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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...
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...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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 29, 2026

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

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Published on: March 31, 2019

CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression.

Daniela Samaniego-Castruita1, Isabella Han1, Roxroy C Morgan1

  • 1Department of Cell and Developmental Biology, Northwestern University, Chicago, IL 60611.

Proceedings of the National Academy of Sciences of the United States of America
|May 27, 2026
PubMed
Summary

DNA G-quadruplexes (G4s) are key DNA structures. This study reveals CCCTC-binding factor (CTCF) binds G4s, influencing genome organization, chromatin looping, and gene expression, establishing G4s

Keywords:
3D genomealternative DNA structuresgene regulationgenome biologygenome topology

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Area of Science:

  • Genomics and molecular biology
  • Structural biology
  • Epigenetics

Background:

  • DNA G-quadruplexes (G4s) are non-B-form DNA structures found in regulatory genomic regions.
  • Their precise roles in genome function remain largely unknown.
  • G4s are conserved across evolution, suggesting fundamental importance.

Purpose of the Study:

  • To identify genomic regulators that bind G4s.
  • To investigate the functional significance of G4 structures in genome regulation.
  • To elucidate the interaction between G4s and the architectural protein CTCF.

Main Methods:

  • Proteomics screening using diverse G4 topologies.
  • Biochemical validation of CTCF-G4 interactions.
  • Development of G4 mapping tools and genetic reconstitution experiments in mouse embryonic stem cells.

Main Results:

  • CCCTC-binding factor (CTCF) identified as a strong G4 binder.
  • A CTCF mutant with enhanced G4 affinity was characterized.
  • A comprehensive catalog of genomic G4s associated with CTCF binding sites was generated.
  • G4-linked chromatin loops exhibit increased strength and persistence.

Conclusions:

  • CTCF directly binds DNA G-quadruplexes.
  • G4 structures play a significant role in regulating CTCF binding, chromatin looping, and gene expression.
  • G4s contribute to the stability and regulation of genome architecture.