{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE308nnn/GSE308938/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Saccharomyces cerevisiae"],"gds_type":[" Expression profiling by high throughput sequencing","Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE308938"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Identification of translation events that drive nonsense-mediated mRNA decay reveals functional roles for alternative RNA isoforms","description":"The nonsense-mediated mRNA decay (NMD) pathway targets mRNAs undergoing premature translation termination for degradation. Previously, RNA-seq of yeast lacking NMD revealed that most genes targeted by NMD lack obvious premature termination codons (PTCs). We developed a combined approach using RNA-seq and a novel 40S ribosome profiling strategy to identify cryptic premature termination events that could account for NMD on nearly all these transcripts, including many non-coding RNA transcript isoforms associated with annotated genes. Many NMD-targeted transcripts appear to be involved in two-promoter gene regulatory systems and share properties with long un-decoded transcript isoforms (LUTIs). In particular, we show that the DAL5 LUTI regulates expression of the DAL5 protein-coding mRNA in response to changes to environmental nitrogen. Our work expands the functional roles for LUTIs and establishes the importance of NMD in their regulation.","dates":{"publication":"2026/09/16"},"accession":"GSE308938","cross_references":{"GSM":["GSM9256519","GSM9256517","GSM9256518","GSM9256522","GSM9256500","GSM9256523","GSM9256501","GSM9256520","GSM9256521","GSM9256504","GSM9256505","GSM9256502","GSM9256503","GSM9256508","GSM9256509","GSM9256506","GSM9256507","GSM9256492","GSM9256493","GSM9256490","GSM9256491","GSM9256496","GSM9256497","GSM9256494","GSM9256495","GSM9256511","GSM9256512","GSM9256498","GSM9256510","GSM9256499","GSM9256515","GSM9256516","GSM9256513","GSM9256514"],"GPL":["23014","27812"],"GSE":["308938"],"taxon":["Saccharomyces cerevisiae"]}}