Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression最新文献

Sphingosine kinase 1 (SphK1) is a lipid kinase implicated in mitogenic signaling pathways in vascular smooth muscle cells. We demonstrate that human coronary artery smooth muscle (HCASM) cells require SphK1 for growth and that SphK1 mRNA and protein levels are elevated in PDGF stimulated HCASM cells. To determine the mechanism of PDGF-induced SphK1 expression, we used pharmacological inhibitors of the PI3K/AKT/mTOR signaling pathway. Wortmannin, SH-5, and rapamycin significantly blocked PDGF-stimulated induction of SphK1 mRNA and protein expression, indicating a regulatory role of the PI3K/AKT/mTOR pathway in SphK1 expression. To determine which isoform of AKT regulates SphK1 mRNA and protein levels, siRNAs specific for AKT1, AKT2, and AKT3 were used. We show that AKT2 siRNA significantly blocked PDGF-stimulated increases in SphK1 mRNA and protein expression levels as well as SphK1 enzymatic activity levels. In contrast, AKT1 or AKT3 siRNA did not have an effect. Together, these results demonstrate that the PI3K/AKT/mTOR signaling pathway is involved in regulation of SphK1, with AKT2 playing a key role in PDGF-induced SphK1 expression in HCASM cells.

Native estrogens and estrogenic chemicals exert their actions primarily through the nuclear estrogen receptors (ERs). The present study is directed towards providing a molecular basis for detection of estrogenic and antiestrogenic effects of compounds. In the present study, we isolated successfully two isoforms of a full-length ER mRNA from the liver of Xenopus (Silurana) tropicalis, and analyzed their expression in various tissues during the development by RT-PCR method. The isolated full-length ERα and ERβ cDNAs contained a 1755-bp and a 1644-bp coding regions, respectively. The deduced amino acid sequence of X. tropicalis ERα was highly homologous to previously published X. tropicalis ERα, Xenopus laevis ERs (xer3, ERα1, and ERα2), and X. laevis ER-related proteins. The N-terminal region of the X. tropicalis ERα amino acid sequence cloned in the present study was more highly homologous to that of the xer3 amino acid sequence than the previously published X. tropicalis ERα sequence. Some amino acid residues in the D domain were absent in this sequence. In contrast, the deduced amino acid sequence of the C and E/F domains in X. tropicalis ERβ was highly homologous to those in teleosts, quail, and human ERβs. The RT-PCR analysis showed that expression of the two ER transcripts was relatively abundant in the brain, liver, and gonad/kidney complex of 2-month-old froglet, but weakly expressed in the heart, stomach, leg muscle, and back skin. Gonadal sex differentiation occurred histologically in the X. tropicalis tadpole between Nieuwkoop and Faber stages 54 and 59. The ERα transcripts in the brain, liver and gonad/kidney complex, and ERβ in the brain were expressed at low levels in the tadpole at stage 51, but became extremely abundant in the tadpole at stage 60, and remained at relatively high levels in the froglet after metamorphosis. In contrast, ERβ transcript was expressed abundantly in a consistent manner in the liver and gonad/kidney complex from stage 51 through metamorphosis. Expression of the two ER transcripts was recognized at almost the same levels in both sexes during the development, except for relatively lower expression of ERβ in the female gonad after metamorphosis. These results taken together suggest that the brain, liver, and gonad/kidney complex of the X. tropicalis tadpole may be more susceptible to toxic influences by exogenous estrogenic substances after sex differentiation.

Expression of CCL23 is induced by external stimuli including PMA in monocytes, but its transcriptional regulation has not been studied to date. Serial deletion analysis of its 5′ flanking region revealed that the region − 293 to + 31 was important for induction by PMA. Cis-acting elements at the − 269/− 264 (NFAT site), − 167/− 159 (NF-κB site), and − 51/− 43 (AP-1 site) positions were identified as the critical sites for the CCL23 expression in U937 cells. We demonstrated the binding of the transcription factors to the consensus sites. Specific inhibitors for signal pathways reduced PMA-induced expression of CCL23, confirming involvement of these transcription factors.

