Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

Abstract

Understanding how precise control of gene expression is specified within regulatory DNA sequences is a key challenge with far-reaching implications. Many studies have focused on the regulatory role of transcription factor-binding sites. Here, we explore the transcriptional effects of different elements, nucleosome-disfavoring sequences and, specifically, poly(dA:dT) tracts that are highly prevalent in eukaryotic promoters. By measuring promoter activity for a large-scale promoter library, designed with systematic manipulations to the properties and spatial arrangement of poly(dA:dT) tracts, we show that these tracts significantly and causally affect transcription. We show that manipulating these elements offers a general genetic mechanism, applicable to promoters regulated by different transcription factors, for tuning expression in a predictable manner, with resolution that can be even finer than that attained by altering transcription factor sites. Overall, our results advance the understanding of the regulatory code and suggest a potential mechanism by which promoters yielding prespecified expression patterns can be designed.

Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise

“…Similar to the effect of TATA-boxes, the increase in expression variability observed with two NF-Y sites or with a higheraffinity site was mediated primarily by an increase in the average burst size, whereas the burst frequency was largely unaffected (Suter et al 2011). Chromatin regulation has also been linked to expression variability (Blake et al 2003;Raser and O'Shea 2004;Field et al 2008;Choi and Kim 2009;Bai et al 2010), with two studies showing that adding nucleosome-disfavoring sequences to a yeast promoter resulted in lower nucleosome occupancy and reduced expression variability (Bai et al 2010;Raveh-Sadka et al 2012). However, in contrast to the effect of TATA-boxes and TF sites, chromatin was suggested to mainly affect the frequency with which promoters transition between transcriptionally active and inactive states (Raser and O'Shea 2004).…”

“…1A, bottom). In contrast, since addition of poly(dA:dT) tracts, which disfavor nucleosome formation (Segal and Widom 2009), was shown to result in lower nucleosome occupancy and more accessible DNA in the vicinity of the tract (Iyer and Struhl 1995;Raveh-Sadka et al 2012), we hypothesized that this would result in faster on/off binding dynamics of a TF to a nearby site, and thus increase expression by increasing the burst frequency (Fig. 1A, middle).…”

“…Several lines of evidence suggested that the effect of the nucleosomedisfavoring sequences was likely mediated by the lower nucleosome occupancy and thus increased accessibility that nucleosomedisfavoring sequences confer over the nearby promoter elements, such as TF sites (Raveh-Sadka et al 2012). Thus, combined with the above studies, an intriguing hypothesis is that the two distinct types of sequence changes in either TF sites or in nucleosome-disfavoring sequences provide a genetic mechanism that may allow partial decoupling of mean expression level and transcriptional noise.…”

“…A recent study showed that the quantitative increase in the mean expression over a cell population that results from adding nucleosome disfavoring sequences can be comparable to the increase in expression achieved when increasing the affinity of a transcription factor (TF) binding site (Raveh-Sadka et al 2012). Several lines of evidence suggested that the effect of the nucleosomedisfavoring sequences was likely mediated by the lower nucleosome occupancy and thus increased accessibility that nucleosomedisfavoring sequences confer over the nearby promoter elements, such as TF sites (Raveh-Sadka et al 2012).…”

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress inC. elegans

“…Poly(dA:dT) tracts disrupt nucleosome formation and tend to increase transcription of downstream genes (Raveh-Sadka et al 2012), while TATA box motifs in yeast are associated with bendable promoters sensitive to chromatin remodelers (Albert et al 2007;Tirosh et al 2007). In C. elegans, the number of T-block motifs (three to five consecutive thymine nucleotides, often spaced at 10-bp periodicity) have been positively correlated with expression: Genes with more than five T-blocks have fivefold higher expression than genes with fewer than four T-blocks (Grishkevich et al 2011), presumably through a reduction in promoter nucleosome occupancy.…”