Abstract
Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution, although the physiological basis of this assumption remains unclear. In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21–27 replicates), and the characteristics of gene-dependent empirical probability density function (ePDF) profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, various types of ePDF of gene expression levels were obtained that were classified as Gaussian, power law-like containing a long tail, or intermediate. These ePDF profiles were well fitted with a Gauss-power mixing distribution function derived from a simple model of a stochastic transcriptional network containing a feedback loop. The fitting function suggested that gene expression levels with long-tailed ePDFs would be strongly influenced by feedback regulation. Furthermore, the features of gene expression levels are correlated with their functions, with the levels of essential genes tending to follow a Gaussian-like ePDF while those of genes encoding nucleic acid-binding proteins and transcription factors exhibit long-tailed ePDF.
Highlights
Stochastic variations in gene expression—known as gene expression noise or phenotype fluctuation—have been observed among individuals in a genetically identical population under the same environmental conditions[1,2,3,4,5,6,7,8,9,10,11]
RNA sequencing (RNA-seq) data from 7- and 22-day-old Arabidopsis shoots cultured under a 12:12-h light/dark cycle were obtained 1, 7, 13, and 19 h after the lights were turned on
Each gene could be classified by parameters of the G-P function fitting its empirical probability density function (ePDF) profile of expression levels
Summary
Stochastic variations in gene expression—known as gene expression noise or phenotype fluctuation—have been observed among individuals in a genetically identical population under the same environmental conditions[1,2,3,4,5,6,7,8,9,10,11]. An analysis of RNA-seq data from a two-condition, 48-replicate experiment using S. cerevisiae revealed that variations in expression levels for each gene conformed to both log-normal and NB distributions[36]. We analyzed RNA-seq data for A. thaliana under eight conditions (21–27 replicates) to observe the empirical probability distribution profiles of gene expression levels among individuals in a homogeneous population. The features of each probability distribution function in gene expression level are expected to be correlated with the strength of feedback regulation for each gene, its average expression level, and its function
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