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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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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.
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...
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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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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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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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Spreading of Chromatin Modifications02:25

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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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Euchromatin01:01

Euchromatin

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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.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
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Heterochromatin02:38

Heterochromatin

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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 that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
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Related Experiment Video

Updated: Jun 30, 2025

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding.

Ziheng Duan1, Siwei Xu1, Shushrruth Sai Srinivasan1

  • 1Department of Computer Science, University of California, Irvine, 92697 CA, USA.

Briefings in Bioinformatics
|March 17, 2024
PubMed
Summary

scENCORE computationally reconstructs chromatin A/B compartments from accessible epigenetic data, offering a cost-effective alternative to single-cell Hi-C for studying DNA structure and disease.

Keywords:
chromatin compartmentsgraph embeddingsingle-cell epigenetics

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Area of Science:

  • Genomics
  • Epigenetics
  • Computational Biology

Background:

  • Eukaryotic DNA compartmentalization into active and repressed states is crucial for transcriptional regulation.
  • Dysregulation of chromatin structure is linked to various diseases.
  • Single-cell Hi-C provides chromosome conformation data but is expensive and inaccessible.

Purpose of the Study:

  • To develop a computational method (scENCORE) for reconstructing chromatin compartments from single-cell epigenetic data.
  • To offer a cost-effective and accessible alternative to single-cell Hi-C for analyzing higher-order chromatin structure.
  • To investigate chromatin conformation changes across different conditions and their relation to disease.

Main Methods:

  • scENCORE constructs a long-range epigenetic correlation graph representing chromatin interaction frequencies.
  • It uses node embeddings to cluster genome regions into A/B compartments.
  • Graphs are aligned to quantify chromatin conformation changes.

Main Results:

  • scENCORE accurately reconstructs cell-type-specific A/B compartments, validated against Hi-C experiments.
  • The method identifies significant chromatin compartment switching events.
  • These switching events are linked to potential regulatory and transcriptional changes in psychiatric disease.

Conclusions:

  • scENCORE enables accurate and cost-effective reconstruction of A/B compartments.
  • It facilitates the delineation of higher-order chromatin structure heterogeneity in complex tissues.
  • This approach aids in understanding the role of chromatin conformation in health and disease.