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Related Concept Videos

Histone Modification02:32

Histone Modification

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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.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
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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
The writer...
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Nucleosome Remodeling02:54

Nucleosome Remodeling

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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...
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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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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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Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
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Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

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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.
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...
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Updated: Jun 14, 2025

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

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Dynamic Changes in Histone Modifications Are Associated with Differential Chromatin Interactions.

Yumin Nie1, Mengjie Wang1

  • 1Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China.

Genes
|August 29, 2024
PubMed
Summary

Chromatin interactions in immune cells change dynamically during viral and interferon responses. Histone modifications, rather than architectural proteins, drive these dynamic chromatin interactions.

Keywords:
CTCFdifferential chromatin interactionhistone modification

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Reconstitution of Nucleosomes with Differentially Isotope-labeled Sister Histones
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Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Eukaryotic genome organization relies on chromatin domains and long-range interactions.
  • Architectural proteins (e.g., CTCF, cohesin) and histone modifications mediate these interactions.

Purpose of the Study:

  • To investigate dynamic regulation of chromatin interactions in human macrophages upon influenza A virus and interferon-beta stimulation.
  • To understand the roles of histone modifications and architectural proteins in differential chromatin interactions (DCIs).

Main Methods:

  • Analysis of published Hi-C and ChIP-seq datasets from human monocyte-derived macrophages.
  • Identification of differential chromatin interactions (DCIs) under specific treatment conditions.
  • Motif scanning to identify potential protein binding sites correlating with histone modification changes.

Main Results:

  • Identified 206 and 127 DCIs in influenza A virus- and interferon-beta-treated cells, respectively.
  • CTCF and RAD21 binding sites remained largely stable within DCIs, while five histone modifications (H3K4me3, H3K27ac, H3K36me3, H3K9me3, H3K27me3) showed significant changes.
  • Histone modifications exhibited more dramatic changes within DCIs compared to CTCF/RAD21, with some modifications showing greater changes outside DCIs.
  • PRDM9, ZNF384, and STAT2 were identified as potential regulators correlating with histone modification dynamics within DCIs.

Conclusions:

  • Histone modifications play a more dynamic role than CTCF and RAD21 in regulating differential chromatin interactions during immune responses.
  • The study provides insights into the dynamic regulation of chromatin architecture and its relationship with epigenetic modifications.