Jonathan Chubb Research Group

Imaging transcriptional dynamics

Despite the generation of transcriptional differences between nearby
related cells being the basis of most differentiation and disease, our standard
measures of RNA synthesis do not register the origins of these differences.
Although useful for a preliminary rough sorting of genes to context, the
widespread techniques of Northern blotting, microarrays, RT-PCR and RNA-Seq
measure bulk RNA levels from homogenous population extracts. These approaches
lose dynamic information from individual cells, and give the impression
transcription is a continuous smooth process. The reality is that transcription
is irregular, with strong variable duration periods of activity, interspersed
by variable duration periods of inactivity (see movie sequences). Averaged over
millions of cells, this appears continuous. But at the individual cell level,
there is considerable variability, and for most genes, very little activity at
any one time.  Transcription of genes, the process which transforms the
stable code written in DNA into the mobile RNA message can occur in
"bursts" or"pulses" (see movie sequence). These phenomena
have recently come to light with the advent of new technologies, to detect RNA
in single cells, allowing precise measurements of RNA number, or RNA emergence
at a gene.  We would like to understand the mechanistic basis of pulsing,
and how it is responsive to signals, developmental and chromatin context. And
we are testing the implications of noisy transcription on the generation of
diversity between cells in developmental and clinical contexts.