Dadiani et al. explored the effects that two types of promoter element have on transcription: nucleosome disfavouring sequences and transcription factor binding sites. It has previously been shown that either increasing the affinity of a transcription factor binding site or adding sequences that disfavour nucleosome formation (that is, poly(dA:dT) tracts) can increase the mean expression of a gene across a population of cells. However, it is predicted that they do so in different ways. Genes are transcribed in bursts, and increased transcription factor binding affinity is expected to increase the number of transcripts produced per burst (because the factor is likely to remain bound for longer). By contrast, increasing nucleosome disfavouring sequences is expected to increase burst frequency (because the DNA is likely to be more accessible for factors to bind).
To test these predictions, the authors used strains of yeast containing a yellow fluorescent protein (YFP) gene driven by the same promoter with changes in a transcription factor binding site or in the length of a poly(dA:dT) tract. They monitored YFP in single cells over time using automated fluorescence microscopy and at single time points using flow cytometry. For equivalent mean expression levels, they found that the longer poly(dA:dT) tracts resulted in faster promoter dynamics (that is, faster on–off switching) and lower transcriptional noise across a cell population compared to promoters with increased transcription factor binding site affinity. Their results are consistent with the predicted effects of the different sequence changes.
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