Trimethylamine n-Oxide (TMAO) Modulates the Expression of Cardiovascular Disease-Related microRNAs and Their Targets

Diet is a well-known risk factor of cardiovascular diseases (CVDs). Some microRNAs (miRNAs) have been described to regulate molecular pathways related to CVDs. Diet can modulate miRNAs and their target genes. Choline, betaine, and l-carnitine, nutrients found in animal products, are metabolized into trimethylamine n-oxide (TMAO), which has been associated with CVD risk. The aim of this study was to investigate TMAO regulation of CVD-related miRNAs and their target genes in cellular models of liver and macrophages. We treated HEPG-2, THP-1, mouse liver organoids, and primary human macrophages with 6 µM TMAO at different timepoints (4, 8, and 24 h for HEPG-2 and mouse liver organoids, 12 and 24 h for THP-1, and 12 h for primary human macrophages) and analyzed the expression of a selected panel of CVD-related miRNAs and their target genes and proteins by real-time PCR and Western blot, respectively. HEPG-2 cells were transfected with anti-miR-30c and syn-miR-30c. TMAO increased the expression of miR-21-5p and miR-30c-5p. PER2, a target gene of both, decreased its expression with TMAO in HEPG-2 and mice liver organoids but increased its mRNA expression with syn-miR-30c. We concluded that TMAO modulates the expression of miRNAs related to CVDs, and that such modulation affects their target genes.

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Artificial microRNA (amiRNA) induced gene silencing in alfalfa (Medicago sativa)

Botany ◽

10.1139/cjb-2012-0166 ◽

2013 ◽

Vol 91 (2) ◽

pp. 117-122 ◽

Cited By ~ 5

Author(s):

Julian C. Verdonk ◽

Michael L. Sullivan

Keyword(s):

Gene Silencing ◽

Medicago Sativa ◽

Target Gene ◽

Target Genes ◽

Mirna Precursor ◽

Crop Species ◽

Forage Crop ◽

Ribonucleic Acids ◽

Endogenous Gene ◽

Medicago Sativa L

Gene silencing is a powerful technique that allows the study of the function of specific genes by selectively reducing their transcription. Several different approaches can be used, however they all have in common the artificial generation of single stranded small ribonucleic acids (RNAs) that are utilized by the endogenous gene silencing machinery of the organism. Artificial microRNAs (amiRNA) can be used to very specifically target genes for silencing because only a short sequence of 21 nucleotides of the gene of interest is used. Gene silencing via amiRNA has been developed for Arabidopsis thaliana (L.) Heynh. and rice using endogenous microRNA (miRNA) precursors and has been shown to also work effectively in other dicot species using the arabidopsis miRNA precursor. Here, we demonstrate that the arabidopsis miR319 precursor can be used to silence genes in the important forage crop species alfalfa (Medicago sativa L.) by silencing the expression of a transgenic beta-glucuronidase (GUSPlus) target gene.

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CHOP-Dependent Stress-Inducible Expression of a Novel Form of Carbonic Anhydrase VI

Molecular and Cellular Biology ◽

10.1128/mcb.19.1.495 ◽

1999 ◽

Vol 19 (1) ◽

pp. 495-504 ◽

Cited By ~ 102

Author(s):

John Sok ◽

Xiao-Zhong Wang ◽

Nikoleta Batchvarova ◽

Masahiko Kuroda ◽

Heather Harding ◽

...

Keyword(s):

Carbonic Anhydrase ◽

Target Gene ◽

Target Genes ◽

Direct Evidence ◽

Nuclear Protein ◽

Intracellular Form ◽

Carbonic Anhydrase Vi ◽

Responsive Element

ABSTRACT CHOP (also called GADD153) is a stress-inducible nuclear protein that dimerizes with members of the C/EBP family of transcription factors and was initially identified as an inhibitor of C/EBP binding to classic C/EBP target genes. Subsequent experiments suggested a role for CHOP-C/EBP heterodimers in positively regulating gene expression; however, direct evidence that this is the case has so far not been uncovered. Here we describe the identification of a positively regulated direct CHOP-C/EBP target gene, that encoding murine carbonic anhydrase VI (CA-VI). The stress-inducible form of the gene is expressed from an internal promoter and encodes a novel intracellular form of what is normally a secreted protein. Stress-induced expression of CA-VI is both CHOP and C/EBPβ dependent in that it does not occur in cells deficient in either gene. A CHOP-responsive element was mapped to the inducibleCA-VI promoter, and in vitro footprinting revealed binding of CHOP-C/EBP heterodimers to that site. Rescue of CA-VIexpression in c/ebpβ−/− cells by exogenous C/EBPβ and a shorter, normally inhibitory isoform of the protein known as LIP suggests that the role of the C/EBP partner is limited to targeting the CHOP-containing heterodimer to the response element and points to a preeminent role for CHOP in CA-VI induction during stress.

