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Related Experiment Videos

Functional noncoding sequences derived from SINEs in the mammalian genome.

Hidenori Nishihara1, Arian F A Smit, Norihiro Okada

  • 1Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.

Genome Research
|May 24, 2006
PubMed
Summary

Ancient SINEs, termed AmnSINE1, are surprisingly conserved in mammalian genomes, challenging their parasitic view. These short interspersed repetitive elements show significant functionality, particularly in their central domains.

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Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Comparative genomic analyses reveal strong selective constraint on numerous non-protein-coding mammalian genomic regions.
  • Short interspersed repetitive elements (SINEs) and other transposable elements are typically considered genomic parasites.

Purpose of the Study:

  • To identify and characterize ancient SINE families, specifically AmnSINE1, residing in conserved genomic regions.
  • To investigate the evolutionary origins and potential functionality of these ancient SINEs across vertebrate genomes.

Main Methods:

  • Comparative sequence analysis of mammalian, avian, and fish genomes.
  • Phylogenetic analysis to determine the evolutionary age and relationships of SINE families.
  • Identification and conservation analysis of AmnSINE1 copies within the human genome and across mammalian orthologs.

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Main Results:

  • Discovery of AmnSINE1, an ancient SINE family predating the mammalian-bird split (310 Mya), present in mammals and birds.
  • AmnSINE1 exhibits a chimeric structure derived from 5S rRNA and tRNA, related to newly characterized SINE families in diverse vertebrates (coelacanth, shark, hagfish, amphioxus).
  • Approximately 105 out of 1000 human AmnSINE1 copies are highly conserved among mammalian orthologs, with strongest conservation in the central domain.

Conclusions:

  • AmnSINE1 represents a significant fraction of transposable elements that have acquired genomic functionality.
  • The findings challenge the traditional view of SINEs as solely parasitic elements, highlighting their potential roles in genome evolution.
  • The DeuSINE superfamily, including AmnSINE1, provides insights into the early evolution of SINEs in deuterostomes.