Mammalian Genes Are Transcribed
with Widely Different Bursting Kinetics
David M. Suter,1 Nacho Molina,2 David Gatfield,1,3 Kim Schneider,1
Ueli Schibler,1†‡ Felix Naef2†‡
In prokaryotes and eukaryotes, most genes appear to be transcribed during short periods
called transcriptional bursts, interspersed by silent intervals. We describe how such bursts
generate gene-specific temporal patterns of messenger RNA (mRNA) synthesis in mammalian
cells. To monitor transcription at high temporal resolution, we established various gene trap cell
lines and transgenic cell lines expressing a short-lived luciferase protein from an unstable
mRNA, and recorded bioluminescence in real time in single cells. Mathematical modeling identified
gene-specific on- and off-switching rates in transcriptional activity and mean numbers of
mRNAs produced during the bursts. Transcriptional kinetics were markedly altered by cis-regulatory
DNA elements. Our analysis demonstrated that bursting kinetics are highly gene-specific,
reflecting refractory periods during which genes stay inactive for a certain time before
switching on again.
Polymerase II–mediated transcription of mammalian genes is a complex process consisting of several consecutive steps (1).
Studies in prokaryotes (2–4), yeast (5–7), and
higher eukaryotes (8–11) have suggested that
genes are transcribed in a discontinuous fashion,
resulting in stochastic production of RNA and
protein molecules. Stochastic gene expression
has been linked to phenotypic variability, for ex-
ample, in the resistance to antibiotics in bacterial
populations or in the control of developmental
transitions in metazoans (8, 12–14). Transcrip-
tional bursts can be abstracted in the random
telegraph model of gene expression (2, 9, 15–17 ),
whereby transcription switches between “on”
and “off” states (Fig. 1A). We monitored tran-
scription kinetics by single-cell time-lapse bio-
luminescence imaging of mouse fibroblasts
expressing a short-lived luciferase reporter gene
controlled by endogenous loci, circadian regula-
tory sequences, or artificial promoters (Fig. 1B).
Mathematical modeling allowed us to reconstruct
temporal changes in mRNA and protein copy
numbers as well as the gene activity state (“on” or
“off”) at a resolution of 5 min over extended
1Department of Molecular Biology, Sciences III, University of
Geneva, and National Centre of Competence in Research Frontiers
in Genetics, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland.
2Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, AAB 021 Station 15, CH-1015 Lausanne, Switzerland.
3Center for Integrative Genomics, University of Lausanne, 1015
*These authors contributed equally to this work.
†These authors contributed equally to this work.
‡To whom correspondence should be addressed. E-mail:
firstname.lastname@example.org (U.S.); email@example.com (F.N.)
Fig. 1. Different transgene insertion sites show
highly stereotyped luminescence profiles. (A) Sche-
matic for a gene switching between “on” and “off”
states and expressing short-lived mRNA and pro-
teins. (B) Schematic representation of the vectors
used to generate the different cell lines. SA, splice
acceptor; IRES, internal ribosomal entry site; Bsd,
blasticidin deaminase; F2A, foot-and-mouth virus
peptide 2A; NLS-luc, destabilized nuclear luciferase; polyA, polyadenylation
signal; ARE, AU-rich element. (C) Examples of single-cell traces. (D and E)
Relationships between transcription rate and kon (D) or koff (E) confirm gene
specificity of transcriptional kinetics. (F) Mean burst size versus percentage
of time during which the gene is active. Ellipses represent means T 2SD.
Color keys are shown on top of (D).