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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

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Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
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What is Gene Expression?01:36

What is Gene Expression?

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

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The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
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Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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Related Experiment Video

Updated: Feb 2, 2026

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells
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Comparative expression profiling reveals widespread coordinated evolution of gene expression across eukaryotes.

Trevor Martin1, Hunter B Fraser2

  • 1Department of Biology, Stanford University, Stanford, CA, 94305, USA.

Nature Communications
|November 25, 2018
PubMed
Summary

This study developed a new method to compare gene expression across many species, revealing coordinated evolution in protein complexes and pathways over vast evolutionary timescales.

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • Comparative gene expression studies offer insights but are limited by species representation.
  • Analyzing gene expression across diverse species is crucial for understanding evolutionary mechanisms.

Purpose of the Study:

  • To develop a novel approach for identifying orthologs between divergent transcriptome assemblies.
  • To analyze gene expression patterns and coevolutionary dynamics in a large set of unicellular eukaryotes.
  • To uncover coordinated evolution of gene expression in conserved protein complexes and pathways.

Main Methods:

  • Developed an ortholog identification method for highly diverged transcriptome assemblies.
  • Applied the method to 657 RNA-sequencing (RNA-seq) gene expression profiles from 309 unicellular eukaryotes.
  • Analyzed gene expression data for coevolutionary patterns and adaptive evolution.

Main Results:

  • Identified several hundred protein complexes and pathways with coordinated expression evolution across species.
  • Discovered gene sets with coordinated expression that show little within-species co-expression.
  • Detected adaptive evolution, such as tRNA ligase levels matching genome-wide codon usage.

Conclusions:

  • Comparative transcriptomics across highly diverse organisms provides novel insights into gene expression evolution.
  • Coordinated evolution impacts even the most conserved eukaryotic protein complexes.
  • The developed ortholog identification approach enables broader comparative genomic studies.