient in transcription-coupled repair. JH Bielas JA Heddle, DNA Repair (Amst) 2004 3 711 717 10.1016/j.dnarep.2004.02.010 (Pubitemid 38716100)
22. DNA repair in differentiated cells: some new answers to old questions. T Nouspikel, Neuroscience 2007 145 1213 1221 10.1016/j.neuroscience.2006.07.006 16920273 (Pubitemid 46602722)
23. The absence of caveolin-1 increases proliferation and anchorage-independent growth by a Rac-dependent, Erk-independent mechanism. A Cerezo MC Guadamillas JG Goetz S Sanchez-Perales E Klein RK Assoian MA del Pozo, Mol Cell Biol 2009 29 5046 5059 10.1128/MCB.00315-09 19620284
24. Interaction between human MCM7 and Rad17 proteins is required for replication checkpoint signaling. CC Tsao C Geisen RT Abraham, EMBO J 2004 23 4660 4669 10.1038/sj.emboj.7600463 15538388 (Pubitemid 39657865)
25. Mechanisms of transcriptional repression by histone lysine methylation. P Hublitz M Albert AH Peters, Int J Dev Biol 2009 53 335 354 10.1387/ijdb. 082717ph 19412890
26. Protective effect of Toll-like receptor 4 in pulmonary vaccinia infection. MA Hutchens KE Luker J Sonstein G Nunez JL Curtis GD Luker, PLoS Pathog 2008 4 1000153 10.1371/journal.ppat.1000153 18802464
27. Immune responses to adenoviruses: viral evasion mechanisms and their implications for the clinic. WS Wold K Doronin K Toth M Kuppuswamy DL Lichtenstein AE Tollefson, Curr Opin Immunol 1999 11 380 386 10.1016/S0952-7915(99)80064-8 10448144 (Pubitemid 29377903)
28. Viruses and apoptosis. A Roulston RC Marcellus PE Branton, Annu Rev Microbiol 1999 53 577 628 10.1146/annurev.micro.53.1.577 10547702 (Pubitemid 29503742)
29. p21 and retinoblastoma protein control the absence of DNA replication in terminally differentiated muscle cells. A Mal D Chattopadhyay MK Ghosh RYC Poon T Hunter ML Harter, J Cell Biol 2000 149 281 292 10.1083/jcb.149.2.281 10769022 (Pubitemid 30227147)
30. Model-based variance-stabilizing transformation for Illumina microarray data. SM Lin P Du W Huber WA Kibbe, Nucleic acids research 2008 36 11 18178591
31. Bioconductor: open software development for computational biology and bioinformatics. RC Gentleman VJ Carey DM Bates B Bolstad M Dettling S Dudoit B Ellis L Gautier Y Ge J Gentry, et al. Genome biology 2004 5 80 10.1186/gb-2004-5-10-r80 15461798
32. lumi: a pipeline for processing Illumina microarray. P Du WA Kibbe SM Lin, Bioinformatics (Oxford, England) 2008 24 1547 1548 10.1093/bioinformatics/ btn224 (Pubitemid 351911712)
33. Analysis of high density expression microarrays with signed-rank call algorithms. WM Liu R Mei X Di TB Ryder E Hubbell S Dee TA Webster CA Harrington MH Ho J Baid, et al. Bioinformatics (Oxford, England) 2002 18 1593 1599 10.1093/bioinformatics/18.12.1593 (Pubitemid 36097724)
34. nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. P Du WA Kibbe SM Lin, Biology direct 2007 2 16 10.1186/1745-6150-2-16 17540033
35. Use and misuse of the gene ontology annotations. SY Rhee V Wood K Dolinski S Draghici, Nat Rev Genet 2008 9 509 515 10.1038/nrg2363 18475267 (Pubitemid 351861540)
36. Ontological analysis of gene expression data: current tools, limitations, and open problems. P Khatri S Draghici, Bioinformatics (Oxford, England) 2005 21 3587 3595 10.1093/bioinformatics/bti565 (Pubitemid 41264092)
37. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Y Benjamini Y Hochberg, J R Statist Soc 1995 57 289 300