Related Experiment Video
Updated: Jun 2, 2026
10:05
Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
Published on: December 12, 2017
Predicting nucleosome positioning in genomes: physical and bioinformatic approaches
Anita Scipioni1, Pasquale De Santis
1Dipartimento di Chimica, Università di Roma La Sapienza, P.le A. Moro, 5 I-00185, Roma, Italy.
Biophysical Chemistry
|April 13, 2011
Summary
Computational methods predict nucleosome positioning in eukaryotic genomes. DNA sequence features intrinsically encode nucleosome organization, guiding gene expression and DNA packaging.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Nucleosomes package eukaryotic DNA and regulate gene expression.
- Accurate prediction of nucleosome positioning is crucial for understanding genome regulation.
- Computational methods are increasingly employed to predict nucleosome occupancy.
Purpose of the Study:
- To review and compare bioinformatic and physical approaches for predicting nucleosome positioning.
- To highlight the role of DNA sequence features in nucleosome organization.
- To discuss the intrinsic encoding of nucleosome organization within eukaryotic genomes.
Main Methods:
- Review of existing bioinformatic analyses focusing on dinucleotide step periodicity.
- Examination of physical models based on sequence-dependent DNA conformational features.
- Comparison of computational approaches for predicting nucleosome occupancy.
Main Results:
- Bioinformatic analyses reveal significant sequence-dependent periodicities related to nucleosome occupancy.
- Eukaryotic DNA intrinsically encodes information for nucleosome organization.
- Physical models demonstrate the influence of DNA free energy on nucleosome formation.
Conclusions:
- DNA sequence features are key determinants of nucleosome organization.
- Computational methods, both bioinformatic and physical, offer valuable tools for predicting nucleosome positioning.
- Understanding nucleosome organization through sequence analysis is vital for deciphering gene regulation.
Related Concept Videos
02:54Nucleosome 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...
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
02:35Chromatin Position Affects Gene Expression
Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area.
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
02:10The 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 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...
01:12The 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.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
02:36Chromatin 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...
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...
01:19The 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...
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...