Abstract
Genome-wide patterns of nucleosome occupancy and positioning have greatly impacted on studies of chromatin structure, yet these studies require extensive computational analysis which is crucial for the quality of the resulting datasets and inferred conclusions. This chapter describes the computational steps required in order to estimate genome-wide patterns of nucleosome occupancy and positioning from raw data obtained from high-throughput sequencing of mononucleosome DNA fragments. Potential pitfalls that may be encountered in such analysis and computational quality controls are further discussed in Subheading 3.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Albert, I., Mavrich, T.N., Tomsho, L.P., Qi, J., Zanton, S.J., Schuster, S.C. and Pugh, B.F. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharo-myces cerevisiae genome. Nature, 446, 572–576.
Lee, W., Tillo, D., Bray, N., Morse, R.H., Davis, R.W., Hughes, T.R. and Nislow, C. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet, 39, 1235–1244.
Shivaswamy, S., Bhinge, A., Zhao, Y., Jones, S., Hirst, M. and Iyer, V.R. (2008) Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol, 6, e65.
Tirosh, I., Sigal, N. and Barkai, N. (2010) Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol Syst Biol, 6, 365.
Weiner, A., Hughes, A., Yassour, M., Rando, O.J. and Friedman, N. (2010) High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res, 20, 90–100.
Whitehouse, I., Rando, O.J., Delrow, J. and Tsukiyama, T. (2007) Chromatin remodelling at promoters suppresses antisense transcription. Nature, 450, 1031–1035.
Yuan, G.C., Liu, Y.J., Dion, M.F., Slack, M.D., Wu, L.F., Altschuler, S.J. and Rando, O.J. (2005) Genome-scale identification of nucleo-some positions in S. cerevisiae. Science, 309, 626–630.
Tirosh, I., Sigal, N. and Barkai, N. (2010) Widespread remodeling of mid-coding sequence nucleosomes by Isw1. Genome Biol, 11, R49.
Li, H., Ruan, J. and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res, 18, 1851–1858.
Smith, A.D., Chung, W.Y., Hodges, E., Kendall, J., Hannon, G., Hicks, J., Xuan, Z. and Zhang, M.Q. (2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25, 2841–2842.
Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 10, R25.
Fan, X., Moqtaderi, Z., Jin, Y., Zhang, Y., Liu, X.S. and Struhl, K. (2010) 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, 107, 17945–17950.
Horz, W. and Altenburger, W. (1981) Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res, 9, 2643–2658.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Tirosh, I. (2012). Computational Analysis of Nucleosome Positioning. In: Morse, R. (eds) Chromatin Remodeling. Methods in Molecular Biology, vol 833. Humana Press. https://doi.org/10.1007/978-1-61779-477-3_27
Download citation
DOI: https://doi.org/10.1007/978-1-61779-477-3_27
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-476-6
Online ISBN: 978-1-61779-477-3
eBook Packages: Springer Protocols