Abstract
Chromatin organization and epigenetic marks play a critical role in stem cell pluripotency and differentiation. Chromatin digestion by micrococcal nuclease (MNase) followed by high-throughput sequencing (MNase-seq) is the most widely used genome-wide method for studying nucleosome organization, that is, the first level of DNA packaging into chromatin. Combined with chromatin immunoprecipitation (ChIP), MNase-ChIP-seq represents a high-resolution method for investigating both chromatin organization and the distribution of epigenetic marks and histone variants. The plot2DO package presented here is a flexible tool for evaluating the quality of MNase-seq and MNase-ChIP-seq data, and for visualizing the distribution of nucleosomes near the functional regions of the genome. The plot2DO package is open-source software, and it is freely available from https://github.com/rchereji/plot2DO under the MIT license.
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Acknowledgement
We thank Natalia Petrenko, Burke Squires, Ming-an Sun, and Yashpal Rawal for insightful discussions and for testing the software. R.V.C. was supported by the Intramural Research Program of the National Institute of Child Health and Human Development, National Institutes of Health. This work utilized the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov).
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Beati, P., Chereji, R.V. (2020). Creating 2D Occupancy Plots Using plot2DO. In: Kidder, B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 2117. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0301-7_5
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DOI: https://doi.org/10.1007/978-1-0716-0301-7_5
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