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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements.

Zhen-Xia Chen1,2,3, Brian Oliver2, Yong E Zhang4,5

  • 1College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, P.R. China.

Genome Biology and Evolution
|March 25, 2017
PubMed
Summary
This summary is machine-generated.

Inverted duplicates, repetitive DNA sequences, are often functional, potentially producing hairpin RNAs. Their structural stability and conservation suggest a role beyond mere genome instability.

Keywords:
Homo sapiensMus musculushairpin RNAinverted repeatsmirror repeatsnoncoding RNA

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Inverted duplicates are repetitive DNA sequences with potential roles in genome instability and functional small RNA production.
  • The evolutionary drivers for the abundance of inverted duplicates in genomes, particularly mammalian genomes, remain unclear.
  • Distinguishing between neutral duplication and positive selection for functionality is challenging.

Purpose of the Study:

  • To investigate the functionality of intergenic inverted duplicates lacking known functions.
  • To use mirror duplicates as a nonfunctional control to assess hairpin formation potential.
  • To determine if inverted duplicates are conserved and expressed in vertebrate genomes.

Main Methods:

  • Identification of inverted duplicates and mirror duplicates in human, mouse, and 19 other vertebrate genomes.
  • Structural analysis to assess the potential for hairpin formation.
  • Expression profiling across various tissues.
  • Phylogenetic dating to analyze conservation patterns.

Main Results:

  • Large numbers of intergenic inverted duplicates were identified across vertebrate genomes.
  • Inverted duplicates showed a higher propensity to form stable hairpins compared to mirror duplicates.
  • A significant percentage of inverted duplicates (7.8% in humans, 5.7% in mice) were expressed.
  • Expressed inverted duplicates were more structurally stable and evolutionarily conserved than mirror duplicates.

Conclusions:

  • Expressed inverted duplicates possess structural features conducive to hairpin RNA formation.
  • Higher conservation of inverted duplicates compared to mirror duplicates suggests functional relevance.
  • These findings support the hypothesis that expressed inverted duplicates may be functional through hairpin RNA production.