Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation

Abstract

Transcription of genes can be discontinuous, occurring in pulses or bursts. It is not clear how properties of transcriptional pulses vary between different genes. We compared the pulsing of five housekeeping and five developmentally induced genes by direct imaging of single gene transcriptional events in individual living Dictyostelium cells. Each gene displayed its own transcriptional signature, differing in probability of firing and pulse duration, frequency, and intensity. In contrast to the prevailing view from both prokaryotes and eukaryotes that transcription displays binary behavior, strongly expressed housekeeping genes altered the magnitude of their transcriptional pulses during development. These nonbinary "tunable" responses may be better suited than stochastic switch behavior for housekeeping functions. Analysis of RNA synthesis kinetics using fluorescence recovery after photobleaching implied modulation of housekeeping-gene pulse strength occurs at the level of transcription initiation rather than elongation. In addition, disparities between single cell and population measures of transcript production suggested differences in RNA stability between gene classes. Analysis of stability using RNAseq revealed no major global differences in stability between developmental and housekeeping transcripts, although strongly induced RNAs showed unusually rapid decay, indicating tight regulation of expression.transcriptional bursting | RNA turnover | stochastic gene expression T ranscription is not adequately described by the smooth, seamless process implied by standard measures of RNA level. Within individual cells, transcription occurs as a series of irregular pulses, interspersed by long, irregular periods of inactivity. Pulsing (or bursting) is a fundamental feature of transcription, conserved from prokaryotes to mammalian cells (1-5). These phenomena have strong implications for our understanding of transcriptional mechanism and may provide a major source of stochasticity in gene expression (6), a driver of cell diversity in differentiation and disease (7,8). However, it is unclear how pulsing behaves for different genes with different functional properties.Pulsing dynamics, and therefore deeper understanding of underlying transcriptional mechanics and regulation of different genes, are masked when averaged over millions of dead cells, as occurs with standard bulk RNA measurement techniques, from Northern blotting to RNA sequencing (RNAseq). The readout from these methods also has a variable contribution from RNA stability. Although strong inferences can be made from heterogeneities in transcript number using hybridization against RNA in single cells (RNA-FISH) (9-11), an erroneous inference of strong transcription from both bulk and fixed-cell RNA techniques emerges if RNA is stable. To appreciate how transcription is regulated and how the process differs between different genes, it is crucial to look at the process itself in living cells at the singlegene level. Live-cell methods using fluorescent protein...

Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage

“…A sustained, non-binary transcriptional activity might be better suited for housekeeping functions (Muramoto et al, 2012). By contrast, stochastic switch behaviour might allow room for developmental decisions, an idea supported by studies from both Dictyostelium and Drosophila (Muramoto et al, 2012;Little et al, 2013).…”

“…When the rate of pre-initiation complex and RNAPII binding and processivity is high, transcription of a gene becomes a sustained event, with only short periods of inactivity between the production of transcripts from the given gene. Often, however, transcription of genes is a rather discontinuous event, with only a few pulses occurring over a discrete time period (Muramoto et al, 2012).…”

Aptamer-based molecular imaging

“…This resulted in a probability of 26% Pol II pausing at a single gene locus. The elongation pausing kinetics of Pol II (Darzacq et al, 2007) and the potential different initiation rate of Pol II (Muramoto et al, 2012) may explain the mRNA transcriptional pulsing dynamics. To correlate chromatin structure with transcription, a 200-copy gene array system as mentioned above with additional tetracycline inducible elements was integrated into chromosome 1 heterochromatic region in human U2OS cells.…”

“…With the progress of development stages, the percent of cells expressing the genes increased for most developmental genes but decreased for most of the housekeeping genes. For transcription pulse behavior (pulse duration, frequency and intensity) at different development stages, most development genes had constant transcription pulse behavior while housekeeping genes showed tunable transcription pulse behavior (Muramoto et al, 2012). To measure the mRNA transcription kinetics (kinetic parameters in promoter binding, initiation and elongation), a gene array of 200 copies of a gene cassette (CFP-SKL) each tagged with 24 units of MS2 aptamer was inserted into a single locus on a chromosome of human U2OS cells.…”

Epigenetic memory and parliamentary privilege combine to evoke discussions on inheritance

“…Single-molecule approaches and live cell imaging have been widely applied to document transcription, revealing that this is a largely discontinuous process in which transcripts are generated in bursts or pulses (Raj and van Oudenaarden, 2008;Muramoto et al, 2012). Using this approach, Jonathan Chubb (University College London, UK) monitored transcriptional events in individual Dictyostelium cells to find out whether transcriptional activity was inherited through mitosis.…”