The potential for chemicals to affect endocrine signaling is commonly evaluated via receptor binding and gene activation, but these assays, especially antagonism assays, have potential artifacts that must be addressed for accurate interpretation. Results are presented from screening 94 chemicals from 54 chemical groups for estrogen receptor (ER) activation in a competitive rainbow trout ER (rtER) binding assay and a trout liver slice vitellogenin mRNA expression assay. Results from true competitive agonists and antagonists, and inactive chemicals with little or no indication of ER binding or gene activation were easily interpreted. However, results for numerous industrial chemicals were more challenging to interpret, including chemicals with: (1) apparent competitive binding curves but no gene activation, (2) apparent binding and gene inhibition with evidence of either cytotoxicity or changes in assay media pH, (3) apparent binding but non-competitive gene inhibition of unknown cause, or (4) no rtER binding and gene inhibition not due to competitive ER interaction but due to toxicity, pH change, or some unknown cause. The use of endpoints such as toxicity, pH, precipitate formation, and determination of inhibitor dissociation constants (Ki) for interpreting the results of antagonism and binding assays for diverse chemicals is presented. Of the 94 chemicals tested for antagonism only two, tamoxifen and ICI-182780, were found to be true competitive antagonists. This report highlights the use of two different concentrations of estradiol tested in combination with graded concentrations of test chemical to provide the confirmatory evidence to distinguish true competitive antagonism from apparent antagonism.
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http://dx.doi.org/10.1089/aivt.2016.0021 | DOI Listing |
Methods Mol Biol
January 2025
Department of Integrative Biology and Physiology, Medical School, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA.
Homeobox genes (HOX), the master regulators, deploy a unique set of target genes to coordinate and orchestrate the spatiotemporal development of an organism. HOX encoded transcriptional factors regulate the expression of target genes by binding to the specific sequences on the genome. Chromatin Immunoprecipitation (ChIP) and Chromatin Immunoprecipitation with Sequencing (ChIP-Seq) are widely used to map and understand specific gene locus and global regulatory regions on the genome.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Department of Pharmacology, Yale School of Medicine, Yale University, New Haven, CT, USA.
Electrophoretic Mobility Shift Assay (EMSA) is a powerful technique for studying nucleic acid and protein interactions. This technique is based on the principle that nucleic acid-protein complex and nucleic acid migrate at different rates due to differences in size and charge. Nucleic acid and protein interactions are fundamental to various biological processes, such as gene regulation, replication, transcription, and recombination.
View Article and Find Full Text PDFMethods Mol Biol
January 2025
Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.
The HOX and PBX genes encode transcription factors that have key roles in development and cancer, both independently and as a heterodimer within a complex of proteins that recognizes specific sequences in DNA and can both activate and repress transcription of target genes. Due to functional redundancy amongst HOX proteins, knock down or knock out studies of individual genes often do not result in an altered phenotype. An alternative approach is to target the interaction between HOX and PBX proteins, which is dependent on a conserved hexapeptide region within HOX.
View Article and Find Full Text PDFDevelopment
January 2025
Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA.
Expression of SRY-box transcription factor 17 (Sox17) in the endodermal region caudal to the hepatic diverticulum during late gastrulation is necessary for hepato-pancreato-biliary system formation. Analysis of an allelic series of promoter-proximal mutations near the transcription start site (TSS) 2 of Sox17 has revealed that gallbladder (GB) and extrahepatic bile duct (EHBD) development is exquisitely sensitive to Sox17 expression levels. Deletion of a SOX17-binding cis-regulatory element in the TSS2 promoter impairs GB&EHBD development by reducing outgrowth of the nascent biliary bud.
View Article and Find Full Text PDFJ Cell Biochem
January 2025
Division of Cell Biology and Physiology, CSIR-Indian Institute of Chemical Biology, Kolkata, India.
Cellular prion protein (PRNP) has been implicated in various physiological processes in different cell types, for decades. Little has been known how PRNP functions in multiple, yet related processes within a particular system. In our current study, with the aid of high-throughput RNA-sequencing technique, we have presented an overall transcriptome profile of rat vascular smooth muscle cells (VSMCs) with Prnp knockdown.
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