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Related Concept Videos

Epigenetic Regulation01:37

Epigenetic Regulation

3.0K
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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Master Transcription Regulators02:23

Master Transcription Regulators

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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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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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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Co-activators and Co-repressors02:04

Co-activators and Co-repressors

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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Related Experiment Video

Updated: Jun 8, 2025

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
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Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

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Methylation Mesa define functional regulatory elements for targeted gene activation.

Y V Liu1,2, J Suryatenggara1, H Wong1

  • 1Cancer Science Institute of Singapore, 117599, Singapore.

Research Square
|November 1, 2024
PubMed
Summary
This summary is machine-generated.

New epigenetic elements called Methylation Mesas (MM) drive gene activation. These self-sustaining regulatory elements use targeted demethylation to initiate long-term gene expression and chromatin rewiring.

Keywords:
CRISPR-DiRDNA MethylationDemethylationGene ActivationGene ExpressionMethylation Sensitive Sites

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Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
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Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

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Related Experiment Videos

Last Updated: Jun 8, 2025

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
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Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

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Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

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Area of Science:

  • Epigenetics
  • Genomics
  • Molecular Biology

Background:

  • Correlation between DNA methylation and mRNA expression lacks consistent causal evidence.
  • Hypothesis: Causal regulatory methylation elements show heightened demethylation sensitivity.

Purpose of the Study:

  • Identify and characterize novel epigenetic regulatory elements.
  • Investigate the causal role of methylation in gene regulation.
  • Develop precise tools for epigenetic manipulation.

Main Methods:

  • Whole-genome bisulfite sequencing of 20 samples before and after demethylation.
  • Identification of narrow-width elements termed Methylation Mesas (MM).
  • Development and application of CRISPR-DiR for targeted demethylation.

Main Results:

  • Methylation Mesas (MM) are narrow-width elements (45-294 bp) with a short plateau signature.
  • MM signature is conserved across species, independent of CpG islands, and correlates with active histone marks.
  • Targeted demethylation of MM triggers significant locus and distal chromatin rewiring, initiating mRNA expression.

Conclusions:

  • Methylation Mesas (MM) are self-sustaining epigenetic regulatory elements.
  • MM maintain long-term gene activation via focused demethylation, leading to histone modifications and distal element interactions.
  • CRISPR-DiR technology enables precise assessment of epigenetic causality.