Gene Expression In Media Research Articles

Catabolite responsive elements as a strategy for the control of heterologous gene expression in lactobacilli.

Genes involved in the transport and catabolism of carbohydrates are usually controlled through the binding of the catabolite control protein A (CcpA) to the catabolite-responsive elements (cre) of target genes in Gram-positive bacteria. In this work, we show how the elimination of the cre sites in Lactobacillus casei BL23 promoters induced by sorbitol (PgutF), maltose (PmalL), and myo-inositol (PiolT) allowed the induction of gene expression in media supplemented with sorbitol, maltose, and myo-inositol, respectively, even in the presence of glucose. This was studied using plasmids encoding the anaerobic fluorescent protein evoglow-Pp1 as a reporter. In addition, gutF cre site was introduced into a bile inducible promoter (P16090) and into the constitutive promoter of the elongation factor P (PEf-P) of L. casei BL23. The existence of the cre site blocked gene expression in the P16090 inducible promoter in the presence of glucose, while it had no influence on the expression of the PEf-P constitutive one. These results demonstrated that the introduction or elimination of cre sites in inducible promoters allows the control and modification of their heterologous genetic expression, showing how the cre site, the transcriptional regulator, and CcpA interact to control gene expression in inducible genes. KEY POINTS: • Cre sequences regulate gene expression in inducible promoters in L. casei BL23. • Cre sites do not affect gene expression in constitutive promoters in L. casei BL23. • Cre sequences could control heterologous genic expression in lactobacilli.

Alterations of aorta intima and media transcriptome in swine fed high-fat diet over 1-year follow-up period and of the switch to normal diet

Background and aimWe previously showed that 12-month high-fat diet (HFD) in pigs led to fattening and increased artery intima-media-thickness, which were partly reversed after 3-month return to control diet (CD). The aim of this study was to decipher underlying mechanism of action by using transcriptomic analyses of intima and media of aorta. Methods and resultsThirty-two pigs were divided into three groups: CD for 12 months; HFD for 12 months; switch diet group (regression diet; RD): HFD for 9 months followed by CD for 3 months. After 12 months, RNA was isolated from aorta intima and media for nutrigenomic analyses. HFD significantly affected gene expression in intima, while RD gene expression profile was distinct from the CD group. This suggests that switch to CD is not sufficient to correct gene expression alterations induced by HFD but counteracted expression of a group of genes. HFD also affected gene expression in media and as for intima, the expression profile of media of pigs on RD differed from that of these on CD. ConclusionsThis study revealed nutrigenomic modifications induced by long-term HFD consumption on arterial intima and media. The return to CD was not sufficient to counteract the genomic effect of HFD.

TRIGONELLA FOENUM-GRAECUM L. EXHIBITS ESTROGENIC EFFECT THROUGH PRESENILIN 2 GENE EXPRESSION IN THE BREAST CANCER CELL LINE MCF-7

Objective: The objective of this study is to investigate the estrogenic and antiestrogenic activity of Fenugreek seeds, Trigonella foenum-graecum L. in the estrogen-dependent breast cancer cell line, MCF-7, including its effect on the expression of estrogen-dependent presenilin 2 (pS2) gene.Methods: An activity guided fractionation was carried out with extracts from fenugreek seeds in MCF-7 cells. Cytotoxic activity assays were conducted with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) assay. Most fractions were also tested also tested in media with estradiol 10 nM We also analysed the expression of pS2 gene. For the analysis of pS2 gene expression we employed PCR primers for pS2 and for β-actin as a housekeeping gene using real-time polymerase chain reaction (RT-PCR).Results: Based on cytotoxic activity assay in MCF-7, the active fractions are ethyl acetic fraction and its phases ethyl acetic (EA) 2 and EA 2.2. The most active fraction was EA 2.2 (IC50=27.129 ppm), which exhibited a biphasic effect; at low concentrations, it stimulated the growth, and at high concentrations it showed strong cytotoxic effects. EA2.2 fraction in concentration 20 ppm, also could induce pS2 gene expression in media with and without estrogen.Conclusion: The most active fraction was the ethyl acetate phase and further subfractions. The most active fraction also induced the expression of pS2 gene which was studied by RT-PCR.

TRIGONELLA FOENUM-GRAECUM L. EXHIBITS ESTROGENIC EFFECT THROUGH PRESENILIN 2 GENE EXPRESSION IN THE BREAST CANCER CELL LINE MCF-7

Objective: The objective of this study is to investigate the estrogenic and antiestrogenic activity of Fenugreek seeds, Trigonella foenum-graecum L. in the estrogen-dependent breast cancer cell line, MCF-7, including its effect on the expression of estrogen-dependent presenilin 2 (pS2) gene.Methods: An activity guided fractionation was carried out with extracts from fenugreek seeds in MCF-7 cells. Cytotoxic activity assays were conducted with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) assay. Most fractions were also tested also tested in media with estradiol 10 nM We also analysed the expression of pS2 gene. For the analysis of pS2 gene expression we employed PCR primers for pS2 and for β-actin as a housekeeping gene using real-time polymerase chain reaction (RT-PCR).Results: Based on cytotoxic activity assay in MCF-7, the active fractions are ethyl acetic fraction and its phases ethyl acetic (EA) 2 and EA 2.2. The most active fraction was EA 2.2 (IC50=27.129 ppm), which exhibited a biphasic effect; at low concentrations, it stimulated the growth, and at high concentrations it showed strong cytotoxic effects. EA2.2 fraction in concentration 20 ppm, also could induce pS2 gene expression in media with and without estrogen.Conclusion: The most active fraction was the ethyl acetate phase and further subfractions. The most active fraction also induced the expression of pS2 gene which was studied by RT-PCR.

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

BackgroundHistone modifications play an important role in gene regulation. Acetylation of histone 3 lysine 9 (H3K9ac) is generally associated with transcription initiation and unfolded chromatin, thereby positively influencing gene expression. Deep sequencing of the 5' ends of gene transcripts using DeepCAGE delivers detailed information about the architecture and expression level of gene promoters. The combination of H3K9ac ChIP-chip and DeepCAGE in a myeloid leukemia cell line (THP-1) allowed us to study the spatial distribution of H3K9ac around promoters using a novel clustering approach. The promoter classes were analyzed for association with relevant genomic sequence features.ResultsWe performed a clustering of 4,481 promoters according to their surrounding H3K9ac signal and analyzed the clustered promoters for association with different sequence features. The clustering revealed three groups with major H3K9ac signal upstream, centered and downstream of the promoter. Narrow single peak promoters tend to have a concentrated activity of H3K9ac in the upstream region, while broad promoters tend to have a concentrated activity of H3K9ac and RNA polymerase II binding in the centered and downstream regions. A subset of promoters with high gene expression level, compared to subsets with low and medium gene expression, shows dramatic increase in H3K9ac activity in the upstream cluster only; this may indicate that promoters in the centered and downstream clusters are predominantly regulated at post-initiation steps. Furthermore, the upstream cluster is depleted in CpG islands and more likely to regulate un-annotated genes.ConclusionsClustering core promoters according to their surrounding acetylation signal is a promising approach for the study of histone modifications. When examining promoters clustered into groups according to their surrounding H3K9 acetylation signal, we find that the relative localization and intensity of H3K9ac is very specific depending on characteristic sequence features of the promoter. Experimental data from DeepCAGE and ChIP-chip experiments using undifferentiated (monocyte) and differentiated (macrophage) THP-1 cells leads us to the same conclusions.