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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
Published on: December 12, 2017
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing
Kaifu Chen1, Yuanxin Xi, Xuewen Pan
1Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
Genome Research
|November 30, 2012
Summary
We developed DANPOS, a bioinformatics pipeline for dynamic nucleosome analysis. DANPOS accurately identifies nucleosome changes at single-nucleotide resolution, revealing distinct biological functions for different nucleosome dynamics.
Area of Science:
- Genomics
- Bioinformatics
- Epigenetics
Background:
- Next-generation sequencing enables whole-genome nucleosome profiling.
- Existing algorithms struggle to accurately define dynamic nucleosomes under environmental changes.
Purpose of the Study:
- To develop a comprehensive bioinformatics pipeline, DANPOS, for dynamic nucleosome analysis at single-nucleotide resolution.
- To enable accurate detection and functional interpretation of nucleosome dynamics.
Main Methods:
- Developed DANPOS, a bioinformatics pipeline for dynamic nucleosome analysis.
- Implemented bias correction and optimal statistical testing for data processing.
- Utilized a uniform statistical framework for analyzing nucleosome position, fuzziness, and occupancy changes.
Main Results:
- DANPOS accurately detects three categories of nucleosome dynamics: position shift, fuzziness change, and occupancy change.
- Bias correction and statistical testing significantly improve the functional interpretation of dynamic nucleosomes.
- Sequencing depth analysis suggests 200-fold coverage may be insufficient for comprehensive dynamic nucleosome identification.
- DANPOS robustly identifies functional dynamic nucleosomes in promoters and distal regulatory regions of mammalian genomes (HSCs and ESCs).
Conclusions:
- DANPOS provides a robust framework for single-nucleotide resolution dynamic nucleosome analysis.
- Nucleosome dynamics are linked to distinct biological functions.
- Further optimization of sequencing depth is needed for complete dynamic nucleosome identification.
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