Abstract
The basic unit of chromatin is double-stranded DNA wrapped around nucleosome core particles, the classic “beads-on-a-string” described by Kornberg and colleagues. The history of chromatin studies has experienced many peaks, from the earliest studies by Miescher to the biochemical studies of the 1960s and 1970s, the appreciation for the influence of histone modifications in controlling gene expression in the 1990s to the genome-wide studies that began in 2006 and show no signs of abating with the introduction of next generation sequencing technologies. Genome-wide studies not only have provided a base line to understand relationships between chromatin structure and gene function but also have begun to provide new insights into chromatin remodelling. Here, we describe the use of genome-wide approaches to determining nucleosome occupancy in yeast.
*Kyle Tsui and Tanja Durbic have equally contributed to this chapter.
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References
Yuan, G.C., et al., Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 2005. 309(5734): p. 626–30.
Lee, W., et al., A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet, 2007. 39(10): p. 1235–44.
Kozarewa, I., et al., Amplification-free Illumina sequencing-library preparation facilitates imp-roved mapping and assembly of (G + C)-biased genomes. Nat Methods, 2009. 6(4): p. 291–5.
Badis, G., et al., A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell, 2008. 32(6): p. 878–87.
Schmiedeberg, L., et al., A temporal threshold for formaldehyde crosslinking and fixation. PLoS One, 2009. 4(2): p. e4636.
Sutherland, B.W., J. Toews, and J. Kast, Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions. J Mass Spectrom, 2008. 43(6): p. 699–715.
Weiner, A., et al., High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res, 2010. 20(1): p. 90–100.
Pugh, B.F., A preoccupied position on nucleosomes. Nat Struct Mol Biol, 2010. 17(8): p. 923.
Fan, X., et al., Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3′-end formation. Proc Natl Acad Sci USA, 2010. 107(42): p. 17945–50.
Chatterjee, C. and T.W. Muir, Chemical approaches for studying histone modifications. J Biol Chem, 2010. 285(15): p. 11045–50.
Rait, V.K., et al., Modeling formalin fixation and antigen retrieval with bovine pancreatic RNase A II. Interrelationship of cross-linking, immunoreactivity, and heat treatment. Lab Invest, 2004. 84(3): p. 300–6.
Rando, O.J., Genome-wide mapping of nucleo-somes in yeast. Methods Enzymol, 2010. 470: p. 105–18.
David, L., et al., A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA, 2006. 103(14): p. 5320–5.
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Tsui, K., Durbic, T., Gebbia, M., Nislow, C. (2012). Genomic Approaches for Determining Nucleosome Occupancy in Yeast. In: Morse, R. (eds) Chromatin Remodeling. Methods in Molecular Biology, vol 833. Humana Press. https://doi.org/10.1007/978-1-61779-477-3_23
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DOI: https://doi.org/10.1007/978-1-61779-477-3_23
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