Transcriptional bursts render substantial biological noise in cellular transcriptomes. Here, we investigated the 8 theoretical extent of monoallelic expression resulting from transcriptional bursting and how it compared to the amounts of 9 monoallelic expression of autosomal genes observed in single-cell RNA-sequencing (scRNA-seq) data. We found that 10 transcriptional bursting can explain frequent observations of autosomal monoallelic gene expression in cells. Importantly, 11 the burst frequency largely determined the fraction of cells with monoallelic expression, whereas both burst frequency and 12 size contributed to allelic imbalance. Allelic observations deviate from the expected when analysed across heterogeneous 13 groups of cells, suggesting that allelic modelling can provide an unbiased assessment of heterogeneity within cells. Finally, 14 large numbers of cells are required for analyses of allelic imbalance to avoid confounding observations from transcriptional 15 bursting. Altogether, our results shed light on the implications of transcriptional burst kinetics on allelic expression patterns 16 and phenotypic variation between cells. 17 18 19Cells of identical background and type may show phenotypic differences (Symmons and Raj, 2016) and stochasticity 20 in the transcriptional process itself is known to generate cellular variability (Elowitz et al., 2002). In mammalian cells, 21 diploidy may give rise to phenotypic differences due to the unequal expression of two functionally different alleles. Indeed, 22 since mammalian genes are transcribed in discrete bursts (Elowitz et al., 2002; Chubb et al., 2006; Raj et al., 2006; 23 Suter et al., 2011) there are periodic fluctuations in the abundance of transcripts originating from each allele, which have 24 implications for the allelic expression within cells over time and may further extend to phenotypic differences (Reinius and 25 Sandberg, 2015). 26 The introduction of allele-sensitive single-cell RNA-sequencing revealed that RNA from substantial numbers of autosomal 27 genes were only detectable from a single allele in individual cells at any given time point (Deng et al., 2014). This autosomal 28 random monoallelic expression (aRME) is consistent with the concept of transcriptional bursting (Nicolas et al., 2017), 29 in particular since subsequent work demonstrated that the allelic patterns were primarily due to a stochastic process in 30 somatic cells rather than a mitotically heritable characteristic (Reinius et al., 2016). Furthermore, allele-specific RNA FISH 31 of autosomal genes in situ has shown that transcriptional bursting can explain the observed aRME in three selected cases 32 (Symmons et al., 2019). However, the explicit relationship between aRME and transcriptional burst kinetics has not been 33 systematically explored.
34The two-state model of transcription (Peccoud and Ycart, 1995; Raj et al., 2006) (Figure 1A) has been extensively used 35 to investigate quantitative relationships between burst kinetics and other gene-le...