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The Nucleosome

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 Nucleosome

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...

The Nucleosome

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...

Nucleosome Remodeling

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 Particle

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...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Related Experiment Video

Updated: May 15, 2026

Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution

Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution

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NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data.

Abhinav Nellore¹, Konstantin Bobkov, Elizabeth Howe

¹Institute for Human Genetics, University of California San Francisco CA, USA ; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco CA, USA.

Frontiers in Genetics

|January 22, 2013

Summary

This summary is machine-generated.

NSeq is a new Java application that efficiently identifies nucleosome positions from sequencing data. It offers a user-friendly interface and computes false discovery rates for accurate results.

Keywords:

nucleosome nucleosome positioning

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Nucleosomes are fundamental units of DNA packaging in eukaryotes.
High-throughput sequencing (HTS) of MNase-digested DNA is a common method for studying nucleosome positioning.
Accurate identification of nucleosome positions from HTS data is crucial for understanding genome regulation.

Purpose of the Study:

To introduce NSeq, a novel Java application designed for rapid and efficient identification of positioned nucleosomes.
To provide researchers with a user-friendly tool for analyzing MNase-digested mononucleosomal DNA sequencing data.
To enhance the accuracy of nucleosome calling through integrated false discovery rate computation.

Main Methods:

Development of a Java application, NSeq, for nucleosome calling.
Implementation of a user-friendly graphical interface (GUI).
Utilization of Monte Carlo simulations for calculating false discovery rates (FDRs).
Parallelization of computations across multiple processor cores for efficiency.
Analysis of high-throughput sequencing data from MNase-digested mononucleosomal DNA.

Main Results:

NSeq provides a fast and efficient method for identifying positioned nucleosomes.
The application includes features for plotting nucleosome coverage and centers.
False discovery rates are computed to assess the reliability of identified nucleosomes.
NSeq leverages multi-core processing for accelerated analysis.

Conclusions:

NSeq is a valuable and accessible tool for researchers studying nucleosome positioning.
The software's efficiency and accuracy facilitate deeper insights into genome organization and function.
NSeq is freely available for download and compatible with major operating systems.