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Related Concept Videos

Nucleosome Remodeling02:54

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
The Nucleosome02:33

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

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Related Experiment Video

Updated: May 10, 2026

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.

Sangsoon Woo1, Xuekui Zhang, Renan Sauteraud

  • 1Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA.

Bioinformatics (Oxford, England)
|June 22, 2013
PubMed
Summary

Researchers developed PING 2.0, an open-source R package for accurate nucleosome positioning. This tool enhances analysis of sequencing data, even with low read counts, advancing chromatin studies.

Related Experiment Videos

Last Updated: May 10, 2026

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Chromatin immunoprecipitation sequencing (ChIP-Seq) and MNase sequencing (MNase-Seq) are key techniques for studying chromatin structure and histone modifications.
  • While tools for identifying enriched regions are abundant, specialized software for precise nucleosome positioning remains limited.
  • Nucleosome positioning is crucial for understanding gene regulation and DNA accessibility.

Purpose of the Study:

  • To introduce PING 2.0, a novel, flexible, and powerful open-source R package designed for accurate nucleosome positioning.
  • To provide a robust tool for analyzing MNase-Seq and ChIP-Seq data, accommodating various sequencing types (single-end and paired-end).
  • To offer a model-based approach for nucleosome prediction, effective even with low sequencing read counts.

Main Methods:

  • Development of the PING 2.0 R package, implementing a model-based approach for nucleosome prediction.
  • Utilizing MNase-Seq data or MNase- or sonicated-ChIP-Seq data with both single-end and paired-end sequencing.
  • Application and comparison of PING 2.0 against existing tools (nucleR and ChIPseqR) using Saccharomyces cerevisiae datasets.

Main Results:

  • PING 2.0 demonstrates effective nucleosome positioning capabilities.
  • The package provides reliable predictions even when sequencing data exhibits low read counts.
  • Performance evaluation shows PING 2.0 as a competitive tool for nucleosome positioning analysis.

Conclusions:

  • PING 2.0 is a valuable open-source resource for the scientific community, addressing the need for advanced nucleosome positioning software.
  • The package enhances the analysis of chromatin-related sequencing data, facilitating deeper insights into chromatin organization.
  • PING 2.0 offers a powerful and flexible solution for researchers studying nucleosome positioning and its implications.