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Related Concept Videos

Mutations01:39

Mutations

Overview
Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
Mutations01:39

Mutations

Overview
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Transcription Attenuation in Prokaryotes02:42

Transcription Attenuation in Prokaryotes

Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...
Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).

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Related Experiment Video

Updated: May 20, 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

Noise-mean relationship in mutated promoters.

Gil Hornung1, Raz Bar-Ziv, Dalia Rosin

  • 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.

Genome Research
|July 24, 2012
PubMed
Summary

Promoter mutations reveal that gene expression burst size is a promoter-specific trait. TATA box interactions with nucleosomes significantly impact burst size and gene expression responsiveness.

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Published on: June 28, 2018

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
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Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biophysics

Background:

  • Gene expression is regulated by transcription burst frequency and burst size, both encoded in promoter sequences.
  • The impact of promoter mutations on burst size and frequency is not well understood.
  • Theoretical models predict that burst size and frequency changes can be distinguished by analyzing gene expression noise.

Purpose of the Study:

  • To investigate how promoter sequence mutations affect gene expression burst size and frequency.
  • To identify principles governing promoter sequence regulation of transcription bursts.
  • To understand the role of specific promoter elements, like the TATA box, in regulating gene expression dynamics.

Main Methods:

  • Randomly mutated 22 yeast promoters to create libraries of sequence variants.
  • Analyzed mean expression (m) and noise (coefficient of variation, η) across variant libraries.
  • Derived a scaling curve (η(2) = b/m + η(ext)(2)) to estimate burst size (b) and frequency contributions.
  • Identified specific mutations (TATA box, translation start site) affecting burst size.

Main Results:

  • A scaling curve relating mean expression and noise was observed, consistent with mutations primarily modulating burst frequency.
  • Estimated burst size (b) varied between promoters, higher in those with TATA boxes and lacking nucleosome-free regions.
  • Mutations in the TATA box or insertions near the start site significantly decreased burst size.
  • TATA box mutations affected gene expression responsiveness to environmental changes.

Conclusions:

  • Gene expression burst size is a promoter-specific property, relatively robust to random mutations.
  • The TATA box and its interaction with promoter nucleosomes are critical determinants of burst size.
  • TATA box integrity is essential for maintaining normal burst size and conditional gene expression responsiveness.