Fig. 2

Paused genes have lower cell-to-cell expression variability than non-paused genes. a Paused genes comprised the majority of expressed (FPKM >1) genes in each cell type. E, expressed genes (FPKM >1); A, All Refseq genes. (***p <0.001, Mann–Whitney U test). b “Hill-shaped” relationship between gene expression and PI in GM12878. We found no linear correlation between the PI and gene expression levels. The broadest range and strongest level of gene expression occurred at intermediate PI values, while extreme PI values were associated with reduced gene expression. c Similar “hill-shaped” relationships were observed in the four other cell lines examined, with the hill peak occurring within a similar PI range for 4/5 cell lines. d Using single cell RNA-seq data for GM12878 [18] and H1 [19], we analyzed the effect of RNAP2 pausing on cell-to-cell gene expression variability. We measured the coefficient of variation (standard deviation/mean) of gene expression across individual cells, stratified by gene expression quintiles based on the single-cell population wide mean expression level. We then compared between paused and non-paused genes. For nearly all expression quintiles in both cell lines, paused genes had lower coefficient of variation on average, suggesting that at the same expression level RNAP2 pausing dampens expression variability. (***p <0.001, NS, not significant; Mann–Whitney U test.)