Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data
Date
2012
Authors
Zhang, Xuekui
Robertson, G.
Woo, S.
Hoffman, B.G.
Gottardo, R.
Journal Title
Journal ISSN
Volume Title
Publisher
PLoS ONE
Abstract
We describe a model-based method, PING, for predicting nucleosome positions in MNase-Seq and MNase- or sonicated-
ChIP-Seq data. PING compares favorably to NPS and TemplateFilter in scalability, accuracy and robustness to low read
density. To demonstrate that PING predictions from widely available sonicated data can have sufficient spatial resolution to
be to be useful for biological inference, we use Illumina H3K4me1 ChIP-seq data to detect changes in nucleosome
positioning around transcription factor binding sites due to tamoxifen stimulation, to discriminate functional and nonfunctional
transcription factor binding sites more effectively than with enrichment profiles, and to confirm that the pioneer
transcription factor Foxa2 associates with the accessible major groove of nucleosomal DNA.
Description
Keywords
Citation
Zhang, X., Robertson, G., Woo, S., Hoffman, B.G., Gottardo, R. (2012). Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data. PLoS ONE, 7(2). https://doi.org/10.1371/journal.pone.0032095