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Related Concept Videos

Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
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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.
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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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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...
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
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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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Updated: Feb 14, 2026

Chromatin Immunoprecipitation ChIP of Histone Modifications from Saccharomyces cerevisiae
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Chromatin Immunoprecipitation ChIP of Histone Modifications from Saccharomyces cerevisiae

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Reading cytosine modifications within chromatin.

Elise A Mahé1, Thierry Madigou1, Gilles Salbert1

  • 1a University of Rennes 1, UMR6290 CNRS , Institute of Genetics and Development of Rennes , Campus de Beaulieu, Rennes Cedex , France.

Transcription
|February 7, 2018
PubMed
Summary
This summary is machine-generated.

Transcription factors can access methylated DNA in cells. Oxidation of 5-methylcytosine to 5-hydroxymethylcytosine may help transcription factors read epigenetic information from nucleosomal DNA.

Keywords:
5-hydroxymethylcytosine chromatin5-methylcytosineDNA methylationten eleven translocationtranscription factors

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Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells
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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Transcription Factor Regulation

Background:

  • Transcription factors bind DNA motifs containing methylated CpG sites in vitro.
  • DNA methylation plays a crucial role in gene regulation.
  • Chromatin structure, including nucleosome packaging and DNA condensation, can hinder transcription factor access to methylated DNA in vivo.

Purpose of the Study:

  • To explore how transcription factors can access methylated DNA motifs within nucleosomes.
  • To investigate the potential role of 5-hydroxymethylcytosine in facilitating transcription factor binding to epigenetic marks.

Main Methods:

  • This study is a discussion/review of existing literature and concepts.
  • It focuses on the chemical properties of DNA modifications and their implications for protein-DNA interactions.
  • Theoretical analysis of chromatin accessibility and epigenetic information readout.

Main Results:

  • In vitro binding of transcription factors to methylated CpG motifs is established.
  • In vivo accessibility is limited by nucleosome structure and condensed chromatin.
  • Oxidation of 5-methylcytosine to 5-hydroxymethylcytosine is proposed as a key step.

Conclusions:

  • 5-hydroxymethylcytosine formation could destabilize chromatin.
  • This modification may provide a crucial clue for transcription factors.
  • Facilitating access to nucleosomal DNA and enabling the reading of epigenetic information.