Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

Ochiai, Hiroshi; Hayashi, Tetsutaro; Umeda, Mana; Yoshimura, Mika; Harada, Akihito; Shimizu, Yukiko; Nakano, Kenta; Saitoh, Noriko; Liu, Zhe; Yamamoto, Takashi; Okamura, Tadashi; Ohkawa, Yasuyuki; Kimura, Hiroshi; Nikaido, Itoshi

Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. However, the mechanism underlying the regulation of transcriptional bursting kinetics (burst size and frequency) in mammalian cells remains elusive. In this study, we performed single-cell RNA sequencing to analyze the intrinsic noise and mRNA levels for elucidating the transcriptional bursting kinetics in mouse embryonic stem cells. Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.