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Mutant Alleles of the Drosophila trithorax Gene Produce Common and Unusual Homeotic and Other Developmental Phenotypes

Genetics ◽

10.1093/genetics/152.1.319 ◽

1999 ◽

Vol 152 (1) ◽

pp. 319-344

Author(s):

Thomas R Breen

Keyword(s):

Target Gene ◽

Target Genes ◽

Protein Isoforms ◽

Homeotic Genes ◽

Set Domain ◽

Human Homologue ◽

Terminal Set ◽

Hypomorphic Alleles ◽

Different Levels ◽

Target Gene Transcription

Abstract trithorax (trx) encodes chromosome-binding proteins required throughout embryogenesis and imaginal development for tissue- and cell-specific levels of transcription of many genes including homeotic genes of the ANT-C and BX-C. trx encodes two protein isoforms that contain conserved motifs including a C-terminal SET domain, central PHD fingers, an N-terminal DNA-binding homology, and two short motifs also found in the TRX human homologue, ALL1. As a first step to characterizing specific developmental functions of TRX, I examined phenotypes of 420 combinations of 21 trx alleles. Among these are 8 hypomorphic alleles that are sufficient for embryogenesis but provide different levels of trx function at homeotic genes in imaginal cells. One allele alters the N terminus of TRX, which severely impairs larval and imaginal growth. Hypomorphic alleles that alter different regions of TRX equivalently reduce function at affected genes, suggesting TRX interacts with common factors at different target genes. All hypomorphic alleles examined complement one another, suggesting cooperative TRX function at target genes. Comparative effects of hypomorphic genotypes support previous findings that TRX has tissue-specific interactions with other factors at each target gene. Some hypomorphic genotypes also produce phenotypes that suggest TRX may be a component of signal transduction pathways that provide tissue- and cell-specific levels of target gene transcription.

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The EAR Motif in the Arabidopsis MADS Transcription Factor AGAMOUS-Like 15 Is Not Necessary to Promote Somatic Embryogenesis

Plants ◽

10.3390/plants10040758 ◽

2021 ◽

Vol 10 (4) ◽

pp. 758

Author(s):

Sanjay Joshi ◽

Christian Keller ◽

Sharyn E. Perry

Keyword(s):

Gene Expression ◽

Somatic Embryogenesis ◽

Target Gene ◽

Target Genes ◽

Domain Family ◽

Binding Factor ◽

Ear Motif ◽

Carboxyl Terminal ◽

Responsive Element ◽

Carboxy Terminal

AGAMOUS-like 15 (AGL15) is a member of the MADS domain family of transcription factors (TFs) that can directly induce and repress target gene expression, and for which promotion of somatic embryogenesis (SE) is positively correlated with accumulation. An ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif of form LxLxL within the carboxyl-terminal domain of AGL15 was shown to be involved in repression of gene expression. Here, we examine whether AGL15′s ability to repress gene expression is needed to promote SE. While a form of AGL15 where the LxLxL is changed to AxAxA can still promote SE, another form with a strong transcriptional activator at the carboxy-terminal end, does not promote SE and, in fact, is detrimental to SE development. Select target genes were examined for response to the different forms of AGL15.

