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Related Concept Videos

Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Updated: Jun 14, 2026

Engineering 'Golden' Fluorescence by Selective Pressure Incorporation of Non-canonical Amino Acids and Protein Analysis by Mass Spectrometry and Fluorescence
11:51

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Positive selection for unpreferred codon usage in eukaryotic genomes.

Daniel E Neafsey1, James E Galagan

  • 1Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. neafsey@broad.mit.edu

BMC Evolutionary Biology
|July 21, 2007
PubMed
Summary
This summary is machine-generated.

Natural selection can favor unpreferred codons, reducing translational efficiency, particularly in regulatory genes. This may help minimize gene expression noise in organisms like Cryptococcus and Drosophila.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Traditionally, natural selection is thought to increase translational efficiency, while reduced efficiency is attributed to neutral processes.
  • This study investigates directional selection for increased unpreferred codon usage, implying reduced translational efficiency.

Purpose of the Study:

  • To search for evidence of natural selection driving unpreferred codon usage in eukaryotic genomes.
  • To determine the extent and nature of this selection across different species.

Main Methods:

  • Utilized an optimal-codon-based metric (Kp/Ku) for genome-wide scans.
  • Analyzed codon usage patterns in three divergent eukaryotic genome clusters.
  • Performed functional enrichment analysis on genes with low Kp/Ku ratios.

Main Results:

  • Found evidence of selection for unpreferred codon usage in Cryptococcus and Drosophila, but not Saccharomyces.
  • Observed a correlation between unpreferred codon selection and upstream open reading frames (uORFs).
  • Identified regulatory genes as particularly enriched for selection favoring unpreferred codons.

Conclusions:

  • Genome-wide scans revealed recent selection for unpreferred codon usage in ~1% of loci in Cryptococcus and some genes in Drosophila.
  • Genes with translation-impeding uORFs are enriched for this selection signal.
  • Selection for reduced translational efficiency in regulatory genes supports the hypothesis of suppressing expression noise.