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Gene Clustering in Eukaryotes

  1. Maja Tarailo-Graovac,
  2. Nansheng Chen

Published Online: 18 OCT 2013

DOI: 10.1002/9780470015902.a0006117.pub3



How to Cite

Tarailo-Graovac, M. and Chen, N. 2013. Gene Clustering in Eukaryotes. eLS. .

Author Information

  1. Simon Fraser University, Burnaby, British Columbia, Canada

  1. Based in part on the previous version of this eLS article ‘Gene Clustering in Eukaryotes’ (2008) by Jeffrey G Lawrence and Thomas Blumenthal.

Publication History

  1. Published Online: 18 OCT 2013


Recent advances in genomics have provided us with better understanding of genomes from many different species, their architectures and evolutionary relationships. Genome architecture (a nonrandom arrangement of functional elements in the genome, such as genes and regulatory regions) is different in eukaryotes than in prokaryotes. Although in prokaryotes, many genes are organised into linearly positioned cotranscribed groups (operons), eukaryotic genomes possess very small number of genes organised into operons. The acquisition of the nuclear membrane, decoupling of transcription and translation and adoption of the ribosome-scanning mechanism for translation initiation (necessitating monocistronic messenger ribonucleic acids (mRNAs)) are possible reasons for the loss of operon structure in eukaryotes. Despite the general trend of low level of gene clustering within operon structures in eukaryotes, there is an evidence for nonrandom linear and spatial organisation of eukaryotic genomes, as a result of multiple mechanisms that can lead to the proximity of coexpressed genes.

Key Concepts:

  • Albeit not as common as the gene clustering within operons observed in bacteria, linear gene clustering does occur in eukaryotes.

  • In eukaryotes, linear gene clusters form predominantly by partially adaptive, but largely neutral processes, such as genome rearrangements.

  • In natal clusters, genes occupy adjacent positions on chromosomes as a result of a tandem duplication and consequent divergence.

  • In embedded clusters, coding sequence of one gene may be entirely positioned within an intron of another gene, or one gene may have exons that interweave with the exons of other genes.

  • In coregulated clusters, genes could be either linearly clustered on chromosomes to share regulatory sequences, or genes could be spatially colocalised within the nucleus forming transcription factories.

  • Linearly coregulated clusters in eukaryotes include: alternatively spliced transcripts, polycistronic messages, uORFs and genes regulated by bidirectional promoters.

  • Spatial sequestration of genes positioned distantly on the same chromosome or even on different chromosomes can modulate coregulated gene expression.


  • linear gene clustering;
  • spatial gene clustering;
  • gene duplication;
  • operons;
  • polycistronic messages;
  • trans-splicing