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On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11269-z ◽

2021 ◽

Author(s):

Philipp Moritz Fricke ◽

Angelika Klemm ◽

Michael Bott ◽

Tino Polen

Keyword(s):

Gene Expression ◽

Acetic Acid ◽

Literature Search ◽

Target Gene ◽

Target Genes ◽

Recombinant Dna ◽

Acetic Acid Bacteria ◽

Homoserine Lactone ◽

Expression Systems ◽

Target Gene Expression

Abstract Acetic acid bacteria (AAB) are valuable biocatalysts for which there is growing interest in understanding their basics including physiology and biochemistry. This is accompanied by growing demands for metabolic engineering of AAB to take advantage of their properties and to improve their biomanufacturing efficiencies. Controlled expression of target genes is key to fundamental and applied microbiological research. In order to get an overview of expression systems and their applications in AAB, we carried out a comprehensive literature search using the Web of Science Core Collection database. The Acetobacteraceae family currently comprises 49 genera. We found overall 6097 publications related to one or more AAB genera since 1973, when the first successful recombinant DNA experiments in Escherichia coli have been published. The use of plasmids in AAB began in 1985 and till today was reported for only nine out of the 49 AAB genera currently described. We found at least five major expression plasmid lineages and a multitude of further expression plasmids, almost all enabling only constitutive target gene expression. Only recently, two regulatable expression systems became available for AAB, an N-acyl homoserine lactone (AHL)-inducible system for Komagataeibacter rhaeticus and an l-arabinose-inducible system for Gluconobacter oxydans. Thus, after 35 years of constitutive target gene expression in AAB, we now have the first regulatable expression systems for AAB in hand and further regulatable expression systems for AAB can be expected. Key points • Literature search revealed developments and usage of expression systems in AAB. • Only recently 2 regulatable plasmid systems became available for only 2 AAB genera. • Further regulatable expression systems for AAB are in sight.

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PPARα Signaling is Activated by Cocoa in Mouse Liver

Natural Product Communications ◽

10.1177/1934578x1300800507 ◽

2013 ◽

Vol 8 (5) ◽

pp. 1934578X1300800

Author(s):

Marco Fidaleo ◽

Claudia Sartori

Keyword(s):

Mouse Liver ◽

Target Genes ◽

Signal Modulation ◽

Sod1 Gene ◽

Serum Triglycerides ◽

Oxidative Balance ◽

Gene Level ◽

Direct Binding ◽

Somatic Index ◽

Oxidation System

In this study we evaluated in mouse liver the effects of cocoa on PPARα signaling. To this aim, mouse diet was supplemented with 10%, w/w, cocoa for one and two weeks. We quantified the expression of PPARα target genes and PPARα gene level and some parameters related to PPARα activation (hepato-somatic index, peroxisomal β-oxidation system and catalase activity). Moreover, we evaluated antioxidant capacity of cocoa by detecting the expression of CAT and SOD1 genes (known to be involved in oxidative balance) and hypolipidemic properties on serum triglycerides. We made a parallel treatment with 0.025%, w/w, ciprofibrate, a well-known PPARα activator, to quantify signal modulation by cocoa. It is known that PPARα activation by ciprofibrate is mediated by direct binding to the receptor and strongly induces expression of target genes. Our results show that cocoa weakly up-regulates PPARα target genes as a consequence of the modulation of the PPARα gene level and does not improve the triglyceride profile in blood. Finally, cocoa increased SOD1 gene expression suggesting an antioxidant effect.

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Microrna-130a Downregulates HCV Replication through an atg5-Dependent Autophagy Pathway

Cells ◽

10.3390/cells8040338 ◽

2019 ◽

Vol 8 (4) ◽

pp. 338 ◽

Cited By ~ 5

Author(s):

Xiaoqiong Duan ◽

Xiao Liu ◽

Wenting Li ◽

Jacinta A. Holmes ◽

Annie J. Kruger ◽

...

Keyword(s):

Immune Responses ◽

Binding Sites ◽

Target Gene ◽

Target Genes ◽

Pyruvate Metabolism ◽

Host Immune Responses ◽

Qrt Pcr ◽

Antiviral Genes ◽

Autophagy Pathway ◽

Host Antiviral Response

We previously identified that miR-130a downregulates HCV replication through two independent pathways: restoration of host immune responses and regulation of pyruvate metabolism. In this study, we further sought to explore host antiviral target genes regulated by miR-130a. We performed a RT² Profiler™ PCR array to identify the host antiviral genes regulated by miR-130a. The putative binding sites between miR-130a and its downregulated genes were predicted by miRanda. miR-130a and predicted target genes were over-expressed or knocked down by siRNA or CRISPR/Cas9 gRNA. Selected gene mRNAs and their proteins, together with HCV replication in JFH1 HCV-infected Huh7.5.1 cells were monitored by qRT-PCR and Western blot. We identified 32 genes that were significantly differentially expressed more than 1.5-fold following miR-130a overexpression, 28 of which were upregulated and 4 downregulated. We found that ATG5, a target gene for miR-130a, significantly upregulated HCV replication and downregulated interferon stimulated gene expression. miR-130a downregulated ATG5 expression and its conjugation complex with ATG12. ATG5 and ATG5-ATG12 complex affected interferon stimulated gene (ISG) such as MX1 and OAS3 expression and subsequently HCV replication. We concluded that miR-130a regulates host antiviral response and HCV replication through targeting ATG5 via the ATG5-dependent autophagy pathway.

