DANPOS

Dynamic analysis of nucleosome position and occupancy by sequencing

Kaifu Chen, Yuanxin Xi, Xuewen Pan, Zhaoyu Li, Klaus Kaestner, Jessica Tyler, Sharon Dent, Xiangwei He, Wei Li

Research output: Contribution to journalArticle

138 Citations (Scopus)

Abstract

Recent developments in next-generation sequencing have enabled whole-genome profiling of nucleosome organizations. Although several algorithms for inferring nucleosome position from a single experimental condition have been available, it remains a challenge to accurately define dynamic nucleosomes associated with environmental changes. Here, we report a comprehensive bioinformatics pipeline, DANPOS, explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution. Using both simulated and real nucleosome data, we demonstrated that bias correction in preliminary data processing and optimal statistical testing significantly enhances the functional interpretation of dynamic nucleosomes. The single-nucleotide resolution analysis of DANPOS allows us to detect all three categories of nucleosome dynamics, such as position shift, fuzziness change, and occupancy change, using a uniform statistical framework. Pathway analysis indicates that each category is involved in distinct biological functions. We also analyzed the influence of sequencing depth and suggest that even 200-fold coverage is probably not enough to identify all the dynamic nucleosomes. Finally, based on nucleosome data from the human hematopoietic stem cells (HSCs) and mouse embryonic stem cells (ESCs), we demonstrated that DANPOS is also robust in defining functional dynamic nucleosomes, not only in promoters, but also in distal regulatory regions in the mammalian genome.

Original languageEnglish (US)
Pages (from-to)341-351
Number of pages11
JournalGenome Research
Volume23
Issue number2
DOIs
StatePublished - Feb 2013
Externally publishedYes

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Nucleosomes
Nucleotides
Genome
Nucleic Acid Regulatory Sequences
Hematopoietic Stem Cells
Computational Biology

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Chen, K., Xi, Y., Pan, X., Li, Z., Kaestner, K., Tyler, J., ... Li, W. (2013). DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing. Genome Research, 23(2), 341-351. https://doi.org/10.1101/gr.142067.112

DANPOS : Dynamic analysis of nucleosome position and occupancy by sequencing. / Chen, Kaifu; Xi, Yuanxin; Pan, Xuewen; Li, Zhaoyu; Kaestner, Klaus; Tyler, Jessica; Dent, Sharon; He, Xiangwei; Li, Wei.

In: Genome Research, Vol. 23, No. 2, 02.2013, p. 341-351.

Research output: Contribution to journalArticle

Chen, K, Xi, Y, Pan, X, Li, Z, Kaestner, K, Tyler, J, Dent, S, He, X & Li, W 2013, 'DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing', Genome Research, vol. 23, no. 2, pp. 341-351. https://doi.org/10.1101/gr.142067.112
Chen, Kaifu ; Xi, Yuanxin ; Pan, Xuewen ; Li, Zhaoyu ; Kaestner, Klaus ; Tyler, Jessica ; Dent, Sharon ; He, Xiangwei ; Li, Wei. / DANPOS : Dynamic analysis of nucleosome position and occupancy by sequencing. In: Genome Research. 2013 ; Vol. 23, No. 2. pp. 341-351.
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