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Related Concept Videos

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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 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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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. 
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Euchromatin01:01

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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
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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.
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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.
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Updated: Dec 13, 2025

Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells
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Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation.

Matt J Barter1, Kathleen Cheung1,2, Julia Falk1

  • 1Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK.

Epigenetics
|August 4, 2020
PubMed
Summary

Interleukin-1 (IL-1) stimulation dynamically alters chromatin accessibility, primarily at enhancer regions, influencing gene expression during inflammation. This study identifies key transcription factors, like RelA, involved in these rapid inflammatory responses.

Keywords:
ATAC-seqchromatingenome-editinginflammationinterleukin-1

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Area of Science:

  • Molecular Biology
  • Genomics
  • Immunology

Background:

  • Dynamic chromatin modifications enable gene regulation by controlling access to condensed genomic regions.
  • Inflammatory cytokines rapidly alter gene expression via signaling pathways and transcription factor activation.

Purpose of the Study:

  • To investigate genome-wide chromatin accessibility changes induced by interleukin-1 (IL-1) stimulation using ATAC-seq.
  • To identify and functionally validate specific regulatory elements involved in IL-1-mediated inflammatory signaling.

Main Methods:

  • Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to map open chromatin regions.
  • Motif enrichment analysis and ChIP-seq to identify transcription factor binding sites (e.g., RelA).
  • CRISPR/Cas9 genome editing and dCas9-activator systems to assess functional roles of identified regions.

Main Results:

  • Identified 126,483 open chromatin regions, with 241 significantly differentially accessible upon IL-1 stimulation.
  • Differentially accessible regions were enriched for enhancers, with overrepresentation of RelA binding motifs.
  • Demonstrated a correlation between chromatin accessibility changes and gene expression, and validated enhancer function of specific regions.

Conclusions:

  • IL-1 stimulation induces dynamic changes in chromatin accessibility, particularly at enhancers, mediated by transcription factors like RelA.
  • These accessible regions play a functional role in regulating inflammatory gene expression.
  • The study provides a comprehensive map and functional validation of chromatin regions involved in inflammatory signaling.