The Effect of an Intervening Promoter Nucleosome on Gene Expression

Rasesh Y. Parikh,Harold D. Kim

doi:10.1371/journal.pone.0063072

Abstract

Nucleosomes, which are the basic packaging units of chromatin, are stably positioned in promoters upstream of most stress-inducible genes. These promoter nucleosomes are generally thought to repress gene expression due to exclusion; they prevent transcription factors from accessing their target sites on the DNA. However, the role of promoter nucleosomes that do not directly occlude transcription factor binding sites is not obvious. Here, we varied the stability of a non-occluding nucleosome positioned between a transcription factor binding site and the TATA box region in an inducible yeast promoter and measured downstream gene expression level. We found that gene expression level depends on the occupancy of the non-occluding nucleosome in a non-monotonic manner. We postulated that a non-occluding nucleosome can serve both as a vehicle of and a barrier to chromatin remodeling activity and built a quantitative, nonequilibrium model to explain the observed nontrivial effect of the intervening nucleosome. Our work sheds light on the dual role of nucleosome as a repressor and an activator and expands the standard model of gene expression to include irreversible promoter chromatin transitions.

Highlights

The effect of promoter nucleosomes is generally thought to be repressive for gene expression because nucleosomes can sterically hinder access of transcription factors to the promoter during transcriptional activation [1]
All known binding sequences of Pho2 [34], a trans-activator which cooperatively interacts with Pho4, were left intact in all Nuc -2 (+) promoter variants. We believe that this nontrivial effect of the non-occluding nucleosome on gene expression level is a result of nucleosome occupancy, not the change in DNA sequence itself
We showed that gene expression level depended on the occupancy of a non-occluding nucleosome in a non-monotonic manner

Summary

Introduction

The effect of promoter nucleosomes is generally thought to be repressive for gene expression because nucleosomes can sterically hinder access of transcription factors to the promoter during transcriptional activation [1]. The TATA box is occluded by nucleosome -1 as the removal of nucleosome -1 is sufficient for transcriptional activation of PHO5pr [24] These evidences point to the notion that promoter nucleosomes in occluding configurations repress gene expression by preventing trans-factors from binding to cis-regulatory elements. Because changing GC% of nucleosome -2 sequence which was similar to the wild-type sequence led to a drop in gene expression level, we explored the possibility that crucial cis regulatory elements could have been unintentionally deleted in the low or high GC% Nuc -2 (+) variant. All known binding sequences of Pho2 [34], a trans-activator which cooperatively interacts with Pho, were left intact in all Nuc -2 (+) promoter variants Based on these results, we believe that this nontrivial effect of the non-occluding nucleosome on gene expression level is a result of nucleosome occupancy, not the change in DNA sequence itself

Discussion

Findings

Materials and Methods