Nucleosome-Depleted Regions in Cell-Cycle-Regulated Promoters Ensure Reliable Gene Expression in Every Cell Cycle

Abstract

Summary Many promoters in eukaryotes have nucleosome depleted regions (NDR) containing transcription factor binding sites (TFBS). However, the functional significance of NDR is not well understood. Here, we examine NDR function in two cell-cycle-regulated promoters, CLN2pr and HOpr, by varying nucleosomal coverage of the binding sites of their activator SBF (SCBs) and probing the corresponding transcriptional activity in individual cells using time-lapse microscopy. Nucleosome-embedded SCBs do not significantly alter peak expression levels. Instead, they induce bimodal, “on/off” activation in individual cell cycles, which displays short-term memory, or epigenetic inheritance, from the mother cycle. In striking contrast, the same SCBs localized in NDR lead to highly reliable activation, once in every cell cycle. We further demonstrate that the high variability in Cln2p expression induced by the nucleosomal SCBs reduces cell fitness. Therefore, we propose that the NDR function in limiting stochasticity in gene expression promotes the ubiquity and conservation of promoter NDR.

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).…”

Stochastic expression and epigenetic memory at the yeast HO promoter

“…Using a cell cycle-regulated CLN2 promoter (CLN2pr) as a model, we found that a nucleosomedepleted region (NDR) over the activator SBF (Swi4/6) binding sites ensures reliable gene expression (4). In particular, when the SBF binding sites on CLN2pr are nucleosome-embedded, they induce "on/off" activation in individual cell cycles.…”

Déplétion des nucléosomes dans les régions promotrices

“…Dans une étude récente [11], nous avons apporté un éclairage nouveau sur ces questions. Dans la plupart des études précédentes, les données transcriptionnelles étaient exprimées comme la moyenne de mesures faites dans des populations de cellules.…”

“…Quelques éléments de réponse peuvent être tirés de notre étude ainsi que d'autres travaux empruntés à la littérature. En premier lieu, l'activation à partir d'un site de fixation nucléo somal peut requé-rir une concentration plus élevée d'activateurs et dépendre davantage des complexes de remodelage de la chromatine [7][8][9][10][11]. Le coût lié à ces deux processus pourrait être bien supérieur à celui nécessaire à la déplétion de quelques nucléosomes.…”