Search results for "binding"

showing 10 items of 3896 documents

Anything but Ordinary - Emerging Splicing Mechanisms in Eukaryotic Gene Regulation.

2021

Splicing of precursor mRNAs (pre-mRNA) is an important step during eukaryotic gene expression. The identification of the actual splice sites and the proper removal of introns are essential for the production of the desired mRNA isoforms and their encoded proteins. While the basic mechanisms of splicing regulation are well understood, recent work has uncovered a growing number of noncanonical splicing mechanisms that play key roles in the regulation of gene expression. In this review, we summarize the current principles of splicing regulation, including the impact of cis and trans regulatory elements, as well as the influence of chromatin structure, transcription, and RNA modifications. We f…

Regulation of gene expression0303 health sciencesRNA SplicingIntronRNAEukaryotaRNA-binding proteinComputational biologyBiologyIntronsChromatin03 medical and health sciencesAlternative Splicing0302 clinical medicineCircular RNARNA splicingGene expressionGeneticsRNA PrecursorsHumansRNA Messenger030217 neurology & neurosurgery030304 developmental biologyTrends in genetics : TIG
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Transcription- and apoptosis-dependent long-range distribution of tight DNA-protein complexes in the chicken alpha-globin gene.

2008

The proteins tightly bound to DNA (TBP) are a group of proteins that remain attached to DNA with covalent or noncovalent bonds after its deproteinization, and have been hypothesized to be involved in regulation of gene expression. To investigate this question further, oligonucleotide DNA arrays were used to determine the distribution of tightly bound proteins along a 100-kb DNA fragment surrounding the chicken alpha-globin gene domain in DNA from chicken erythrocytes, liver, and AEV-transformed HD3 (erythroblast) cells in different physiological conditions. DNA was fractionated into TBP-free (F) and TBP-enriched (R) fractions by separation on nitrocellulose, and these fractions were used as…

Regulation of gene expressionErythrocytesMicroarrayTranscription GeneticOligonucleotideApoptosisCell BiologyGeneral MedicineBiologyMolecular biologyGlobinsDNA-Binding Proteinschemistry.chemical_compoundchemistryCovalent bondApoptosisTranscription (biology)GeneticsAnimalsMolecular BiologyGeneChickensDNAOligonucleotide Array Sequence AnalysisDNA and cell biology
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Systematic Comparative Protein Expression Profiling of Clear Cell Renal Cell Carcinoma

2009

Proteome-based technologies represent powerful tools for the analysis of protein expression profiles, including the identification of potential cancer candidate biomarkers. Thus, here we provide a comprehensive protein expression map for clear cell renal cell carcinoma established by systematic comparative two-dimensional gel electrophoresis-based protein expression profiling of 16 paired tissue systems comprising clear cell renal cell carcinoma lesions and corresponding tumor-adjacent renal epithelium using overlapping narrow pH gradients. This approach led to the mapping of 348 distinct spots corresponding to 248 different protein identities. By implementing restriction criteria concernin…

Regulation of gene expressionGel electrophoresisTwo-dimensional gel electrophoresisTissue microarrayBiologymedicine.diseaseProteomicsBiochemistryMolecular biologyAnalytical ChemistryClear cell renal cell carcinomaProteomemedicineFatty Acid Binding Protein 3Molecular BiologyMolecular & Cellular Proteomics
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Competing endogenous RNA and interactome bioinformatic analyses on human telomerase.

