Allele-specific mRNA expression analysis in 129/CAST hybrid mESCs by single-cell full-length total RNA-sequencing

Cell-to-cell heterogeneity in gene expression can even be observed in the same type of cells, present in a similar environment. Transcriptional bursting is thought to be one of contributing factors to the heterogeneity, but it remains elusive how the kinetic properties of transcriptional bursting (e.g. burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. Here, by using single-cell, full-length total RNA-sequencing, we performed genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs). We found that the kinetics of transcriptional bursting is gene-specific and is determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors. To study kinetic properties of transcriptional bursting genome-wide, we analyzed allele-specific mRNA levels in 129/CAST hybrid mESCs (grown on Laminin-511 (LN511) without feeder cells in G1 phase) by RamDA-Seq - a highly sensitive RNA-Seq method capable of determining the full-length of transcript at single cell level (Hayashi et al., 2018).