Computational identification of conserved transcription factor binding sites upstream of genes induced in rat brain by transient focal ischemic stroke

Brain Research

Volumn 1495, Issue , 2013, Pages 76-85

  Pulliam, John V K ^a,b   Xu, Zhenfeng ^a   Ford, Gregory D ^a,c   Liu, Cuimei ^a,d   Li, Yonggang ^a   Stovall, Kyndra C ^a,b   Cannon, Virginetta S ^a   Tewolde, Teclemichael ^a   Moreno, Carlos S ^b   Ford, Byron D ^a  

^a MOREHOUSE SCHOOL OF MEDICINE   (United States)

^b EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c MOREHOUSE COLLEGE   (United States)

^d CENTRAL SOUTH UNIVERSITY   (China)

Author keywords

Ischemia; Microarray; Rat; Reperfusion; Stroke; Transcription factor

Indexed keywords

MESSENGER RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ETS 1;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BINDING SITE; BRAIN INJURY; BRAIN ISCHEMIA; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION; GENETIC TRANSCRIPTION; IMMUNOHISTOCHEMISTRY; MALE; MICROARRAY ANALYSIS; MIDDLE CEREBRAL ARTERY OCCLUSION; NERVE CELL; NONHUMAN; PRIORITY JOURNAL; RAT;

ANIMALS; BINDING SITES; BRAIN; GENE EXPRESSION REGULATION; IMMUNOHISTOCHEMISTRY; INFARCTION, MIDDLE CEREBRAL ARTERY; ISCHEMIC ATTACK, TRANSIENT; LASER-DOPPLER FLOWMETRY; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; PROTO-ONCOGENE PROTEIN C-ETS-1; RATS; RATS, SPRAGUE-DAWLEY; TRANSCRIPTOME;

ANIMALIA; RATTUS;

EID: 84872391013     PISSN: 00068993     EISSN: 18726240     Source Type: Journal    
DOI: 10.1016/j.brainres.2012.11.052     Document Type: Article

References (36)

