Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data DOI Creative Commons

Augustinas Sukys,

Ramon Grima

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(7)

Published: March 31, 2025

Bursty gene expression is characterized by two intuitive parameters, burst frequency and size, the cell-cycle dependence of which has not been extensively profiled at transcriptome level. In this study, we estimate parameters per allele in G1 G2/M phases for thousands mouse genes fitting mechanistic models to messenger RNA count data, obtained sequencing single cells whose position inferred using a deep-learning method. We find that upon DNA replication, median approximately halves, while size remains mostly unchanged. Genome-wide distributions parameter ratios between are broad, indicating substantial heterogeneity transcriptional regulation. also observe significant negative correlation ratios, suggesting regulatory processes do independently control parameters. show accurately must explicitly account copy number variation extrinsic noise due coupling transcription cell age across cycle, but corrections technical imperfect capture molecules experiments less critical.

Language: Английский

Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data DOI Creative Commons

Augustinas Sukys,

Ramon Grima

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(7)

Published: March 31, 2025

Bursty gene expression is characterized by two intuitive parameters, burst frequency and size, the cell-cycle dependence of which has not been extensively profiled at transcriptome level. In this study, we estimate parameters per allele in G1 G2/M phases for thousands mouse genes fitting mechanistic models to messenger RNA count data, obtained sequencing single cells whose position inferred using a deep-learning method. We find that upon DNA replication, median approximately halves, while size remains mostly unchanged. Genome-wide distributions parameter ratios between are broad, indicating substantial heterogeneity transcriptional regulation. also observe significant negative correlation ratios, suggesting regulatory processes do independently control parameters. show accurately must explicitly account copy number variation extrinsic noise due coupling transcription cell age across cycle, but corrections technical imperfect capture molecules experiments less critical.

Language: Английский

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