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Related Concept Videos

The Eukaryotic Promoter Region02:40

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
The Eukaryotic Promoter Region02:40

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
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...
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...

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Related Experiment Video

Updated: May 8, 2026

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
10:16

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Published on: June 28, 2018

Mapping the fine structure of a eukaryotic promoter input-output function.

Arun S Rajkumar1, Nicolas Dénervaud, Sebastian J Maerkl

  • 1Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.

Nature Genetics
|August 20, 2013
PubMed
Summary

Researchers precisely tuned gene expression by altering transcription factor binding sites. In vitro binding affinities accurately predicted promoter output, enabling fine-tuning of gene regulation in yeast.

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Area of Science:

  • Molecular Biology
  • Systems Biology
  • Genetics

Background:

  • Transcriptional regulatory networks require precise gene expression tuning for optimal function.
  • Transcription factors (TFs) play a crucial role in regulating gene expression by binding to specific DNA sequences.
  • Understanding the quantitative relationship between TF binding and gene output is vital for systems biology.

Purpose of the Study:

  • To quantify the impact of transcription factor binding site variations on promoter output.
  • To determine if in vitro measured binding affinities can predict in vivo promoter activity.
  • To explore the potential for precise gene expression tuning through TF binding site modification.

Main Methods:

  • Construction and analysis of 209 variants of the Saccharomyces cerevisiae PHO5 promoter.
  • In vitro determination of transcription factor (Pho4) binding affinities to promoter variants.
  • Quantitative measurement of promoter output (gene expression levels) in yeast.

Main Results:

  • In vitro binding affinities quantitatively predicted the output of the PHO5 promoter.
  • Promoter output was precisely tunable by altering binding-site affinity (changes < 3 kcal mol(-1)).
  • Subtle modifications (1-2 base changes) were sufficient for significant tuning of gene expression.

Conclusions:

  • In vitro binding-energy landscapes of transcription factors can accurately predict native yeast promoter output.
  • Quantitative models of transcriptional regulatory networks are feasible.
  • TF binding sites offer a mechanism for precise and tunable gene expression control, with implications for network evolution and synthetic biology.