ATP-dependent chromatin remodeling is performed by multi-subunit protein complexes. Over the last years, the identity of these factors has been unveiled in yeast and many parallels have been drawn with animal and plant systems, indicating that sophisticated chromatin transactions evolved prior to their divergence. Here we review current knowledge pertaining to the molecular mode of action of ATP-dependent chromatin remodeling, from single molecule studies to genome-wide genetic and proteomic studies. We focus on the budding yeast versions of SWI/SNF, RSC, DDM1, ISWI, CHD1, INO80 and SWR1.

Glypican 3 (GPC3) is an X-linked gene that has its peak expression during development and is down-regulated in all studied tissues after birth. We have shown that GPC3 was expressed in neuroblastoma and Wilms' tumor. To understand the mechanisms regulating the transcription of this gene in neuroblastoma cells, we have focused our study on the identification of putative transcription factors binding the promoter. In this report we performed in vivo dimethylsulfate, UV type C irradiation and DNaseI footprinting analyses coupled with ligation-mediated PCR on nearly 1000 bp of promoter in two neuroblastoma cell lines, SJNB-7 (expressing GPC3) and SK-N-FI (not expressing GPC3). Nucleosome signature footprints were observed in the most distal part of the studied region in both cell lines. We detected eight large differentially protected regions, suggesting the presence of binding proteins in both cell lines but more DNA–protein interactions in GPC3-expressing cells. Sp1 was previously shown to be able to bind some of these regions. Here by combining electromobility shift assays and chromatin immunoprecipitations we showed that the transcription factor NFY was part of the DNA–protein complex found in footprinted regions upstream of the described minimal promoter. These studies performed on chromatin in situ suggest that NFY and yet unknown cell type-specific factors may play an important role in the regulation of GPC3.

PNPase is a phosphate-dependent exonuclease of Escherichia coli required for growth in the cold. In this work we explored the effect of specific mutations in its two RNA binding domains KH and S1 on RNA binding, enzymatic activities, autoregulation and ability to grow at low temperature. We removed critical motifs that stabilize the hydrophobic core of each domain, as well as made a complete deletion of both (ΔKHS1) that severely impaired PNPase binding to RNA. Nevertheless, a residual RNA binding activity, possibly imputable to catalytic binding, could be observed even in the ΔKHS1 PNPase. These mutations also resulted in significant changes in the kinetic behavior of both phosphorolysis and polymerization activities of the enzyme, in particular for the double mutant Pnp-ΔKHS1-H. Additionally, PNPases with mutations in these RNA binding domains did not autoregulate efficiently and were unable to complement the growth defect of a chromosomal Δpnp mutation at 18 °C. Based on these results it appears that in E. coli the RNA binding domains of PNPase, in particular the KH domain, are vital at low temperature, when the stem–loop structures present in the target mRNAs are more stable and a machinery capable to degrade structured RNA may be essential.

Members of transforming growth factor-β (TGF-β) superfamily play important roles in diverse biological functions including early development. These extracellular factors exert their effects by interacting with membrane receptors followed by signal transduction by a group of Smad proteins. Smad7 is an inhibitory Smad protein that specifically antagonizes TGF-β and activin signaling. To characterize the developmental role of Smad7, a transgenic mouse model was generated using a 4.3 kb mouse Smad7 promoter driving β-galactosidase expression. In these mice, the Smad7 promoter defined a restrictive expression pattern of β-galactosidase in a tightly regulated temporal and spatial manner. The β-galactosidase gene was transiently expressed in the cardiovascular structures including heart cushion tissues and the endothelium of major arteries at E11.5 to E12.5. Through E12.5 to E17.5, β-galactosidase expression was prominently detected in the epithelium of developing cochlea and nasolacrimal duct. In addition, it was temporally expressed in trigeminal ganglion, the skeletal muscles surrounding major joints, primordium of the jaws, as well as genital tubercle. These studies indicated that the 4.3 kb Smad7 promoter contains sufficient regulatory elements to define controlled gene expression during mouse development.

