Abstract
Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors determine nucleosome positioning in regions that are not close to genes. We mapped both nucleosome positioning and DNase I hypersensitive site (DHS) datasets across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Phased nucleosomes were also found to flank DHSs in the human genome. Our results suggest the barrier model may represent a general feature of nucleosome organization in eukaryote genomes. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome.
Highlights
The fundamental unit of chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around a histone octamer containing four core histones (H3, H4, H2A, and H2B) [1]
We discovered that DNase I hypersensitive site (DHS) associated with different genomic regions, including promoters, genes, and intergenic regions, were all flanked by strongly phased nucleosome arrays
We applied a strategy of mapping both nucleosome positioning and DHS datasets to examine whether nucleosome positioning is associated with all cisregulatory elements across the rice genome
Summary
The fundamental unit of chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around a histone octamer containing four core histones (H3, H4, H2A, and H2B) [1]. Since the DNA has to bend sharply around the surface of the histone octamer, flexible or intrinsically curved sequences are favorable for nucleosome formation [2]. Poly(dA:dT) stretches, which are intrinsically stiff, have been shown to be unfavorable for nucleosome formation and are more enriched in linker sequences [3,4,5]. In vitro nucleosome assembly studies in yeast (Saccharomyces cerevisiae) and Caenorhabditis elegans have confirmed the DNA sequence preferences in nucleosome formation [7,8]. Nucleosome organization in vivo is determined by several factors that can override the sequence preferences, including gene transcription, action of nucleosome remodeling complexes, and presence of histone variants and histone modifications [2,6]. A sequence preference-based model could only explain ,50% of the in vivo nucleosome positions in S. cerevisiae [9]. It is important to take such numbers with caution, as the calculations are affected by the sequencing methodology and the cell/tissue types used in analysis [10]
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