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Related Concept Videos

Transcription Factors02:16

Transcription Factors

75.5K
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...
75.5K
General Transcription Factors01:30

General Transcription Factors

5.1K
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

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...
6.8K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.3K
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...
6.3K
Combinatorial Gene Control02:33

Combinatorial Gene Control

8.3K
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...
8.3K
Ribosome Profiling02:24

Ribosome Profiling

3.4K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.4K

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Related Experiment Video

Updated: May 23, 2025

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

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Protocol to identify transcription factor target genes using TargetOrtho2.

Jonathan D Rumley1, Jee Hun Kim2, Oliver Hobert1

  • 1Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, New York, NY 10027, USA.

STAR Protocols
|March 8, 2025
PubMed
Summary
This summary is machine-generated.

TargetOrtho2 predicts transcription factor targets in C. elegans using phylogenetic footprinting. This study details a protocol for using the updated TargetOrtho2 software to identify target genes and manage genomes.

Keywords:
BioinformaticsGene ExpressionGenomicsModel OrganismsMolecular BiologySequence analysis

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Identification of Transcription Factor Regulators using Medium-Throughput Screening of Arrayed Libraries and a Dual-Luciferase-Based Reporter
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

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Related Experiment Videos

Last Updated: May 23, 2025

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

Published on: April 16, 2018

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Identification of Transcription Factor Regulators using Medium-Throughput Screening of Arrayed Libraries and a Dual-Luciferase-Based Reporter
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Identification of Transcription Factor Regulators using Medium-Throughput Screening of Arrayed Libraries and a Dual-Luciferase-Based Reporter

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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Transcription factors regulate gene expression.
  • Identifying transcription factor targets is crucial for understanding gene regulation.
  • Phylogenetic footprinting aids in identifying conserved regulatory elements.

Purpose of the Study:

  • To present an updated protocol for TargetOrtho2.
  • To guide users in predicting transcription factor targets in C. elegans.
  • To facilitate the addition and updating of genomes within TargetOrtho2.

Main Methods:

  • Utilizing transcription factor binding site information.
  • Employing an in silico phylogenetic footprinting approach.
  • Providing installation and usage instructions for TargetOrtho2.

Main Results:

  • A refined protocol for TargetOrtho2 is described.
  • Instructions cover software installation and genome management.
  • The method enables prediction of transcription factor target genes.

Conclusions:

  • The updated TargetOrtho2 protocol simplifies the identification of transcription factor targets.
  • This tool aids in the analysis of gene regulation in C. elegans.
  • The software is adaptable for new genome additions.