In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2

A. thaliana sulfur deficiency-induced 1 and sulfur deficiency-induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency and their transcription is strongly induced by this condition. However, little is currently known about the cis- and trans-factors that regulate SDI expression. To identify potential transcription factors and DNA sequence element regulators of SDI expression we performed a comparative in silico analysis of their promoter sequences cataloguing known and potentially new cis-elements. We further screened an arrayed library of Arabidopsis transcription factors (TF) for binding to the SDI1 and SDI2 promoters. In total 14 candidate TF regulators of SDIs were identified with yeast-one-hybrid analyses, of which five bound to both promoters, 4 were specific to SDI1, and 5 were specific SDI2. Direct association between particular cis-elements in these promoter regions and specific TFs was established via electrophoretic mobility shift assays. SLIM1 was shown to bind SURE cis-element(s) in the proximal promoter region of both SDI1 and SDI2. The bZIP core cis-element in the proximal promoter region of SDI2 was shown to be important for bZIP16, bZIP44, and HYH binding. GBF1 was shown to bind the E-box in the proximal promoter region of SDI2. Additionally, we performed a meta-analysis of expression changes of these 14 TF candidates in a variety of conditions that alter SDI expression. These data will allow for more detailed future analysis of the molecular factors required for transcriptional regulation of SDIs under a range of physiological and metabolic conditions, apart from sulfur deficiency.

Abstract 359: Negative Regulation Of The Fgf-16 Gene Promoter By Doxorubicin Is Associated With A Decrease In Nkx2.5 Binding

Doxorubicin (DOX) is a widely used and effective anti-cancer drug, but it is also cardiotoxic, which can lead to heart failure, and so strategies are needed to protect the heart. Fibroblast growth factor 16 (FGF-16) is preferentially expressed and released from cardiomyocytes after birth. Evidence suggests that FGF-16 decreases the risk of heart damage and limits the negative effects of heart remodeling (hypertrophy and fibrosis) after injury in vivo. Exogenous addition of FGF-16 also increased resistance to the loss of contractility in an isolated heart model of acute DOX-induced injury. Thus, how endogenous FGF-16 production and by extension function is affected by DOX treatment is of interest. The FGF-16 gene is highly conserved between human and murine species. Alignment of sequences indicates a conserved Nkx2.5 binding site in the proximal promoter region that is associated with a previously characterized TATA box. Nkx2.5 is an important factor in vertebrate heart development and congenital disease. Furthermore, Nkx2.5 RNA levels are decreased with DOX treatment. Thus, the possibility that DOX negatively affects FGF-16, perhaps through an effect on Nkx2.5 levels or binding, was investigated. Neonatal rat cardiomyocytes were treated with DOX, and FGF-16 RNA levels decreased 75% within 6 hours as assessed by qPCR. Inhibition of transcription with actinomycinD had no effect on the DOX-induced decrease in FGF-16 RNA levels. Further support for an effect of DOX on FGF-16 transcription was obtained by transfection of cardiomyocytes with a hybrid 747 bp mouse FGF-16 promoter/luciferase reporter gene that was treated with DOX; a significant decrease in luciferase activity was observed. Electrophoretic mobility shift and chromatin immunoprecipitation assays suggest reduced Nkx2.5 protein-DNA interaction with this site after DOX treatment in vitro and in situ, respectively. These data indicate that DOX decreases FGF-16 RNA expression and this correlates with a decrease in Nkx2.5 levels and association with the proximal promoter region. A direct effect of Nkx2.5 on FGF-16 promoter activity awaits further testing. Thus, a decrease or loss of FGF-16 synthesis might contribute to the DOX-induced damage and/or response to injury.

Epigenetic changes in hypothalamic appetite regulatory genes may underlie the developmental programming for obesity in rat neonates subjected to a high-carbohydrate dietary modification

Earlier, we showed that rearing of newborn rats on a high-carbohydrate (HC) milk formula resulted in the onset of hyperinsulinemia, its persistence in the post-weaning period and adult-onset obesity. DNA methylation of CpG dinucleotides in the proximal promoter region and modifications in the N-terminal tail of histone 3 associated with the neuropeptide Y (Npy) and pro-opiomelanocortin (Pomc) genes were investigated to decipher the molecular mechanisms supporting the development of obesity in HC females. Although there were no differences in the methylation status of CpG dinucleotides in the proximal promoter region of the Pomc gene, altered methylation of specific CpG dinucleotides proximal to the transcription start site was observed for the Npy gene in the hypothalami of 16- and 100-day-old HC rats compared with their methylation status in mother-fed (MF) rats. Investigation of histone tail modifications on hypothalamic chromatin extracts from 16-day-old rats indicated decreased acetylation of lysine 9 in histone 3 (H3K9) for the Pomc gene and increased acetylation for the same residue for the Npy gene, without changes in histone methylation (H3K9) in both genes in HC rats. These findings are consistent with the changes in the levels of Npy and Pomc mRNAs in the hypothalami of HC rats compared with MF animals. Our results suggest that epigenetic modifications could contribute to the altered gene expression of the Npy and Pomc genes in the hypothalami of HC rats and could be a mechanism leading to hyperphagia and the development of obesity in adult female HC rats.