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Related Concept Videos

Transcription Initiation01:47

Transcription Initiation

Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
Transcription Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a...
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...
General Transcription Factors01:30

General 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...

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Related Experiment Video

Updated: Jul 10, 2026

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision
09:27

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

Published on: December 23, 2016

Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis.

Ryan K Shultzaberger1, Derek Y Chiang, Alan M Moses

  • 1Department of Molecular and Cell Biology, University of California, Berkeley, United States of America.

Plos One
|November 22, 2007
PubMed
Summary

We developed an information theory method to understand transcription factor cooperativity in eukaryotic gene expression. Our model accurately identifies genes regulated by Met4, showing binding site strength is key, not spacing.

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Area of Science:

  • Molecular Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Eukaryotic gene expression relies on transcription factors acting cooperatively.
  • Structural constraints limit transcription factor binding and define functional cooperativity rules.
  • Understanding these rules helps infer molecular binding characteristics.

Purpose of the Study:

  • To develop an information theory-based method for approximating physical limitations of cooperative transcription factor interactions.
  • To apply this method to understand the coordinated binding of Met4 by Cbf1 and Met31.
  • To create a predictive model for Met4-regulated genes.

Main Methods:

  • Developed an information theory-based approach.
  • Compared sequence analysis with microarray expression data.
  • Applied the method to the Met4, Cbf1, and Met31 regulatory system.

Main Results:

  • Created a combinatorial model that accurately identifies Met4-regulated genes.
  • Found that the sum of binding site strengths for Cbf1 and Met31 is the primary determinant of Met4 regulation.
  • Observed minimal energetic costs associated with the spacing of binding sites.

Conclusions:

  • The developed information theory method effectively models cooperative transcription factor binding.
  • Binding site strength is a more critical factor than spacing in Met4-mediated gene regulation.
  • This approach advances the understanding of gene regulation mechanisms and predictive modeling.