title: Computational identification of conserved transcription factor binding sites upstream of genes induced in rat brain by transient focal ischemic stroke.
abstract: Microarray analysis has been used to understand how gene regulation plays a critical role in neuronal injury, survival and repair following ischemic stroke. To identify the transcriptional regulatory elements responsible for ischemia-induced gene expression, we examined gene expression profiles of rat brains following focal ischemia and performed computational analysis of consensus transcription factor binding sites (TFBS) in the genes of the dataset. In this study, rats were sacrificed 24 h after middle cerebral artery occlusion (MCAO) stroke and gene transcription in brain tissues following ischemia/reperfusion was examined using Affymetrix GeneChip technology. The CONserved transcription FACtor binding site (CONFAC) software package was used to identify over-represented TFBS in the upstream promoter regions of ischemia-induced genes compared to control datasets. CONFAC identified 12 TFBS that were statistically over-represented from our dataset of ischemia-induced genes, including three members of the Ets-1 family of transcription factors (TFs). Microarray results showed that mRNA for Ets-1 was increased following tMCAO but not pMCAO. Immunohistochemical analysis of Ets-1 protein in rat brains following MCAO showed that Ets-1 was highly expressed in neurons in the brain of sham control animals. Ets-1 protein expression was virtually abolished in injured neurons of the ischemic brain but was unchanged in peri-infarct brain areas. These data indicate that TFs, including Ets-1, may influence neuronal injury following ischemia. These findings could provide important insights into the mechanisms that lead to brain injury and could provide avenues for the development of novel therapies.
authors.affiliation: Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA.
authors.forename: John V K
authors.initials: JV
authors.lastname: Pulliam
authors.forename: Zhenfeng
authors.initials: Z
authors.lastname: Xu
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Ford
authors.forename: Cuimei
authors.initials: C
authors.lastname: Liu
authors.forename: Yonggang
authors.initials: Y
authors.lastname: Li
authors.forename: Kyndra C
authors.initials: KC
authors.lastname: Stovall
authors.forename: Virginetta S
authors.initials: VS
authors.lastname: Cannon
authors.forename: Teclemichael
authors.initials: T
authors.lastname: Tewolde
authors.forename: Carlos S
authors.initials: CS
authors.lastname: Moreno
authors.forename: Byron D
authors.initials: BD
authors.lastname: Ford
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D001921:Brain; D005786:Gene Expression Regulation / Q000235:genetics*; D007150:Immunohistochemistry; D020244:Infarction, Middle Cerebral Artery / Q000235:genetics; D002546:Ischemic Attack, Transient / Q000235:genetics*; D017078:Laser-Doppler Flowmetry; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D050784:Proto-Oncogene Protein c-ets-1 / Q000096:biosynthesis / Q000235:genetics*; D051381:Rats; D017207:Rats, Sprague-Dawley; D059467:Transcriptome
chemical_list: D050784:Proto-Oncogene Protein c-ets-1