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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.
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What is Gene Expression?01:36

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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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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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Chromatin Position Affects Gene Expression02:35

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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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mRNA Stability and Gene Expression02:51

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The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
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Fruits form from a mature flower ovary. As seeds develop from the ovules contained within, the ovary wall undergoes a series of complex changes to form fruit. In some fruits, such as soybeans, the ovary wall dries; in other fruits, such as grapes, it remains fleshy. In some cases, organs other than the ovary contribute to fruit formation; such fruits are called accessory fruits.
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Updated: Feb 4, 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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Gene expression cartography of a developing neuronal structure.

Leonardo Tadini1, Lilia Younsi2, Isabel Holguera1

  • 1Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France.

Developmental Biology
|February 2, 2026
PubMed
Summary
This summary is machine-generated.

Researchers created a 3D gene expression atlas of the Drosophila optic lobe using the Novosparc algorithm. This tool maps cell types and gene patterns, aiding the study of brain development and circuit formation.

Keywords:
Developing nervous systemDrosophila optic lobeNeurodevelopmental 3D-atlasNovosparcSingle-cell mRNA sequencingSpatial transcriptomics

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Area of Science:

  • Neuroscience
  • Developmental Biology
  • Computational Biology

Background:

  • Brains feature billions of neurons from diverse origins, requiring precise spatial organization for circuit integration.
  • Existing single-cell mRNA sequencing atlases lack essential spatial information for understanding brain structure.
  • Spatial transcriptomics is crucial for mapping neuronal organization and developmental processes.

Purpose of the Study:

  • To reconstruct the spatial distribution of gene expression and cell types in the developing Drosophila optic lobe.
  • To develop a 3D atlas for visualizing gene expression patterns and identifying spatially patterned transcription factors.
  • To provide a tool for understanding how diverse neuronal lineages integrate into functional brain circuits.

Main Methods:

  • Utilized the gene expression cartography algorithm, Novosparc, to analyze spatial transcriptomic data.
  • Generated a comprehensive three-dimensional (3D) atlas of the Drosophila optic lobe.
  • Identified spatially patterned transcription factors defining specific neuronal types within the atlas.

Main Results:

  • Successfully created a 3D atlas of the Drosophila optic lobe, detailing gene expression and cell localization (https://larva3dnovosparc.ijm.fr).
  • Identified key transcription factors with spatial expression patterns that define distinct neuronal types.
  • Highlighted limitations and potential improvements for the Novosparc algorithm in spatial transcriptomic analysis.

Conclusions:

  • The 3D Drosophila optic lobe atlas is a valuable resource for studying gene expression patterns in brain development.
  • This work demonstrates the potential of spatial transcriptomics and algorithmic approaches for mapping complex brain structures.
  • The study paves the way for generating 3D brain atlases of more complex structures, advancing our understanding of neural circuit formation.