Comparative analysis between single-cell RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise
Comparative analysis between single-cell 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 scRNA-seq 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. Graphical Abstractbiorxiv;2023.03.14.532632v1/UFIG1F1ufig1
Calia Giuliana P.、Weinberger Leor S.、Zuckerman Binyamin、Chen Xinyue
Gladstone|UCSF Center for Cell Circuitry, University of CaliforniaGladstone|UCSF Center for Cell Circuitry, University of California||Department of Biochemistry and Biophysics, University of California||Department of Pharmaceutical Chemistry, University of CaliforniaGladstone|UCSF Center for Cell Circuitry, University of CaliforniaGladstone|UCSF Center for Cell Circuitry, University of California
分子生物学细胞生物学生物科学研究方法、生物科学研究技术
noise enhancer moleculetranscriptional noisesingle-cell RNA sequencing
Calia Giuliana P.,Weinberger Leor S.,Zuckerman Binyamin,Chen Xinyue.Comparative analysis between single-cell RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise[EB/OL].(2025-03-28)[2025-05-14].https://www.biorxiv.org/content/10.1101/2023.03.14.532632.点此复制
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