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Series GSE242874 Query DataSets for GSE242874
Status Public on Nov 01, 2023
Title RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size
Organisms Schizosaccharomyces pombe; Saccharomyces cerevisiae; Nakaseomyces glabratus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary A fundamental feature of cellular growth is that total protein and RNA amounts increase with cell size to keep concentrations approximately constant. A key component to this is that global transcription rates increase in larger cells. Here, we identify RNAPII as the limiting factor scaling mRNA transcription with cell size in budding yeast, as transcription is highly sensitive to the dosage of RNAPII but not to other components of the transcriptional machinery. Our experiments support a dynamic equilibrium model where global RNAPII transcription at a given size is set by the mass-action recruitment kinetics of unengaged nucleoplasmic RNAPII to the genome. However, this only drives a sub-linear increase in transcription with size, which is then partially compensated for by a decrease in mRNA decay rates as cells enlarge. Thus, limiting RNAPII and feedback on mRNA stability work in concert to scale mRNA amounts with cell size.
 
Overall design ChIP-seq and RNA-seq experiments using S. cerevisiae with a spike-in of S. pombe or C. glabrata cells for spike-in normalisation.
 
Contributor(s) Swaffer MP, Marinov GK, Zheng H, Fuentes Valenzuela L, Tsui CY, Jones AW, Greenwood J, Kundaje A, Greenleaf WJ, Reyes-Lamothe R, Skotheim JM
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Submission date Sep 11, 2023
Last update date Nov 01, 2023
Contact name Georgi Kolev Marinov
Organization name STANFORD UNIVERSITY
Department Genetics
Street address 279 Campus Drive West, Beckman Center, B-257A/259
City Stanford
State/province California
ZIP/Postal code 94305-5101
Country USA
 
Platforms (2)
GPL29170 Illumina NovaSeq 6000 (Saccharomyces cerevisiae; Schizosaccharomyces pombe)
GPL33750 Illumina NovaSeq 6000 (Nakaseomyces glabratus; Saccharomyces cerevisiae)
Samples (782)
GSM7773406 180415LA_exp180227_MS01-MS99_SCGE-ratio-0.0625_anti-H3
GSM7773407 180415LB_exp180227_MS01-MS99_SCGE-ratio-0.25_anti-H3
GSM7773408 180415LC_exp180227_MS01-MS99_SCGE-ratio-0.50_anti-H3
Relations
BioProject PRJNA1015207

Download family Format
SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE242874_RAW.tar 11.3 Gb (http)(custom) TAR (of BIGWIG)
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Raw data are available in SRA
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