DOI: 10.5061/dryad.tb2rbp06x
title: Ribosome demand links transcriptional bursts to protein expression noise

description: The translation process modulates stochastic fluctuations in mRNA numbers
 and determines noise in protein expression. Studies across different
 organisms have revealed a positive correlation between translational
 efficiency and protein noise. However, the molecular basis of this
 correlation has remained unknown. Through stochastic modeling of
 translation in single mRNA molecules and empirical measurement of protein
 noise, we demonstrate that ribosome demand associated with high
 translational efficiency leads to the correlation between translational
 efficiency and protein noise. We also show that this correlation is
 present only in promoters with bursty transcription, where ribosome demand
 varies with stochastic fluctuations in mRNA numbers. Thus, our work shows
 how transcriptional bursts are translated into protein noise, which has
 implications for investigating noise and phenotypic heterogeneity across
 biological systems.
description: Clones of wild-type GFP gene and each mutant
 variant were grown in SCD medium (0.67% YNB + 0.079% complete synthetic
 supplement + 2% glucose) at 30℃ with shaking at 220 rpm. Yeast cells from
 glycerol stock were inoculated in SCD medium, were grown for 24 hrs, and
 were then diluted 1:100 in fresh medium. This process was repeated one
 more time.  The cells were then diluted 1:50 in fresh SCD and were grown
 for 4 hours. In the next step, cells were centrifuged and washed twice
 with 1X PBS (Phosphate Buffered Saline) buffer, and were finally
 resuspended in 1X PBS buffer for flow cytometry. In flow cytometry, the
 data were acquired for 2,00,000 cells for each sample in a BD LSR Fortessa
 cell analyzer.
description: # Ribosome demand links transcriptional bursts to protein expression noise
 [https://doi.org/10.5061/dryad.tb2rbp06x](https://doi.org/10.5061/dryad.tb2rbp06x) The dataset contains raw fcs files from flow cytometer of yeast strains carrying wild type and mutant versions of GFP gene.  ## Description of the data and file structure The dataset contains fcs files for an experiment dated 1st June, 2022. Therefore, the file names are written as 20220601_* The "Strain_names.docx" file describes the mutant GFP variants and the specific mutations that they carry. Individual fcs file annotations are as follows -  20220601_BY4741.fcs - This is the negative control strain that does not carry any GFP gene  20220601_RPG1_NGFP_c1.fcs - Strain carrying a GFP gene under the control of RPG1 promoter (Clone 1) 20220601_RPG1_NGFP_c2.fcs - Strain carrying a GFP gene under the control of RPG1 promoter (Clone 2) 20220601_RPG1_NGFPM4_c1.fcs - Strain carrying a mutant version (M4) of the GFP gene under the control of RPG1 promoter (Clone 1) 20220601_RPG1_NGFPM4_c2.fcs - Strain carrying a mutant version (M4) of the GFP gene under the control of RPG1 promoter (Clone 2) 20220601_RPG1_NGFPM4_c3.fcs - Strain carrying a mutant version (M4) of the GFP gene under the control of RPG1 promoter (Clone 3) 20220601_RPG1_NGFPM5F_c1.fcs - Strain carrying a mutant version (M5F) of the GFP gene under the control of RPG1 promoter (Clone 1) 20220601_RPG1_NGFPM5F_c2.fcs - Strain carrying a mutant version (M5F) of the GFP gene under the control of RPG1 promoter (Clone 2) 20220601_RPG1_NGFPM5F_c3.fcs - Strain carrying a mutant version (M5F) of the GFP gene under the control of RPG1 promoter (Clone 3) 20220601_RPG1_NGFPM6_c1.fcs - Strain carrying a mutant version (M6) of the GFP gene under the control of RPG1 promoter (Clone 1) 20220601_RPG1_NGFPM6_c2.fcs - Strain carrying a mutant version (M6) of the GFP gene under the control of RPG1 promoter (Clone 2) 20220601_RPG1_NGFPM6_c3.fcs - Strain carrying a mutant version (M6) of the GFP gene under the control of RPG1 promoter (Clone 3) 20220601_RPG1_NGFPM7_c1.fcs - Strain carrying a mutant version (M7) of the GFP gene under the control of RPG1 promoter (Clone 1) 20220601_RPG1_NGFPM7_c2.fcs - Strain carrying a mutant version (M7) of the GFP gene under the control of RPG1 promoter (Clone 2) 20220601_RPG1_NGFPM7_c3.fcs - Strain carrying a mutant version (M7) of the GFP gene under the control of RPG1 promoter (Clone 3) 20220601_RPL35_NGFP_c1.fcs - Strain carrying the GFP gene under the control of RPL35A promoter (Clone 1) 20220601_RPL35_NGFP_c2.fcs - Strain carrying the GFP gene under the control of RPL35A promoter (Clone 2) 20220601_RPL35_NGFPM4_c1.fcs - Strain carrying a mutant version (M4) of the GFP gene under the control of RPL35A promoter (Clone 1) 
 
 Each fcs file contains the following information:  FSC - Forward scatter
 values of the cells  SSC - Side scatter values of the cells  FITC - GFP
 signal intensity (arbitrary units) from individual cells  PE-Texas-Red -
 Blank signal in the PE channel (control)  
 
 ## Code/Software The code used for processing fcs files are available at:
 [https://github.com/riddhimandhar/TranslationModNoise](https://github.com/riddhimandhar/TranslationModNoise) The flow cytometry data processing was done using the R/Bioconductor package 'flowCore' ([https://www.bioconductor.org/packages/release/bioc/html/flowCore.html](https://www.bioconductor.org/packages/release/bioc/html/flowCore.html))