Biology subjects

Shahrezaei, V.

Publications and source records attributed to Shahrezaei, V..

3 recordsLinked to original sources

bioRxiv2018

bayNorm: Bayesian gene expression recovery, imputation and normalisation for single cell RNA-sequencing data

Normalisation of single cell RNA sequencing (scRNA-seq) data is a prerequisite to their interpretation. The marked technical variability and high amounts of missing observations typical of scRNA-seq datasets make this task particularly challenging. Here, we introduce bayNorm, a novel Bayesian approach for scaling and inference of scRNA-seq counts. The methods likelihood function follows a binomial model of mRNA capture, while priors are estimated from expression values across cells using an empirical Bayes approach. We demonstrate using publicly-available scRNA-seq datasets and simulated expression data that bayNorm allows robust imputation of missing values generating realistic transcript distributions that match single molecule FISH measurements. Moreover, by using priors informed by dataset structures, bayNorm improves accuracy and sensitivity of differential expression analysis and reduces batch effect compared to other existing methods. Altogether, bayNorm provides an efficient, integrated solution for global scaling normalisation, imputation and true count recovery of gene expression measurements from scRNA-seq data.

bioinformatics↗

bioRxiv2018

Single-cell phenotyping and RNA sequencing reveal novel patterns of gene expression heterogeneity and regulation during growth and stress adaptation in a unicellular eukaryote

Cell-to-cell variability is central for microbial populations and contributes to cell function, stress adaptation and drug resistance. Gene-expression heterogeneity underpins this variability, but has been challenging to study genome-wide. Here, we report an integrated approach for imaging of individual fission yeast cells followed by single-cell RNA sequencing (scRNA-seq) and novel Bayesian normalisation. We analyse >2000 single cells and >700 matching RNA controls in various environmental conditions and identify sets of highly variable genes. Combining scRNA-seq with cell-size measurements provides unique insights into genes regulated during cell growth and division in single cells, including genes whose expression does not scale with cell size. We further analyse the heterogeneity and dynamics of gene expression during adaptive and acute responses to changing environments. Entry into stationary phase is preceded by a gradual, synchronised adaptation in gene regulation, followed by highly variable gene expression when growth decreases. Conversely, a sudden and acute heat-shock leads to a stronger and coordinated response and adaptation across cells. This analysis reveals that the extent and dynamics of global gene-expression heterogeneity is regulated in response to different physiological conditions within populations of a unicellular eukaryote. In summary, this works illustrates the potential of combined transcriptomics and imaging analysis in single cells to provide comprehensive and unbiased mechanistic understanding of cell-to-cell variability in microbial communities.

genomics↗

bioRxiv2017

Impact of division rate and cell size on gene expression noise

The cell division rate, size, and gene expression programmes change in response to external conditions. These global changes impact on average concentrations of biomolecule and their variability or noise. Gene expression is inherently stochastic, and noise levels of individual proteins depend on synthesis and degradation rates as well as on cell-cycle dynamics. We have modelled stochastic gene expression inside growing and dividing cells to study the effect of division rates on noise in mRNA and protein expression. We use assumptions and parameters relevant to Escherichia coli, for which abundant quantitative data are available. We find that coupling of transcription, but not translation rates to the rate of cell division can result in protein concentration and noise homeostasis across conditions. Interestingly, we find that the increased cell size at fast division rates, observed in E. coli d other unicellular organisms, buffers noise levels even for proteins with decreased expression at faster growth. We then investigate the functional importance of these regulations using gene regulatory networks that exhibit bi-stability and oscillations. We find that network topology affects robustness to changes in division rate in complex and unexpected ways. In particular, a simple model of persistence, based on global physiological feedback, predicts increased proportion of persistors cells at slow division rates. Altogether, our study reveals how cell size regulation in response to cell division rate could help controlling gene expression noise. It also highlights that understanding of circuits robustness across growth conditions is key for the effective design of synthetic biological systems.

systems biology↗