Real-time monitoring of gene expression reveals transcription kinetics of mammalian genes.

SwissRegulon (Author Webpage) is a database containing genome-wide annotations of regulatory sites in the intergenic regions of genomes. The regulatory site annotations are produced using a number of recently developed algorithms that operate on multiple alignments of orthologous intergenic regions from related genomes in combination with, whenever available, known sites from the literature, and ChIP-on-chip binding data. Currently SwissRegulon contains annotations for yeast and 17 prokaryotic genomes. The database provides information about the sequence, location, orientation, posterior probability and, whenever available, binding factor of each annotated site. To enable easy viewing of the regulatory site annotations in the context of other features annotated on the genomes, the sites are displayed using the GBrowse genome browser interface and can be queried based on any annotated genomic feature. The database can also be queried for regulons, i.e. sites bound by a common factor.

Significance: Recent single-cell studies showed that gene transcription in mammals is fundamentally stochastic, occurring in short and intense transcriptional bursts. However, less is known on how transcriptional bursting is modulated upon stimulation. Here, we monitor the transcriptional response of a single allele of the endogenous connective tissue growth factor gene, encoding a secreted protein involved in wound healing and response to shear stress, to two different physiological stimuli in single cells. Analysis using stochastic modeling shows that both stimuli cause acute transcriptional responses characterized by transiently modified gene activities, and increased transcription rates that may last longer depending on the stimulus. These results provide insights on how transcriptional bursting kinetics can be adjusted to increase gene expression upon physiological stimulations.

Mammalian transcription occurs stochastically in short bursts interspersed by silent intervals showing a refractory period. However, the underlying processes and consequences on fluctuations in gene products are poorly understood. Here, we use single allele time‐lapse recordings in mouse cells to identify minimal models of promoter cycles, which inform on the number and durations of rate‐limiting steps responsible for refractory periods. The structure of promoter cycles is gene specific and independent of genomic location. Typically, five rate‐limiting steps underlie the silent periods of endogenous promoters, while minimal synthetic promoters exhibit only one. Strikingly, endogenous or synthetic promoters with TATA boxes show simplified two‐state promoter cycles. Since transcriptional bursting constrains intrinsic noise depending on the number of promoter steps, this explains why TATA box genes display increased intrinsic noise genome‐wide in mammals, as revealed by single‐cell RNA‐seq. These findings have implications for basic transcription biology and shed light on interpreting single‐cell RNA‐counting experiments.