Prostaglandin endoperoxide H synthase-1 gene expression is described as inducible in a few contexts such as differentiation of megakaryoblastic MEG-01 cells into platelet-like structures. In the MEG-01 cells model of PGHS-1 gene induction, we previously reported a delay in protein synthesis and identified the translational step of gene expression as being regulated. In the current study, we mapped PGHS-1 mRNA sequences regulating translational efficiency and identified an RNA binding protein. The 5′UTR and first two exons of the PGHS-1 5′ mRNA decreased the synthesis of Luciferase protein by approximately 80% without significant changes in mRNA levels when compared to controls. Both the PGHS-1 5′-UTR and the first two exons were required for activity. Sucrose density gradient fractionations of cytoplasmic extracts from MEG-01 cells infected with reporter constructs, either controls or containing PGHS-1 sequence, presented a similar profile of distribution of reporter transcripts between polysomal and non-polysomal fractions. RNA/protein interaction studies revealed nucleolin binding to the 135 nt PGHS-1 sequence. Mutation of the two NRE elements located in the 5′end of PGHS-1 mRNA sequence partially reduced the negative activity of the 135 nt sequence. Stable secondary structures predicted at the 5′ end of the transcript are potentially involved in translational regulation. We propose that the 5′end of PGHS-1 mRNA represses translation and could delay the synthesis of PGHS-1 enzyme.

The correlation between diet and variation in gene-expression is an important field which could be considered to approach cancer pathways comprehension. We examined the effects of lycopene on breast cancer cell lines using pangenomic arrays. Lycopene is derived predominantly from tomatoes and tomato products and there is some epidemiologic evidence for a preventive role in breast cancer. Previously, we investigated lycopene in breast cancer using a dedicated breast cancer microarray. To confirm these results and explore pathways other than those implicated in breast cancer, for this study we used pangenomic arrays containing 25,000 oligonucleotides. This in vitro study assayed two human mammary cancer cell lines (MCF-7 and MDA-MB-231), and a fibrocystic breast cell line (MCF-10a) treated or not with 10 μM lycopene for 48 h. A competitive hybridization was performed between Cy3-labeled lycopene treated RNA and Cy5-labeled untreated RNA to define differentially expressed genes. Using t-test analysis, a subset of 391 genes was found to be differentially modulated by lycopene between estrogen-positive cells (MCF-7) and estrogen-negative cells (MDA-MB-231, MCF-10a). Hierarchical clustering revealed 726 discriminatory genes between breast cancer cell lines (MCF-7, MDA-MB-231) and the fibrocystic breast cell line (MCF-10a). Modified gene expression was observed in various molecular pathways, such as apoptosis, cell communication, MAPK and cell cycle as well as xenobiotic metabolism, fatty acid biosynthesis and gap junctional intercellular communication.

The human RFC (hRFC) gene is regulated by five major 5′ non-coding exons, characterized by alternate transcription start sites and splice forms. The result is up to 14 hRFC transcripts for which different 5′ untranslated regions (UTRs) are fused to a common coding sequence. By in vitro translation assays with hRFC constructs corresponding to the major transcript forms, most of the forms were translated poorly. Upon expression of the 5′UTR-hRFC constructs in hRFC-null HeLa cells, a range of steady state hRFC proteins and transcripts were detected that reflected relative transcript stabilities and, to a lesser extent, translation efficiencies. Transcripts including 5′ UTRs derived from non-coding exon A encoded a modified hRFC protein translated from an upstream initiation site. When this modified hRFC protein was expressed in hRFC-null K562 cells, there were only minor differences in surface targeting, stability, or transport function from wild type hRFC. Our results demonstrate an important role for posttranscriptional determinants of cellular hRFC levels and activity.