2014

We present a classic interactome bioinformatic analysis and a study on competing endogenous (ce) RNAs for hTERT. The hTERT gene codes for the catalytic subunit and limiting component of the human telomerase complex. Human telomerase reverse transcriptase (hTERT) is essential for the integrity of telomeres. Telomere dysfunctions have been widely reported to be involved in aging, cancer, and cellular senescence. The hTERT gene network has been analyzed using the BioGRID interaction database (http://thebiogrid.org/) and related analysis tools such as Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index) and GeneMANIA (http://genemania.org/). The network of interaction of hTERT transcripts h…

Regulation of gene expressionGeneticsAgingbiologyCompeting endogenous RNAProtein subunitRNAComputational BiologyInteractomeTelomereCell biologyHistoneGene Expression Regulationbiology.proteinHumansRNATelomerase reverse transcriptaseRNA MessengerGeriatrics and GerontologyTelomeraseProtein BindingRejuvenation research
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Complex Contribution of the 3′-Untranslated Region to the Expressional Regulation of the Human Inducible Nitric-oxide Synthase Gene

2000

Cytokine stimulation of human DLD-1 cells resulted in a marked expression of nitric-oxide synthase (NOS) II mRNA and protein accompanied by only a moderate increase in transcriptional activity. Also, there was a basal transcription of the NOS II gene, which did not result in measurable NOS II expression. The 3′-untranslated region (3′-UTR) of the NOS II mRNA contains four AUUUA motifs and one AUUUUA motif, known to destabilize the mRNAs of proto-oncogenes, nuclear transcription factors, and cytokines. Luciferase reporter gene constructs containing the NOS II 3′-UTR showed a significantly reduced luciferase activity. The embryonic lethal abnormal vision (ELAV)-like protein HuR was found to b…

Regulation of gene expressionMessenger RNAGeneral transcription factorThree prime untranslated regionELAV-Like Protein 1LuciferaseRNA-binding proteinCell BiologyBiologyMolecular BiologyBiochemistryMolecular biologyTranscription factorJournal of Biological Chemistry
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Respiration and low cAMP-dependent protein kinase activity are required for high-level expression of the peroxisomal thiolase gene in Saccharomyces c…

1996

Transcription of genes for peroxisomal proteins is repressed by glucose and induced by oleate. At least for the peroxisomal thiolase gene (POT1) there is a third regulatory mechanism, mediated by the transcription factor Adr1p, which is responsible for the high-level expression of the gene in stationary phase. Here we show that a region in the POT1 promoter that extends from positions -238 to -152 mediates this mechanism, and we suggest that Adr1p acts indirectly on POT1. We have also analyzed the role of the cAMP-dependent protein kinase (PKA) in the transcriptional regulation of POT1. PKA exerts a negative control: the high, unregulated PKA activity in a bcy1 mutant maintains POT1 transcr…

Regulation of gene expressionSaccharomyces cerevisiae ProteinsTranscription GeneticThiolaseSaccharomyces cerevisiaeBiologyRegulatory Sequences Nucleic AcidCAMP-dependent protein kinase activityCyclic AMP-Dependent Protein KinasesMicrobodiesMitochondriaDNA-Binding ProteinsFungal ProteinsBiochemistryRegulatory sequenceGene Expression Regulation FungalGeneticsTranscriptional regulationRas2Acetyl-CoA C-AcetyltransferaseProtein kinase APromoter Regions GeneticMolecular BiologyTranscription factorTranscription FactorsMoleculargeneral genetics : MGG
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The putative sponge aggregation receptor. Isolation and characterization of a molecule composed of scavenger receptor cysteine-rich domains and short…

1998

Porifera (sponges) are the oldest extant metazoan phylum. Dissociated sponge cells serve as a classic system to study processes of cell reaggregation. The reaggregation of dissociated cells is mediated by an extracellularly localized aggregation factor (AF), based on heterophilic interactions of the third order; the AF bridges two cells by ligating a cell-surface-bound aggregation receptor (AR). In the present study we report cloning, expression and immunohistochemical localization of a polypeptide from the marine sponge Geodia cydonium, which very likely represents the AR. The presumed AR gene gives rise to at least three forms of alternatively spliced transcripts of 6.5, 4.9 and 3.9 kb, a…

