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

• Type of Material: Article
• Authors: John V.K. Pulliam, Morehouse School of Medicine; Zhengfeng Xu, Morehouse School of Medicine; Gregory D. Ford, Morehouse School of Medicine; Cuimei Liu, Morehouse School of Medicine; Yonggang Li, Morehouse School of Medicine; Kyndra Stovall, Morehouse School of Medicine; Virginetta S. Cannon, Morehouse School of Medicine; Teclemichael Tewolde, Morehouse School of Medicine; Carlos Moreno, Emory University; Byron D. Ford, Morehouse School of Medicine
• Language: English
• Date: 2013-02-07
• Publisher: Elsevier: 12 months
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2012 Elsevier B.V.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1016/j.brainres.2012.11.052
• Title of Journal or Parent Work: Brain Research
• ISSN: 0006-8993
• Volume: 1495
• Start Page: 76
• End Page: 85
• Grant/Funding Information: This work was supported by NIH grants R01 NS34194 (B.F.), U01 NS 057993 (B.F.), U54 NS060659 (B.F.), K12 GM000680 (J.P.) and the W.M. Keck Foundation.; The project described was supported by Grants Number U54 RR026137, G12RR003034 and S21MD000101 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH) and its contents are solely the responsibility of the authors and do not necessarily represent the official views of NCRR or NIH.
• Keywords: Transcription factor; NF-KAPPA-B; EXPRESSION; Microarray; FACTOR ETS-1; Rat; Science & Technology; PERMANENT; CEREBRAL-ISCHEMIA; INFLAMMATION; Stroke; Life Sciences & Biomedicine; CELL-DEATH; Reperfusion; NEUREGULIN-1; Neurosciences & Neurology; NEUROPROTECTION; Neurosciences; Ischemia; PROMOTER ANALYSIS
• Research Categories: Biology, Neuroscience; Health Sciences, General

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.