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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 Nucleosome Core Particle02:10

The Nucleosome Core Particle

Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
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...
The Nucleosome01:19

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can 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.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

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Related Experiment Video

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In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy
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Published on: September 6, 2024

Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data.

Xuekui Zhang1, Gordon Robertson, Sangsoon Woo

  • 1Statistics Department, University of British Columbia, Vancouver, British Columbia, Canada.

Plos One
|March 7, 2012
PubMed
Summary

We developed PING, a new method for predicting nucleosome positions from sequencing data. PING is accurate, scalable, and robust, outperforming existing tools for genomic analysis.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Nucleosome positioning is crucial for gene regulation and DNA accessibility.
  • Accurate prediction of nucleosome positions is essential for understanding these processes.
  • Existing methods face challenges in scalability, accuracy, and robustness, especially with low read density data.

Purpose of the Study:

  • To introduce PING, a novel model-based method for predicting nucleosome positions.
  • To evaluate PING's performance against established methods like NPS and TemplateFilter.
  • To demonstrate the utility of PING predictions from sonicated sequencing data for biological inference.

Main Methods:

  • PING utilizes a model-based approach for nucleosome position prediction.
  • The method is applied to MNase-Seq and sonicated ChIP-Seq datasets.
  • Performance is assessed based on scalability, accuracy, and robustness to varying read densities.

Main Results:

  • PING demonstrates superior scalability, accuracy, and robustness compared to NPS and TemplateFilter.
  • Predictions from PING using sonicated data possess sufficient spatial resolution for biological insights.
  • PING enabled detection of nucleosome positioning changes around transcription factor binding sites and discrimination of functional sites.

Conclusions:

  • PING offers a significant advancement in predicting nucleosome positions, enhancing genomic analysis.
  • The method's performance and utility are validated using real-world ChIP-seq data.
  • PING facilitates deeper understanding of transcription factor binding and its relationship with nucleosome organization.