Repetitive Sequences Amino Acidmedicine.drug_classMolecular Sequence DataReceptors Cell SurfaceCell CommunicationMonoclonal antibodyPolymerase Chain Reactionlaw.inventionAntigenlawComplementary DNAConsensus SequencemedicineAnimalsAmino Acid SequenceCloning MolecularReceptors ImmunologicReceptorCell AggregationReceptors LipoproteinRepetitive Sequences Nucleic AcidReceptors ScavengerbiologyMolecular massBase SequenceSequence Homology Amino AcidMembrane ProteinsCell BiologySequence Analysis DNAScavenger Receptors Class BMolecular biologyRecombinant ProteinsPoriferaTransmembrane domainBiochemistrybiology.proteinRecombinant DNAAntibodyProtein Binding
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Mboat7 down-regulation by hyper-insulinemia induces fat accumulation in hepatocytes.

2020

Background: Naturally occurring variation in Membrane-bound O-acyltransferase domain-containing 7 (MBOAT7), encoding for an enzyme involved in phosphatidylinositol acyl-chain remodelling, has been associated with fatty liver and hepatic disorders. Here, we examined the relationship between hepatic Mboat7 down-regulation and fat accumulation. Methods: Hepatic MBOAT7 expression was surveyed in 119 obese individuals and in experimental models. MBOAT7 was acutely silenced by antisense oligonucleotides in C57Bl/6 mice, and by CRISPR/Cas9 in HepG2 hepatocytes. Findings: In obese individuals, hepatic MBOAT7 mRNA decreased from normal liver to steatohepatitis, independently of diabetes, inflammatio…

Research paperTGFβ Transforming Growth Factor BetaIntracellular SpaceCRISPR Clustered Regularly Interspaced Short Palindromic RepeatshHEPS Human HepatocytesMice0302 clinical medicineLPIAT1DAG Diacylglyceroli.p. Intraperitonealmedia_commonFatty AcidsGeneral Medicine3. Good health030220 oncology & carcinogenesisHOMA-IR homeostasis Model Assessment of Insulin ResistanceMPO morpholinolcsh:Medicine (General)medicine.medical_specialtyPE Phosphatidyl-EthanolamineNashGeneral Biochemistry Genetics and Molecular Biology03 medical and health sciencesTNFα tumor Necrosis Factor AlphaLDL Low Density LipoproteinsHyperinsulinismNAFLDSD Standard Dietmedia_common.cataloged_instanceHumansCPT1 Carnitine Palmitoyltransferase IPhosphatidylinositolGene SilencingEuropean unionVLDL Very Low Density Lipoproteinlcsh:RhHSC Human Hepatic Stellate Cellsmedicine.diseaseLipid MetabolismOA Oleic AcidCI Confidence IntervalMboat7 Membrane bound O-acyltransferase domain containing 7MCD methionine choline deficient diet030104 developmental biologyEndocrinologychemistryCDP Cytidine-DiphosphateFOXO1 Forkhead Box protein O1NAFLD nonalcoholic fatty liver diseaseSteatohepatitisBMI Body Mass IndexCL CardiolipinAcyltransferases0301 basic medicineAlcoholic liver diseaseCXCL10 C-X-C Motif Chemokine 10lcsh:Medicinechemistry.chemical_compoundNon-alcoholic Fatty Liver DiseaseIFG Impaired Fasting GlucoseAPOB Apolipoprotein BNonalcoholic fatty liver diseasePIP Phosphatidyl-Inositol-PhosphateSteatohepatitisqRT-PCR quantitative Real Time Polymerase Chain ReactionMice Knockoutlcsh:R5-920ORO Oil Red O StainingPI PhosphatidylinositolFatty liverTM6SF2 Transmembrane 6 Superfamily Member 2PhospholipidTAG TriglyceridesNASH Nonalcoholic SteatohepatitisLipogenesisLPA Lyso-Phosphatidic AcidPhosphatidylinositolSignal TransductionPS Phosphatidyl-SerinePA Palmitic AcidALD alcoholic liver diseasePC Phosphatidylcholinei.v. IntravenousFATP1 Fatty Acid Transport Protein 1Models BiologicalInternal medicinemedicineAnimalsNonalcoholic fatty liver diseasePPARα Peroxisome Proliferator-Activated Receptor alphaObesityG3P Glyceraldehyde-3-PhosphateSREBP1c Sterol Regulatory Element-Binding Protein 1HDL High Density Lipoproteinsbusiness.industryPI3K Phosphatidylinositol 3 KinaseMembrane ProteinsNHEJ Non-Homologues End JoiningPNPLA3 Patatin-like Phospholipase Domain-containing-3MTTP Microsomal Triglyceride Transfer ProteinLPIAT1 Lysophosphatidylinositol Acyltransferase 1TMC4 Transmembrane Channel-Like 4Disease Models AnimalGene Expression RegulationHepatocytesFOXA2 Forkhead Box A2mTOR mammalian target of RapamycinSteatosisInsulin ResistancebusinessPG Phosphatidyl-GlycerolFABP1 Fatty Acid-Binding Protein 1 FAS Fatty Acid SynthaseT2DM Type 2 Diabetes MellitusEBioMedicine
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Potential of human serum albumin as chiral selector of basic drugs in affinity electrokinetic chromatography-partial filling technique

