The Effect of Nucleosome Stability on Gene Expression Level

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Nucleosomes, which are the basic packaging units of chromatin, are stably positioned in promoters upstream of most stress-induced genes. These promoter nucleosomes are generally thought to repress gene expression due to exclusion; they prevent transcription factors from accessing their binding sites on the DNA. Some promoter nucleosomes, however, do not directly occlude transcription factor binding sites, and therefore their role in gene expression remains unknown. To understand the non-exclusive role of nucleosomes in gene expression, we designed a model promoter in budding yeast where a nucleosome intervenes between a transcription factor binding site in nucleosome depleted region and the transcription start site. To vary nucleosome stability, we constructed promoter variants with several different GC contents in the nucleosomal DNA sequence. We then measured the downstream gene expression level from these promoter variants at different induction levels using a fluorescent protein reporter. Our preliminary data show that relatively high nucleosome stability does not always correlate with relatively low gene expression level. This result suggests that nucleosomes might contribute to gene expression in a cooperative manner either by bringing otherwise distant DNA sites close together or by anchoring the SWI/SNF chromatin remodeling complex for efficient removal of adjacent nucleosomes.