{"doi":"10.1093/nar/gkac411","title":"Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:p>In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells’ total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1—the main 5′-3′ mRNA exonuclease—which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5′-3′ degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5′-3′ exonucleolytic pathway rather than its outputs.</jats:p>","journal":"Nucleic Acids Research","year":2022,"id":655427,"datarank":0.5050943744979712,"base_score":3.367295829986474,"endowment":3.367295829986474,"self_citation_contribution":0.5050943744979712,"citation_network_contribution":0.0,"self_endowment_contribution":0.5050943744979712,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":28,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"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":1589344,"name":"Daphna Joseph-Strauss","orcid":"0000-0002-2742-9873","position":1,"is_corresponding":false},{"id":1710971,"name":"Omer Gershon","orcid":null,"position":2,"is_corresponding":false},{"id":11210,"name":"Nir Friedman","orcid":"0000-0002-9678-3550","position":3,"is_corresponding":false},{"id":626000,"name":"Alon Chappleboim","orcid":"0000-0001-7676-956X","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:p>In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells’ total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1—the main 5′-3′ mRNA exonuclease—which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5′-3′ degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5′-3′ exonucleolytic pathway rather than its outputs.</jats:p>","is_dataset_classified":null,"base_score":3.367295829986474,"endowment":3.367295829986474,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35640599","pmcid":"PMC9177992","openalex_id":"https://openalex.org/W4282941443","authors":[],"funders":[{"funder_name":"Israel Science Foundation","grant_id":"1064/19","title":null},{"funder_name":"Azrieli Foundation","grant_id":"","title":null}],"total_grants":2,"fwci":1.805,"citation_percentile":0.85543143,"influential_citations":0,"citation_trend":[{"year":2022,"count":3},{"year":2023,"count":5},{"year":2024,"count":9},{"year":2025,"count":6},{"year":2026,"count":5}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/50/10/5864/43977191/gkac411.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/50/10/5864/43977191/gkac411.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkac411","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/35640599","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9177992","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC9177992","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9177992?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["RNA Research and Splicing","RNA and protein synthesis mechanisms","RNA modifications and cancer","Exoribonucleases","Feedback","RNA Stability","RNA, Messenger"],"mesh_terms":["Exoribonucleases","Feedback","RNA, Messenger","RNA Stability"],"keywords":["Biology","Messenger RNA","Exonuclease","Transcription (linguistics)","Cell biology","Nonsense-mediated decay","Molecular biology","RNA","Genetics","RNA splicing","Gene"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-11T10:50:16.599311Z","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":[]}