@article {Annaloradmd.119.089102, author = {Andrew J. Annalora and Craig B. Marcus and Patrick L. Iversen}, title = {Alternative Splicing in the Nuclear Receptor Superfamily Redirects Human Metabolic Homeostasis.}, elocation-id = {dmd.119.089102}, year = {2020}, doi = {10.1124/dmd.119.089102}, publisher = {American Society for Pharmacology and Experimental Therapeutics}, abstract = {TThe human genome encodes 48 nuclear receptor (NR) genes, whose translated products transform chemical signals from endo-xenobiotics into pleotropic RNA transcriptional profiles that refine drug metabolism. This review describes the remarkable diversification of the 48 human NR genes, which are potentially processed into over 1000 distinct mRNA transcripts by alternative splicing (AS). The average human NR expresses ~21 transcripts per gene and is associated with ~7000 single nucleotide polymorphisms (SNP). However, the rate of SNP accumulation does not appear to drive the AS process, highlighting the resilience of NR genes to mutation. Here we summarize the altered tissue distribution/function of well-characterized NR splice variants associated with human disease. We also describe a cassette exon visualization pictograph (CEViP) methodology for illustrating the location of modular, cassette exons in genes, which can be skipped in-frame, to facilitate the study of their functional relevance to both drug metabolism and NR evolution. We find cassette exons associated with all of the functional domains of NR genes including the DNA- and ligand-binding domains. The matrix of inclusion or exclusion for functional domain-encoding cassette exons is extensive and capable of significant alterations in cellular phenotypes that modulate endo-xenobiotic metabolism. Exon inclusion options are differentially distributed across NR subfamilies, suggesting group-specific conservation of resilient functionalities. A deeper understanding of this transcriptional plasticity expands our understanding of how chemical signals are refined and mediated by NR genes. This expanded view of the NR transcriptome informs new models of chemical toxicity, disease diagnostics and precision-based approaches to personalized medicine.SIGNIFICANCE STATEMENT This review explores the impact of AS on the human NR superfamily and highlights the dramatic expansion of \>1,000 potential transcript variants from 48 individual genes. Xenobiotics are increasingly recognized for their ability to perturb gene splicing events, but the physiological impact of AS remains poorly understood. Here we explore the differential sensitivity of NR genes to AS and discuss how their differential expression profiles may augment cellular resilience to stress and fine-tune adaptive, metabolic responses to endo-xenobiotic exposure.}, issn = {0090-9556}, URL = {https://dmd.aspetjournals.org/content/early/2020/01/24/dmd.119.089102}, eprint = {https://dmd.aspetjournals.org/content/early/2020/01/24/dmd.119.089102.full.pdf}, journal = {Drug Metabolism and Disposition} }