1. K. Barton, N. Muthusamy, C. Fischer, C.N. Ting, T.L. Walunas, L.L. Lanier, and J.M. Leiden The Ets-1 transcription factor is required for the development of natural killer cells in mice Immunity 9 1998 555 563
2. J.C. Bories, D.M. Willerford, D. Grevin, L. Davidson, A. Camus, P. Martin, D. Stehelin, and F.W. Alt Increased T-cell apoptosis and terminal B-cell differentiation induced by inactivation of the Ets-1 proto-oncogene Nature 377 1995 635 638
3. Y.H. Chen, M.D. Layne, S.W. Chung, K. Ejima, R.M. Baron, S.F. Yet, and M.A. Perrella Elk-3 is a transcriptional repressor of nitric-oxide synthase 2 J. Biol. Chem. 278 2003 39572 39577
4. S.W. Chung, Y.H. Chen, S.F. Yet, M.D. Layne, and M.A. Perrella Endotoxin-induced down-regulation of Elk-3 facilitates heme oxygenase-1 induction in macrophages J. Immunol. 176 2006 2414 2420
5. P. Crepieux, J. Coll, and D. Stehelin The Ets family of proteins: weak modulators of gene expression in quest for transcriptional partners Crit. Rev. Oncog. 5 1994 615 638
6. J. Dittmer The biology of the Ets1 proto-oncogene Mol. Cancer 2 2003 29
7. M. Fisher, G. Feuerstein, D.W. Howells, P.D. Hurn, T.A. Kent, S.I. Savitz, and E.H. Lo Update of the stroke therapy academic industry roundtable preclinical recommendations Stroke 40 2009 2244 2250
8. G. Ford, Z. Xu, A. Gates, J. Jiang, and B.D. Ford Expression Analysis Systematic Explorer (EASE) analysis reveals differential gene expression in permanent and transient focal stroke rat models Brain Res. 1071 2006 226 236
9. N. Hashiya, N. Jo, M. Aoki, K. Matsumoto, T. Nakamura, Y. Sato, N. Ogata, T. Ogihara, Y. Kaneda, and R. Morishita In vivo evidence of angiogenesis induced by transcription factor Ets-1: Ets-1 is located upstream of angiogenesis cascade Circulation 109 2004 3035 3041
10. J.A. Hillion, Y. Li, D. Maric, A. Takanohashi, D. Klimanis, J.L. Barker, and J.M. Hallenbeck Involvement of Akt in preconditioning-induced tolerance to ischemia in PC12 cells J. Cereb. Blood Flow Metab. 26 2006 1323 1331
11. P.C. Hollenhorst, L.P. McIntosh, and B.J. Graves Genomic and biochemical insights into the specificity of ETS transcription factors Annu. Rev. Biochem. 80 2011 437 471
12. C. Iadecola, and J. Anrather The immunology of stroke: from mechanisms to translation Nat. Med. 17 2011 796 808
13. R. Kapadia, K. Tureyen, K.K. Bowen, H. Kalluri, P.F. Johnson, and R. Vemuganti Decreased brain damage and curtailed inflammation in transcription factor CCAAT/enhancer binding protein beta knockout mice following transient focal cerebral ischemia J. Neurochem. 98 2006 1718 1731
14. S. Karanam, and C.S. Moreno CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets Nucleic Acids Res. 32 2004 W475 W484
15. F.D. Karim, L.D. Urness, C.S. Thummel, M.J. Klemsz, S.R. McKercher, A. Celada, C. Van Beveren, R.A. Maki, C.V. Gunther, and J.A. Nye The ETS-domain: a new DNA-binding motif that recognizes a purine-rich core DNA sequence Genes Dev. 4 1990 1451 1453
16. J.H. Kim, Y.W. Lee, K.A. Park, W.T. Lee, and J.E. Lee Agmatine attenuates brain edema through reducing the expression of aquaporin-1 after cerebral ischemia J. Cereb. Blood Flow Metab. 30 2010 943 949
17. B. Kramer, K. Wiegmann, and M. Kronke Regulation of the human TNF promoter by the transcription factor Ets J. Biol. Chem. 270 1995 6577 6583
18. P. Kury, M. Schroeter, and S. Jander Transcriptional response to circumscribed cortical brain ischemia: spatiotemporal patterns in ischemic vs. remote non-ischemic cortex Eur. J. Neurosci. 19 2004 1708 1720
19. Y. Li, Z. Xu, G.D. Ford, D.R. Croslan, T. Cairobe, Z. Li, and B.D. Ford Neuroprotection by neuregulin-1 in a rat model of permanent focal cerebral ischemia Brain Res. 1184 2007 277 283
20. Y. Li, P.J. Lein, C. Liu, D.A. Bruun, T. Tewolde, G. Ford, and B.D. Ford Spatiotemporal pattern of neuronal injury induced by DFP in rats: A model for delayed neuronal cell death following acute OP intoxication Toxicol. Appl. Pharmacol. 253 2011 261 269
21. W. Liu, G. Wang, and A.G. Yakovlev Identification and functional analysis of the rat caspase-3 gene promoter J. Biol. Chem. 277 2002 8273 8278
22. A. Lu, Y. Tang, R. Ran, J.F. Clark, B.J. Aronow, and F.R. Sharp Genomics of the periinfarction cortex after focal cerebral ischemia J. Cereb. Blood Flow Metab. 23 2003 786 810
23. N. Muthusamy, K. Barton, and J.M. Leiden Defective activation and survival of T cells lacking the Ets-1 transcription factor Nature 377 1995 639 642
24. P. Oettgen Regulation of vascular inflammation and remodeling by ETS factors Circ. Res. 99 2006 1159 1166
25. D.A. Ridder, and M. Schwaninger NF-kappaB signaling in cerebral ischemia Neuroscience 158 2009 995 1006
26. D.A. Ridder, S. Bulashevska, G.V. Chaitanya, P.P. Babu, B. Brors, R. Eils, A. Schneider, and M. Schwaninger Discovery of transcriptional programs in cerebral ischemia by in silico promoter analysis Brain Res. 1272 2009 3 13
27. R. Rodriguez-Mercado, G.D. Ford, Z. Xu, E.N. Kraiselburd, M.I. Martinez, V. Eterovic, E. Colon, I.V. Rodriguez, P. Portilla, P.A. Ferchmin, L. Gierbolini, M. Rodriguez-Carrasquillo, M.D. Powell, Pulliam JVK, C.O. McCraw, A. Gates, and B.D. Ford Acute neuronal injury and blood genomic profiles in a nonhuman primate model for ischemic stroke J. Comp. Med. 62 2012 427 438
28. L. Russell, and L.A. Garrett-Sinha Transcription factor Ets-1 in cytokine and chemokine gene regulation Cytokine 51 2010 217 226
29. A. Salminen, P.K. Liu, and C.Y. Hsu Alteration of transcription factor binding activities in the ischemic rat brain Biochem. Biophys. Res. Commun. 212 1995 939 944
30. A.S. Sarabi, H. Shen, Y. Wang, B.J. Hoffer, and C.M. Backman Gene expression patterns in mouse cortical penumbra after focal ischemic brain injury and reperfusion J. Neurosci. Res. 86 2008 2912 2924
31. A. Schneider, A. Martin-Villalba, F. Weih, J. Vogel, T. Wirth, and M. Schwaninger NF-kappaB is activated and promotes cell death in focal cerebral ischemia Nat. Med. 5 1999 554 559
32. J. Tsai, R. Sultana, Y. Lee, G. Pertea, S. Karamycheva, V. Antonescu, J. Cho, B. Parvizi, F. Cheung, and J. Quackenbush RESOURCERER: a database for annotating and linking microarray resources within and across species Genome Biol. 2:SOFTWARE0002 2001
33. R.L. Vangilder, J.D. Huber, C.L. Rosen, and T.L. Barr The transcriptome of cerebral ischemia Brain Res. Bull 2012
34. J. Wang, M.F. Shannon, and I.G. Young A role for Ets1, synergizing with AP-1 and GATA-3 in the regulation of IL-5 transcription in mouse Th2 lymphocytes Int Immunol 18 2006 313 323
35. D. Watanabe, H. Takagi, K. Suzuma, I. Suzuma, H. Oh, H. Ohashi, S. Kemmochi, A. Uemura, T. Ojima, E. Suganami, N. Miyamoto, Y. Sato, and Y. Honda Transcription factor Ets-1 mediates ischemia- and vascular endothelial growth factor-dependent retinal neovascularization Am. J. Pathol. 164 2004 1827 1835
36. Z. Xu, G.D. Ford, D.R. Croslan, J. Jiang, A. Gates, R. Allen, and B.D. Ford Neuroprotection by neuregulin-1 following focal stroke is associated with the attenuation of ischemia-induced pro-inflammatory and stress gene expression Neurobiol. Dis. 19 2005 461 470