Abstract
We introduce NSeq, a fast and efficient Java application for finding positioned nucleosomes from the high-throughput sequencing of MNase-digested mononucleosomal DNA. NSeq includes a user-friendly graphical interface, computes false discovery rates (FDRs) for candidate nucleosomes from Monte Carlo simulations, plots nucleosome coverage and centers, and exploits the availability of multiple processor cores by parallelizing its computations. Java binaries and source code are freely available at https://github.com/songlab/NSeq. The software is supported on all major platforms equipped with Java Runtime Environment 6 or later.
Highlights
Eukaryotic DNA is organized into chromatin, consisting of repeating nucleosomes adjoined by linker DNA
This paper introduces NSeq, an open-source Java application that rigorously identifies positioned nucleosomes from the nextgeneration sequencing of micrococcal nuclease (MNase)-digested mononucleosomal DNA
The nucleosome coverage plot is obtained as described in Zhang et al (2008b): NSeq extends a positive-strand read by 75 bases to the right, and a negativestrand read by 75 bases to the left
Summary
Eukaryotic DNA is organized into chromatin, consisting of repeating nucleosomes adjoined by linker DNA. Nucleosomes are highly dynamic, being subjected to thermal fluctuations and ATP-dependent remodeling (Blossey and Schiessel, 2011), some nucleosomes are well-localized across populations of a given cell type Such positioned nucleosomes are likely to be more functional than delocalized nucleosomes and may be under selection and regulatory forces (Yuan et al, 2005; Ozsolak et al, 2007; Field et al, 2008; Song et al, 2008). MNase preferentially cuts linker DNA, leaving nucleosomal DNA largely intact. This ideally gives rise to clusters of reads on both sides of a positioned nucleosome, with the mean 5 -end positions of reads in the forward- and reversestrand clusters separated by ∼146 bp. The “Methods” section provides a detailed description of NSeq’s algorithm
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