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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...
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...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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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Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
09:07

Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation

Published on: June 21, 2016

Prediction of regulatory elements.

Albin Sandelin1

  • 1The Bioinformatics Centre, Department of Molecular Biology and Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.

Methods in Molecular Biology (Clifton, N.J.)
|August 21, 2008
PubMed
Summary
This summary is machine-generated.

Identifying functional transcription factor binding sites (TFBS) is crucial for understanding gene expression. This study presents computational methods to predict TFBS, improving efficiency over costly lab experiments.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Gene expression regulation is a key challenge in biomedical research.
  • Identifying functional transcription factor binding sites (TFBS) is essential for understanding gene regulation.
  • Experimental methods for TFBS identification are time-consuming and expensive.

Purpose of the Study:

  • To present computational methods for predicting TFBS.
  • To develop quantitative models for transcription factor binding preferences.
  • To provide a protocol for scanning gene promoters using phylogenetic footprinting.

Main Methods:

  • Building quantitative models of transcription factor binding preferences from literature data.
  • Utilizing cross-species comparison (phylogenetic footprinting) to scan gene promoters.
  • Developing computational approaches to enhance the efficiency of TFBS identification.

Main Results:

  • Demonstrated methods for building predictive models of TFBS.
  • Presented a protocol for promoter scanning using phylogenetic footprinting.
  • Showcased the potential of computational methods to accelerate TFBS discovery.

Conclusions:

  • Computational methods can significantly increase the efficiency of identifying functional TFBS.
  • Quantitative models and phylogenetic footprinting offer powerful tools for regulatory genomics.
  • These approaches can guide and optimize experimental validation in TFBS research.