{"doi":"10.1101/2023.03.14.532632","title":"Comparative analysis between RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise","abstract":"Stochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability, but the physiological roles of noise have remained difficult to determine in the absence of generalized noise-modulation approaches. Previous single-cell RNA sequencing (scRNA-seq) suggested that the pyrimidine-base analog (5′-iodo-2′ deoxyuridine, IdU) could generally amplify noise without substantially altering mean expression levels but scRNA-seq technical drawbacks potentially obscured the penetrance of IdU-induced transcriptional noise amplification. Here we quantify global-vs.-partial penetrance of IdU induced noise amplification by assessing scRNAseq data using numerous normalization algorithms and directly quantifying noise using single-molecule RNA FISH (smFISH) for a panel of genes from across the transcriptome. Alternate scRNA-seq analyses indicate IdU-induced noise amplification for ~90% of genes, and smFISH data verified noise amplification for ~90% of tested genes. Collectively, this analysis indicates which scRNA-seq algorithms are appropriate for quantifying noise and argues that IdU is a globally penetrant noise enhancer molecule that could enable investigations of the physiological impacts of transcriptional noise.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":390697,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9583,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":478760,"name":"Xinyue Chen","orcid":"0000-0001-8288-7685","position":1,"is_corresponding":false},{"id":1157577,"name":"B. M. Zuckerman","orcid":"0000-0002-6216-011X","position":2,"is_corresponding":false},{"id":345114,"name":"Leor S. Weinberger","orcid":"0000-0002-9987-6357","position":3,"is_corresponding":false},{"id":897509,"name":"Giuliana Calia","orcid":"0000-0001-7394-9565","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":null,"created_at":"2026-07-19T01:18:37.743462Z","pmid":"36993609","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":[]}