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Related Concept Videos

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...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

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...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Master Transcription Regulators02:23

Master Transcription Regulators

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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Related Experiment Video

Updated: May 28, 2026

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

CpG deamination creates transcription factor-binding sites with high efficiency.

Tomasz Zemojtel1, Szymon M Kielbasa, Peter F Arndt

  • 1Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany. zemojtel@molgen.mpg.de

Genome Biology and Evolution
|October 22, 2011
PubMed
Summary
This summary is machine-generated.

CpG deamination, a common mutation, efficiently creates transcription factor-binding sites (TFBSs). This process significantly impacts gene regulation evolution by driving TFBS formation more effectively than other mutations.

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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
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Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
10:28

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

Area of Science:

  • Evolutionary Biology
  • Genetics
  • Molecular Biology

Background:

  • The formation of new transcription factor-binding sites (TFBSs) is crucial for the evolution of gene regulatory networks.
  • Single nucleotide mutations can create TFBSs, but the relative contribution of different mutation types is unclear.
  • CpG deamination (C → T) is the most frequent base substitution in the human genome and occurs at methylated CpG dinucleotides.

Purpose of the Study:

  • To investigate whether molecular processes inducing single nucleotide mutations contribute equally to TFBS creation.
  • To analyze the role of CpG deamination in generating TFBSs in human gene promoters and key transcription factor-bound regions.

Main Methods:

  • Analysis of single nucleotide mutational events in human gene promoters.
  • Examination of genomic regions bound by transcription factors Oct4, NANOG, and c-Myc.
  • Comparison of TFBS creation efficiency by CpG deamination versus other mutational events.

Main Results:

  • CpG deamination events were found to create TFBSs with significantly higher efficiency compared to other mutational events.
  • Previous work showed CpG deamination creating thousands of p53-binding sites in Alu transposons.
  • A specific Alu sequence region can form functional p53-, PAX-6-, and Myc-binding sites depending on CpG deamination patterns.

Conclusions:

  • CpG deamination is a highly efficient mechanism for creating TFBSs.
  • Deamination of methylated CpGs acts as an evolutionary force shaping TFBS formation.
  • This mechanism contributes to variability in gene regulation through TFBS evolution.