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HSP105 Recruits Protein Phosphatase 2A To Dephosphorylate β-Catenin

Molecular and Cellular Biology ◽

10.1128/mcb.01307-14 ◽

2015 ◽

Vol 35 (8) ◽

pp. 1390-1400 ◽

Cited By ~ 25

Author(s):

Nancy Yu ◽

Michael Kakunda ◽

Victoria Pham ◽

Jennie R. Lill ◽

Pan Du ◽

...

Keyword(s):

Protein Phosphatase ◽

Target Gene ◽

Target Genes ◽

Glycogen Synthase ◽

Protein Phosphatase 2A ◽

Breast Cancer Patients ◽

Poor Overall Survival ◽

Protein Levels ◽

Phosphatase 2A ◽

Unidentified Component

The Wnt/β-catenin pathway causes accumulation of β-catenin in the cytoplasm and its subsequent translocation into the nucleus to initiate the transcription of the target genes. Without Wnt stimulation, β-catenin forms a complex with axin (axis inhibitor), adenomatous polyposis coli (APC), casein kinase 1α (CK1α), and glycogen synthase kinase 3β (GSK3β) and undergoes phosphorylation-dependent ubiquitination. Phosphatases, such as protein phosphatase 2A (PP2A), interestingly, also are components of this degradation complex; therefore, a balance must be reached between phosphorylation and dephosphorylation. How this balance is regulated is largely unknown. Here we show that a heat shock protein, HSP105, is a previously unidentified component of the β-catenin degradation complex. HSP105 is required for Wnt signaling, since depletion of HSP105 compromises β-catenin accumulation and target gene transcription upon Wnt stimulation. Mechanistically, HSP105 depletion disrupts the integration of PP2A into the β-catenin degradation complex, favoring the hyperphosphorylation and degradation of β-catenin. HSP105 is overexpressed in many types of tumors, correlating with increased nuclear β-catenin protein levels and Wnt target gene upregulation. Furthermore, overexpression of HSP105 is a prognostic biomarker that correlates with poor overall survival in breast cancer patients as well as melanoma patients participating in the BRIM2 clinical study.

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Target Gene Specificity of E2F and Pocket Protein Family Members in Living Cells

Molecular and Cellular Biology ◽

10.1128/mcb.20.16.5797-5807.2000 ◽

2000 ◽

Vol 20 (16) ◽

pp. 5797-5807 ◽

Cited By ~ 162

Author(s):

Julie Wells ◽

Kathryn E. Boyd ◽

Christopher J. Fry ◽

Stephanie M. Bartley ◽

Peggy J. Farnham

Keyword(s):

Cell Cycle ◽

Target Gene ◽

Target Genes ◽

Protein Complexes ◽

Current Model ◽

Family Members ◽

Living Cells ◽

Gene Promoters ◽

Pocket Protein ◽

Protein Dna Interactions

ABSTRACT E2F-mediated transcription is thought to involve binding of an E2F-pocket protein complex to promoters in the G0 phase of the cell cycle and release of the pocket protein in late G1, followed by release of E2F in S phase. We have tested this model by monitoring protein-DNA interactions in living cells using a formaldehyde cross-linking and immunoprecipitation assay. We find that E2F target genes are bound by distinct E2F-pocket protein complexes which change as cells progress through the cell cycle. We also find that certain E2F target gene promoters are bound by pocket proteins when such promoters are transcriptionally active. Our data indicate that the current model applies only to certain E2F target genes and suggest that Rb family members may regulate transcription in both G0 and S phases. Finally, we find that a given promoter can be bound by one of several different E2F-pocket protein complexes at a given time in the cell cycle, suggesting that cell cycle-regulated transcription is a stochastic, not a predetermined, process.

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