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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...
Chromatin Position Affects Gene Expression02:35

Chromatin 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...
Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying DNA...
Histone Variants at the Centromere02:30

Histone Variants at the Centromere

Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3 variants are also...
Chromatin Packaging01:32

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...

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Related Experiment Video

Updated: May 17, 2026

Chromatin Immunoprecipitation from Human Embryonic Stem Cells
10:36

Chromatin Immunoprecipitation from Human Embryonic Stem Cells

Published on: July 22, 2008

Genome-wide nucleosome positioning during embryonic stem cell development.

Vladimir B Teif1, Yevhen Vainshtein, Maïwen Caudron-Herger

  • 1Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum, Heidelberg, Germany. v.teif@dkfz.de

Nature Structural & Molecular Biology
|October 23, 2012
PubMed
Summary

Genome-wide nucleosome mapping reveals how DNA packaging changes during cell differentiation. Nucleosome repositioning plays a key role in regulating gene expression and cell fate.

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CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells
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Chromatin Immunoprecipitation from Human Embryonic Stem Cells
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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells
11:13

CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells

Published on: May 25, 2018

Area of Science:

  • Genomics
  • Epigenetics
  • Developmental Biology

Background:

  • Cell differentiation involves complex gene regulation.
  • Nucleosome positioning is crucial for controlling DNA accessibility and gene expression.

Purpose of the Study:

  • To investigate genome-wide nucleosome occupancies in mouse embryonic stem cells and their differentiated counterparts (neural progenitors and embryonic fibroblasts).
  • To identify features of nucleosome positioning associated with lineage commitment and transcription factor binding.
  • To understand the role of nucleosome repositioning in cell differentiation.

Main Methods:

  • Genome-wide nucleosome occupancy profiling in different cell types.
  • Analysis of transcription factor binding preferences in relation to nucleosome occupancy.
  • Correlation analysis between nucleosome occupancy, histone modifications, and gene activity.
  • Measurement of nucleosome repeat length changes during differentiation.

Main Results:

  • Identified cell-type- and protein-specific transcription factor binding preferences linked to nucleosome occupancy levels.
  • Observed distinct patterns of nucleosome-depleted regions around transcription start and termination sites, particularly for active genes.
  • Found correlations between genome-wide nucleosome occupancy and specific histone modifications (methylation and acetylation).
  • Documented an increase in average nucleosome repeat length during differentiation.

Conclusions:

  • Nucleosome repositioning is a significant regulatory mechanism during cell differentiation.
  • Changes in nucleosome occupancy and organization influence transcription factor binding and gene expression.
  • Histone modifications and nucleosome repeat length dynamics contribute to lineage commitment.