Abstract
Understanding chromatin function requires knowing the precise location of nucleosomes. MNase-seq methods have been widely applied to characterize nucleosome organization in vivo, but generally lack the accuracy to determine the precise nucleosome positions. Here we develop a computational approach leveraging digestion variability to determine nucleosome positions at a base-pair resolution from MNase-seq data. We generate a variability template as a simple error model for how MNase digestion affects the mapping of individual nucleosomes. Applied to both yeast and human cells, this analysis reveals that alternatively positioned nucleosomes are prevalent and create significant heterogeneity in a cell population. We show that the periodic occurrences of dinucleotide sequences relative to nucleosome dyads can be directly determined from genome-wide nucleosome positions from MNase-seq. Alternatively positioned nucleosomes near transcription start sites likely represent different states of promoter nucleosomes during transcription initiation. Our method can be applied to map nucleosome positions in diverse organisms at base-pair resolution.
Highlights
The eukaryotic genome is compacted into chromatin (Kornberg, 1974) which is comprised of nucleosomes, each consisting of approximately 147 base pairs of DNA wound around a histone protein octamer (Kornberg and Lorch, 1999)
Since the overall digestion of nucleosomes is reflected in the length of nucleosomal DNA fragments, we tested the idea that we might be able to estimate the variation in the midpoints from the length of digested nucleosomes (Figure 1—figure supplement 1), and use this information to infer the positions of individual nucleosomes through deconvolution
The variability of digested nucleosomes could come from two sources: the technical variation that is associated with nuclease cleavage, such as variable trimming at nucleosome ends, and biological variation that directly influences the length of DNA wound around histones, such as nucleosome breathing and remodeling (Polach and Widom, 1995)
Summary
The eukaryotic genome is compacted into chromatin (Kornberg, 1974) which is comprised of nucleosomes, each consisting of approximately 147 base pairs (bp) of DNA wound around a histone protein octamer (Kornberg and Lorch, 1999). Shifting the histones relative to the DNA sequence by a few base pairs can change the accessibility of sequence elements to DNA binding proteins if they are located in the linker sequences between nucleosomes, or may switch these elements between facing towards and away from nucleosomes if they are located within nucleosomal DNA (Jiang and Pugh, 2009b; Segal and Widom, 2009b; Zhang and Pugh, 2011). Nucleosomes restrict the accessibility of DNA sequences to protein factors, such as transcriptional regulators and the transcription machinery (John et al, 2011; Li et al, 2007; Liu et al, 2006; Zhou and O’Shea, 2011). The positions and occupancy of nucleosomes can influence the interplay between transcription factors (Mirny, 2010) and the level (Carey et al, 2013; Kim and O’Shea, 2008), dynamics (Lam et al, 2008), and differences in gene expression between cells
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