Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells

Area of Science:

• Quantitative biology
• Molecular cell biology
• Genomics

Background:

• The relationship between messenger RNA (mRNA) and protein levels is a fundamental question in molecular biology.
• Understanding this relationship is crucial for interpreting gene expression and cellular function.

Purpose of the Study:

• To investigate the correlation between mRNA and protein abundance in single human cells.
• To identify factors influencing the mRNA-protein relationship, including cell phenotype and population context.
• To develop a predictive model for single-cell protein abundance.

Main Methods:

• Utilized a combination of cell lines with fluorescently tagged endogenous genomic loci.
• Employed quantitative immunofluorescence and branched DNA single-molecule fluorescence in situ hybridization.
• Applied computer vision for high-throughput single-cell analysis of mRNA and protein levels, phenotypic state, and population context for 23 genes.

Main Results:

• Observed a mean single-cell correlation of 0.732 between mRNA and protein abundance at steady state.
• Identified specific phenotypic states and population contexts for outliers deviating from linear correlations.
• Demonstrated that single-cell protein abundance can be predicted by integrating mRNA levels with phenotypic state and microenvironment.

Conclusions:

• Single-cell protein abundance is not solely determined by mRNA levels but is modulated by cellular context.
• The findings provide a more nuanced understanding of gene expression regulation at the single-cell level.
• This integrated approach advances the prediction of protein levels and interpretation of gene expression dynamics.