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Articles by Y Gan
Total Records ( 2 ) for Y Gan
  Y Gan , J Guan and S. Zhou

Motivation: Identification of core promoters is a key clue in understanding gene regulations. However, due to the diverse nature of promoter sequences, the accuracy of existing prediction approaches for non-CpG island (simply CGI)-related promoters is not as high as that for CGI-related promoters. This consequently leads to a low genome-wide promoter prediction accuracy.

Results: In this article, we first systematically analyze the similarities and differences between the two types of promoters (CGI- and non-CGI-related) from a novel structural perspective, and then devise a unified framework, called PNNP (Pattern-based Nearest Neighbor search for Promoter), to predict both CGI- and non-CGI-related promoters based on their structural features. Our comparative analysis on the structural characteristics of promoters reveals two interesting facts: (i) the structural values of CGI- and non-CGI-related promoters are quite different, but they exhibit nearly similar structural patterns; (ii) the structural patterns of promoters are obviously different from that of non-promoter sequences though the sequences have almost similar structural values. Extensive experiments demonstrate that the proposed PNNP approach is effective in capturing the structural patterns of promoters, and can significantly improve genome-wide performance of promoters prediction, especially non-CGI-related promoters prediction.

  Y Gan , Y Zhang , D. J DiGirolamo , J Jiang , X Wang , X Cao , K. R Zinn , D. P Carbone , T. L Clemens and S. J. Frank

GH promotes longitudinal growth and regulates multiple cellular functions in humans and animals. GH signals by binding to GH receptor (GHR) to activate the tyrosine kinase, Janus kinase 2 (JAK2), and downstream pathways including signal transducer and activator of transcription 5 (STAT5), thereby regulating expression of genes including IGF-I. GH exerts effects both directly and via IGF-I, which signals by activating the IGF-I receptor (IGF-IR). IGF-IR is a cell surface receptor that contains intrinsic tyrosine kinase activity within its intracellular domain. In this study, we examined the potential role of IGF-IR in facilitating GH-induced signal transduction, using mouse primary calvarial osteoblasts with Lox-P sites flanking both IGF-IR alleles. These cells respond to both GH and IGF-I and in vitro infection with an adenovirus that drives expression of Cre recombinase (Ad-Cre) dramatically reduces IGF-IR abundance without affecting the abundance of GHR, JAK2, STAT5, or ERK. Notably, infection with Ad-Cre, but not a control adenovirus, markedly inhibited acute GH-induced STAT5 activity (more than doubling the ED50 and reducing the maximum activity by nearly 50%), while sparing GH-induced ERK activity, and markedly inhibited GH-induced transactivation of a STAT5-dependent luciferase reporter. The effect of Ad-Cre on GH signaling was specific, as platelet-derived growth factor-induced signaling was unaffected by Ad-Cre-mediated reduction of IGF-IR. Ad-Cre-mediated inhibition of GH signaling was reversed by adenoviral reexpression of IGF-IR, but not by infection with an adenovirus that drives expression of a hemagglutination-tagged somatostatin receptor, which drives expression of the unrelated somatostatin receptor, and Ad-Cre infection of nonfloxed osteoblasts did not affect GH signaling. Notably, infection with an adenovirus encoding a C-terminally truncated IGF-IR that lacks the tyrosine kinase domain partially rescued both acute GH-induced STAT5 activity and GH-induced IGF-I gene expression in cells in which endogenous IGF-IR was reduced. These data, in concert with our earlier findings that GH induces a GHR-JAK2-IGF-IR complex, suggest a novel function for IGF-IR. In addition to its role as a key IGF-I signal transducer, this receptor may directly facilitate acute GH signaling. The implications of these findings are discussed.

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