2006

The enantiomeric resolution of compounds using HSA by means of affinity EKC (AEKC)-partial filling technique is the result of a delicate balance between different experimental variables such as protein concentration, running pH (background electrophoretic buffer (BGE), protein, and compound solutions), and plug length. In this paper, the possibility of using HSA as chiral selector for enantioseparation of 28 basic drugs using this methodology is studied. The effect of the physicochemical parameters, the structural properties of compounds, and compound-HSA protein binding percentages over their chiral resolution with HSA is outlined. Based on the results obtained, a decision tree is proposed…

Resolution (mass spectrometry)Clinical BiochemistryPlasma protein bindingBuffersBiochemistryChromatography AffinityAnalytical ChemistryElectrokinetic phenomenaMolar volumemedicineHumansSerum AlbuminChromatography Micellar Electrokinetic CapillaryChromatographyMolecular StructureChemistryStereoisomerismHydrogen-Ion ConcentrationHuman serum albuminChiral resolutionbody regionsElectrophoresisPharmaceutical Preparationsembryonic structuresEnantiomerHydrophobic and Hydrophilic Interactionsmedicine.drugELECTROPHORESIS
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The peroxisome proliferator response element (PPRE) present at positions -681/-669 in the rat liver 3-ketoacyl-CoA thiolase B gene functionally inter…

2000

Although previous data showed that the putative thiolase B PPRE located at -681/-669 bind the PPARalpha-RXRalpha heterodimer in vitro (Kliewer et al. (1992) Nature 358, 771-774), there is no evidence about the functional role of this element. By gel mobility-shift assay, we found an interaction of this PPRE with not only PPARalpha but also with HNF-4. By transfection of cells with the putative PPRE-driven luciferase reporter vector and PPARalpha, we found no significant activation of the luciferase gene expression, in contrast to the case with reporter expression driven by the PPRE of the peroxisomal bifunctional enzyme. On the other hand, HNF-4 activated the luciferase gene expression driv…

Response elementBiophysicsReceptors Cytoplasmic and NuclearBiologyTransfectionBiochemistryDNA-binding proteinPeroxisomal Bifunctional EnzymeGenes ReporterGene expressionAnimalsMolecular BiologyGeneDNA PrimersBase SequenceThiolaseCell BiologyTransfectionDNAAcetyl-CoA C-AcyltransferasePhosphoproteinsMolecular biologyRatsDNA-Binding ProteinsHepatocyte nuclear factor 4Hepatocyte Nuclear Factor 4LiverCOS CellsPeroxisome ProliferatorsTranscription FactorsBiochemical and biophysical research communications
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