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Related Concept Videos

Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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 timing and level of...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.

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Related Experiment Video

Updated: May 17, 2026

CRISPR-Mediated Reorganization of Chromatin Loop Structure
09:20

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Published on: September 14, 2018

Chromatin loops, gene positioning, and gene expression.

Sjoerd Holwerda1, Wouter de Laat

  • 1Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht Utrecht, Netherlands.

Frontiers in Genetics
|October 23, 2012
PubMed
Summary

3D genome structure influences gene function. Studies show regulatory DNA contacts genes, organized by proteins like CTCF and cohesin, affecting transcription and gene positioning within the nucleus.

Keywords:
chromatin domainsgene expressiongenome structurenuclear organizationnuclear periphery

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Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
21:55

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation

Published on: April 30, 2012

Area of Science:

  • Genomics and Molecular Biology
  • Cell Biology
  • Epigenetics

Background:

  • Recent technological advances have significantly improved understanding of the genome's three-dimensional (3D) structure.
  • The spatial organization of the genome within the cell nucleus is increasingly recognized as a key determinant of gene function and regulation.

Purpose of the Study:

  • To summarize topological studies on key model gene loci, including globin, antigen receptor, H19-Igf2, and Hox gene clusters.
  • To elucidate the mechanisms by which 3D genome architecture influences gene transcription and expression patterns.

Main Methods:

  • Review of topological studies focusing on the 3D organization of specific gene loci.
  • Analysis of the roles of structural proteins (CTCF, cohesin), nuclear lamina, and transcription machinery in genome folding.
  • Examination of studies investigating non-random gene positioning within the nucleus.

Main Results:

  • Physical contact between regulatory DNA sequences and genes is essential for controlling gene transcription.
  • Proteins such as CTCF and cohesin, along with the transcription machinery and nuclear lamina, are critical for establishing the genome's 3D configuration.
  • Genes occupy specific, non-random positions within the nucleus, suggesting a functional role for nuclear architecture.

Conclusions:

  • The 3D genome structure is a critical layer of gene regulation.
  • Cell-specific genome conformations can facilitate long-range interactions between regulatory elements and genes, potentially across different chromosomes.
  • These interactions can lead to altered gene expression in specific cell subpopulations, highlighting the importance of nuclear organization in cellular heterogeneity.