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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...
Position-effect Variegation02:32

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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 is an enzyme that can...
Heterochromatin02:38

Heterochromatin

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 9th...
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...

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Updated: May 22, 2026

Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates
09:13

Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates

Published on: May 12, 2023

The discrepancy between chromatin factor location and effect.

Tineke L Lenstra1, Frank C P Holstege

  • 1Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, The Netherlands.

Nucleus (Austin, Tex.)
|May 11, 2012
PubMed
Summary
This summary is machine-generated.

Chromatin factors

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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
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Last Updated: May 22, 2026

Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates
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Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates

Published on: May 12, 2023

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

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Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells
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Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells

Published on: April 2, 2018

Area of Science:

  • Molecular Biology
  • Genetics
  • Yeast Biology

Background:

  • Chromatin's role in cellular processes is significant.
  • Studies on individual genes provided foundational models.
  • Genome-wide analyses challenge these simplified models.

Purpose of the Study:

  • To investigate the genome-wide location and gene expression effects of chromatin factors.
  • To compare the overlap between chromatin factor occupancy and gene expression changes.
  • To understand the discrepancy between chromatin factor location and functional impact.

Main Methods:

  • Genome-wide location analysis of chromatin factors in Saccharomyces cerevisiae.
  • Gene expression profiling across the genome.
  • Comparative analysis of location data and expression data.

Main Results:

  • A significant disconnect exists between chromatin factor occupancy and gene expression changes (only 2.5% overlap).
  • A substantial portion of gene expression effects (24%) are not directly linked to chromatin factor occupancy.
  • Most chromatin factor perturbations impact specific gene subsets, suggesting gene-specific requirements.

Conclusions:

  • The discrepancy highlights inherent properties of chromatin-mediated gene regulation in yeast.
  • Gene-specific properties and functional redundancy likely explain the observed disconnect.
  • Future research should focus on elucidating these gene-specific properties to understand chromatin's regulatory role.