{"doi":"10.1196/annals.1359.026","title":"Stability Regulation of mRNA and the Control of Gene Expression","abstract":"<jats:p>Microarray technology has become highly valuable for identifying complex global changes in gene expression patterns. Standard techniques measure changes in total cellular poly(A) mRNA levels. The assumption that changes in gene expression as measured by these techniques are directly and well correlated with changes in rates of new gene synthesis form the basis of attempts to connect coordinated changes in gene expression with shared transcription regulatory elements. Yet systematic attempts at this approach remain difficult to demonstrate convincingly. One reason for this difficulty may result from the intricate convergence of both transcriptional and mRNA turnover events which, together, directly influence steady‐state mRNA levels. Recent technical advances have led to the successful scale‐up and application of nuclear run‐on procedures directly to microarrays. This development has allowed a gene‐by‐gene comparison between new gene synthesis in the nucleus and measured changes in total cellular polyA mRNA. Results from these studies have begun to challenge the strict interpretation of changes in gene expression measured by conventional microarrays as being closely correlated with changes in mRNA transcription rate, but rather they tend to support the significant expansion of the role played by changes in mRNA stability regulation to standard analyses of gene expression. Gene expression profiles obtained from both polyA mRNA (whole‐cell) and nuclear run‐on (newly transcribed) RNA across a time course of one hour following the activation of human Jurkat T cells with PMA plus ionomycin revealed that regulation of mRNA stability may account for as much as 50% of all measurements of changes in total cellular polyA mRNA in this system. Stability regulation was inferred by the absence of corresponding regulation of nuclear gene transcription activity for groups of genes strongly regulated at the whole cell level and which were also resistant to inhibition by Actinomycin D pre‐treatment. Consistent patterns across the time course were observed for both transcribed and stability‐regulated genes. It is proposed that the regulation of mRNA stability in response to external stimuli contributes significantly to observed changes in gene expression as measured by high throughput systems.</jats:p>","journal":"Annals of the New York Academy of Sciences","year":2005,"id":44941,"datarank":5.683922722374938,"base_score":4.672828834461906,"endowment":4.672828834461906,"self_citation_contribution":0.7009243251692859,"citation_network_contribution":4.982998397205652,"self_endowment_contribution":0.7009243251692859,"citer_contribution":4.982998397205652,"corpus_percentile":null,"corpus_rank":null,"citation_count":106,"citer_count":100,"citers_with_citation_signal":90,"citers_with_endowment":90,"datacite_reuse_total":4,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":210682,"name":"JINSHUI FAN","orcid":null,"position":1,"is_corresponding":false},{"id":210683,"name":"YOON S. CHO‐CHUNG","orcid":null,"position":2,"is_corresponding":false},{"id":210684,"name":"THOMAS WERNER","orcid":null,"position":3,"is_corresponding":false},{"id":210685,"name":"JILL RAY","orcid":null,"position":4,"is_corresponding":false},{"id":210686,"name":"LANA DO","orcid":null,"position":5,"is_corresponding":false},{"id":210687,"name":"MYRIAM GOROSPE","orcid":null,"position":6,"is_corresponding":false},{"id":210688,"name":"KEVIN G. BECKER","orcid":null,"position":7,"is_corresponding":false},{"id":210681,"name":"CHRIS CHEADLE","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":4.672828834461906,"endowment":4.672828834461906,"datacite_reuse_total":4,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"16394137","pmcid":null,"openalex_id":"https://openalex.org/W2093869340","authors":[],"funders":[],"total_grants":0,"fwci":4.043,"citation_percentile":0.94429637,"influential_citations":1,"citation_trend":[{"year":2012,"count":6},{"year":2013,"count":7},{"year":2014,"count":8},{"year":2015,"count":8},{"year":2016,"count":4},{"year":2017,"count":3},{"year":2018,"count":1},{"year":2019,"count":4},{"year":2020,"count":2},{"year":2021,"count":2},{"year":2022,"count":4},{"year":2023,"count":1},{"year":2024,"count":1},{"year":2025,"count":2}],"oa_status":"closed","license":"http://onlinelibrary.wiley.com/termsAndConditions#vor","oa_locations":[{"url":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1196%2Fannals.1359.026","host_type":"publisher"},{"url":"https://nyaspubs.onlinelibrary.wiley.com/doi/pdf/10.1196/annals.1359.026","host_type":"publisher"},{"url":"https://doi.org/10.1196/annals.1359.026","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/16394137","host_type":"repository"}],"fields_of_study":["RNA Research and Splicing","Molecular Biology Techniques and Applications","Genomics and Chromatin Dynamics","Biology","Medicine","Cell Line, Tumor","Cell Nucleus","Dactinomycin","Gene Expression","Gene Expression Regulation","Humans","Ionomycin","Jurkat Cells","Oligonucleotide Array Sequence Analysis","Phorbol Esters","RNA","RNA, Messenger","Time Factors","Transcription, Genetic"],"mesh_terms":["Cell Nucleus","Dactinomycin","Gene Expression Regulation","Humans","Phorbol Esters","RNA","RNA, Messenger","Time Factors","Transcription, Genetic","Ionomycin","Gene Expression","Jurkat Cells","Oligonucleotide Array Sequence Analysis","Cell Line, Tumor"],"keywords":["Gene expression","DNA microarray","Biology","Gene","Messenger RNA","Regulation of gene expression","Transcription (linguistics)","Genetics","Cell biology","Computational biology","Molecular biology"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.21087347.v1","title":"Additional file 14 of Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.21087347","title":"Additional file 14 of Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.21087353.v1","title":"Additional file 2 of Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.21087353","title":"Additional file 2 of Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation","publisher":"figshare","resource_type":"JournalArticle"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-01T23:33:49.885200Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}