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Related Concept Videos

General Transcription Factors01:30

General Transcription Factors

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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...
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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...
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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...
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Master Transcription Regulators02:23

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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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Cell Specific Gene Expression

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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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Related Experiment Video

Updated: Oct 18, 2025

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

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CGGBP1-dependent CTCF-binding sites restrict ectopic transcription.

Divyesh Patel1,2, Manthan Patel1, Subhamoy Datta1

  • 1HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India.

Cell Cycle (Georgetown, Tex.)
|September 29, 2021
PubMed
Summary

CGGBP1-dependent CTCF binding sites act as barriers to ectopic transcription. Loss of CGGBP1 and CTCF binding unleashes this transcription, suggesting a role in restricting unwanted gene expression genome-wide.

Keywords:
CGGBP1-dependent CTCF-binding sitesCT (control non-targeting shRNA)ChIP (chromatin immunoprecipitation)H3K9me3KD (anti-cggbp1 shRNA)RNA polymerase 2RNA-sequencingSV40 (simian virus 40)transcription

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • CTCF binding sites are crucial genomic landmarks.
  • CGGBP1 regulates CTCF binding at LINE-1 repeats.
  • These sites may function as epigenetic barriers, influencing H3K9me3 and RNA levels.

Purpose of the Study:

  • To investigate the function of CGGBP1-dependent CTCF binding sites.
  • To determine their role in regulating transcription.

Main Methods:

  • Cloning candidate sites into an SV40 promoter-enhancer episomal system.
  • Performing strand-specific reverse transcription PCR.
  • Utilizing RNA-sequencing.

Main Results:

  • CGGBP1-dependent CTCF binding sites inhibit ectopic transcription from the SV40 promoter.
  • Loss of CGGBP1 and CTCF binding leads to increased ectopic transcription and promoter bidirectionality.
  • These sites function as genome-wide transcription barriers.

Conclusions:

  • CGGBP1-dependent CTCF binding sites restrict ectopic transcription.
  • CGGBP1 and CTCF binding are essential for maintaining transcription barrier function.
  • These sites play a significant role in genome-wide transcriptional regulation.