A Locally Convoluted Cluster Model for Nucleosome Positioning Signals in Chemical Maps

Liqun Xi, Kristin Brogaard, Qingyang Zhang, Bruce Lindsay, Jonathan Widom and Ji-Ping Wang

Journal of the American Statistical Association, 2014, vol. 109, issue 505, 48-62

Abstract: The nucleosome is the fundamental packing unit of DNA in eukaryotic cells, and its positioning plays a critical role in regulation of gene expression and chromosome functions. Using a recently developed chemical mapping method, nucleosomes can be potentially mapped with an unprecedented single-base-pair resolution. Existence of overlapping nucleosomes due to cell mixture or cell dynamics, however, causes convolution of nucleosome positioning signals. In this article, we introduce a locally convoluted cluster model and a maximum likelihood deconvolution approach, and illustrate the effectiveness of this approach in quantification of the nucleosome positional signal in the chemical mapping data. Supplementary materials for this article are available online.

Date: 2014
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DOI: 10.1080/01621459.2013.862169

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