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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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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.
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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X-Inactivation01:58

X-Inactivation

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The human X chromosome contains over ten times the number of genes as in the Y chromosome. Since males have only one X chromosome, and females have two, one might expect females to produce twice as many of the proteins, with undesirable results.
41.5K
Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

2.1K
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...
2.1K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

24.6K
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. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
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Related Experiment Video

Updated: Jan 15, 2026

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

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4D Chromatin Dynamics Resolved During Early Random X Chromosome Inactivation.

Xiaowen Liu1,2, Hao Xie1, Zhiyuan Liu1,3

  • 1Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China.

Genomics, Proteomics & Bioinformatics
|January 13, 2026
PubMed
Summary
This summary is machine-generated.

X chromosome inactivation involves significant 3D reorganization. New HiRES multi-omics reveals transient states and chromatin changes accompanying gene silencing during this crucial process in female mammals.

Keywords:
3D genomeChromatin reorganizationMulti-omicsSingle-cellX chromosome inactivation

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Combined DNA-RNA Fluorescent In situ Hybridization FISH to Study X Chromosome Inactivation in Differentiated Female Mouse Embryonic Stem Cells
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A Non-random Mouse Model for Pharmacological Reactivation of Mecp2 on the Inactive X Chromosome
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A Non-random Mouse Model for Pharmacological Reactivation of Mecp2 on the Inactive X Chromosome

Published on: May 22, 2019

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Area of Science:

  • Genetics and Genomics
  • Epigenetics and Chromatin Biology
  • Developmental Biology

Background:

  • X chromosome inactivation (XCI) is essential for dosage compensation in female mammals.
  • XCI involves extensive three-dimensional (3D) chromatin reorganization.
  • Understanding the dynamics of early XCI stages remains challenging.

Purpose of the Study:

  • To investigate the four-dimensional (4D) chromatin dynamics during early XCI stages.
  • To characterize single-cell inactivation trajectories and associated chromatin remodeling.
  • To elucidate the role of Xist expression in XCI initiation.

Main Methods:

  • Application of HiRES (Hi-C and RNA-seq simultaneously) multi-omics sequencing.
  • Analysis of mouse embryonic stem cells undergoing induced random XCI.
  • Single-cell resolution of 3D genome and transcriptome.

Main Results:

  • Identified distinct inactivation trajectories at single-cell resolution.
  • Discovered a transient structural state shared by both X chromosomes during biallelic Xist expression.
  • Demonstrated that most chromatin remodeling accompanies or follows gene silencing.
  • Revealed that topologically associating domain (TAD) attenuation initiates from anchor interaction loss.

Conclusions:

  • Provides a detailed, fine-scale depiction of chromatin reorganization during XCI initiation.
  • Highlights the dynamic interplay between 3D genome structure and gene silencing.
  • Establishes HiRES as a powerful tool for studying dynamic multi-omics processes.