Identification of Transcription Factor Binding Sites Upstream of Human Genes Regulated by the Phosphatidylinositol 3-Kinase and MEK/ERK Signaling Pathways

Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA.
Journal of Biological Chemistry (Impact Factor: 4.57). 06/2004; 279(19):20167-77. DOI: 10.1074/jbc.M309260200
Source: PubMed


We have taken an integrated approach in which expression profiling has been combined with the use of small molecule inhibitors and computational analysis of transcription factor binding sites to characterize regulatory sequences of genes that are targets of specific signaling pathways in growth factor-stimulated human cells. T98G cells were stimulated with platelet-derived growth factor (PDGF) and analyzed by DNA microarrays, which identified 74 immediate-early gene transcripts. Cells were then treated with inhibitors to identify subsets of genes that are targets of the phosphatidylinositol 3-kinase (PI3K) and MEK/ERK signaling pathways. Four groups of PDGF-induced genes were defined: independent of PI3K and MEK/ERK signaling, dependent on PI3K signaling, dependent on MEK/ERK signaling, and dependent on both pathways. The upstream regions of all genes in the four groups were scanned using TRANSFAC for putative cis-elements as compared with a background set of non-induced genes. Binding sites for 18 computationally predicted transcription factors were over-represented in the four groups of co-expressed genes compared with the background sequences (p < 0.01). Many of the cis-elements identified were conserved in orthologous mouse genes, and many of the predicted elements and their cognate transcription factors were consistent with previous experimental data. In addition, chromatin immunoprecipitation assays experimentally verified nine predicted SRF binding sites in T98G cells, including a previously unknown SRF site upstream of DUSP5. These results indicate that groups of human genes regulated by discrete intracellular signaling pathways share common cis-regulatory elements.

18 Reads
  • Source
    • "n , 2011 ) . Interestingly , although defi - ciency of GM - CSF has been shown to induce complete re - sistance to the induction of EAE , the expression of only Honma et al . , 2002 ; Miyazaki et al . , 2002 ) . Microarray analy - sis performed in human glioblastoma cells described tran - scriptional regulation of DEC1 through PI3K and MEK / ERK ( Tullai et al . , 2004 ) , suggesting these signaling pathways as potential candidates linking CD28 activation and DEC1 ex - pression in T cells . Nevertheless , other members of the B7 co - stimulation family could participate in the transcriptional regulation of DEC1 during T cell activation ( Sharpe and Freeman , 2002 ) . Microarray analyses performed to c"
    [Show abstract] [Hide abstract]
    ABSTRACT: During the initial hours after activation, CD4(+) T cells experience profound changes in gene expression. Co-stimulation via the CD28 receptor is required for efficient activation of naive T cells. However, the transcriptional consequences of CD28 co-stimulation are not completely understood. We performed expression microarray analysis to elucidate the effects of CD28 signals on the transcriptome of activated T cells. We show that the transcription factor DEC1 is highly induced in a CD28-dependent manner upon T cell activation, is involved in essential CD4(+) effector T cell functions, and participates in the transcriptional regulation of several T cell activation pathways, including a large group of CD28-regulated genes. Antigen-specific, DEC1-deficient CD4(+) T cells have cell-intrinsic defects in survival and proliferation. Furthermore, we found that DEC1 is required for the development of experimental autoimmune encephalomyelitis because of its critical role in the production of the proinflammatory cytokines GM-CSF, IFN-γ, and IL-2. Thus, we identify DEC1 as a critical transcriptional mediator in the activation of naive CD4(+) T cells that is required for the development of a T cell-mediated autoimmune disease.
    Journal of Experimental Medicine 07/2013; 210(8). DOI:10.1084/jem.20122387 · 12.52 Impact Factor
  • Source
    • "The identification of potential regulatory elements acting in meiotically-active promoters can be a useful tool for understanding regulatory networks [e.g. [20,23-26]]. We scanned enriched cis-acting regulatory DNA elements (CREs) in the promoters of our study to obtain clues about possible co-regulation of meiotically-active genes. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Homologous recombination, together with selection, laid the foundation for traditional plant breeding. The recombination process that takes place during meiotic cell division is crucial for the creation of novel variations of highly desired traits by breeders. Gaining control over this process is important for molecular breeding to achieve more precise, large-scale and quicker plant improvement. As conventional ubiquitous promoters are neither tissue-specific nor efficient in driving gene expression in meiocytes, promoters with high meiotic activities are potential candidates for manipulating the recombination process. So far, only a few meiotically-active promoters have been reported. Recently developed techniques to profile the transcriptome landscape of isolated meiocytes provided the means to discover promoters from genes that are actively expressed in meiosis. In a screen for meiotically-active promoters, we examined ten promoter sequences that are associated with novel meiotic candidate genes. Each promoter was tested by expressing a GFP reporter gene in Arabidopsis. Characterization of regulatory regions revealed that these meiotically-active promoters possessed conserved motifs and motif arrangement. Some of the promoters unite optimal properties which are invaluable for meiosis-directed studies such as delivering specific gene expression in early meiosis I and/or meiosis II. Furthermore, the examination of homologs of the corresponding genes within green plants points to a great potential of applying the information from Arabidopsis to other species, especially crop plants. We identified ten novel meiotically-active promoters; which, along with their homologs, are prime candidates to specifically drive gene expression during meiosis in plants and can thus provide important tools for meiosis study and crop breeding.
    BMC Plant Biology 07/2012; 12(1):104. DOI:10.1186/1471-2229-12-104 · 3.81 Impact Factor
  • Source
    • "There are three isozyme in Raf family, Raf-1, A-Raf, and B-Raf [40]. Raf-1 has been reported to be activated by Ras.GTP acts as a key protein kinase to activate dual protein kinase MEK [41]. MEK in turn activates ERKs by phosphorylating their threonine and tyrosine residues [42]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Electroacupuncture (EA) therapy has been widely accepted as a useful therapeutic technique with low or no risk in the clinical prevention of cardiac hypertrophy. However, the signaling transduction mechanism underlying this effect remains unclear. The current study investigates the effects of EA on the signaling pathways of myocardial hypertrophy (MH) in rats. Up to 40 3-month-old Sprague-Dawley (SD) rats were randomly divided into normal, model, PC6 (Neiguan), and LI4 (Hegu) groups, with ten rats in each group. All the rats except for the normal group received 3 mg/kg·d of isoprinosine hydrochloride (ISO) injection into the back skin. The rats in the PC6 and LI4 groups received EA for 14 days. On the 15th day, electrocardiograms were recorded, and the ultrastructure of the myocardial cells was observed. The myocardial hypertrophy indices (MHIs), electrocardiograph (ECG), ultrastructure observation, levels of plasma angiotensin II (Ang II) and endothelin (ET), as well as protein expression of extracellular signal-regulated kinase (ERK), and phosphorylation extracellular signal regulating kinase (p-ERK) in the left ventricular myocardial tissue were measured. The results indicated that EA can improve cardiac function in MH rats by modulating upstream neuroendocrine cytokines that regulate the ERK signaling pathways.
    Evidence-based Complementary and Alternative Medicine 01/2012; 2012:792820. DOI:10.1155/2012/792820 · 1.88 Impact Factor
Show more


18 Reads