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Related Concept Videos

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.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
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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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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
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Epigenetic Regulation01:37

Epigenetic Regulation

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Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...
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Epigenetic Regulation01:46

Epigenetic Regulation

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Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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Related Experiment Video

Updated: Feb 23, 2026

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
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Sparse conserved under-methylated CpGs are associated with high-order chromatin structure.

Xueqiu Lin1,2,3, Jianzhong Su1,2, Kaifu Chen1,2

  • 1Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.

Genome Biology
|September 2, 2017
PubMed
Summary

Researchers developed a new computational method to identify sparse conserved under-methylated CpGs (scUMCs). These novel epigenetic features are linked to high-order chromatin structure and gene regulation.

Keywords:
Chromatin structureChromatin-loop factorsDNA methylationInteracting anchorMulti-sample-based methodSparse conserved under-methylated CpGWhole-genome bisulfite sequencing

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Area of Science:

  • Genomics
  • Epigenetics
  • Computational Biology

Background:

  • Whole-genome bisulfite sequencing (WGBS) is crucial for DNA methylation analysis.
  • Existing computational methods primarily focus on gene regulatory regions.

Purpose of the Study:

  • To develop a novel computational method for identifying single, isolated under-methylated CpGs (UMCs) across the genome.
  • To investigate the functional importance and genomic context of these sparse conserved UMCs (scUMCs).

Main Methods:

  • A multi-sample-based computational approach was employed.
  • Analysis of 31 high-quality methylomes to identify scUMCs.
  • Investigated enrichment in distal interacting regions and association with chromatin factors.

Main Results:

  • Identified 9421 scUMCs, enriched in distal interacting anchor regions.
  • scUMCs are co-occupied by multiple chromatin-loop factors and flanked by methylated CpGs.
  • Cell lineage-specific scUMCs associate with developmental genes and chromatin remodelers.
  • scUMC methylation dynamics correlate with chromatin interactions, looping factors, and gene expression.

Conclusions:

  • Introduced an innovative computational method for scUMC identification.
  • scUMCs represent novel epigenetic features linked to high-order chromatin structure.
  • This work opens new avenues for studying DNA methylation and chromatin structure interplay.