Functional noncoding sequences derived from SINEs in the mammalian genome

  1. Hidenori Nishihara1,
  2. Arian F.A. Smit2, and
  3. Norihiro Okada1,3
  1. 1 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan;
  2. 2 Institute for Systems Biology, Seattle, Washington 98103, USA

Abstract

Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective constraint. Here, we report that some of these loci have been derived from a newly defined family of ancient SINEs (short interspersed repetitive elements). This is a surprising result, as SINEs and other transposable elements are commonly thought to be genomic parasites. We named the ancient SINE family AmnSINE1, for Amniota SINE1, because we found it to be present in mammals as well as in birds, and some copies predate the mammalian-bird split 310 million years ago (Mya). AmnSINE1 has a chimeric structure of a 5S rRNA and a tRNA-derived SINE, and is related to five tRNA-derived SINE families that we characterized here in the coelacanth, dogfish shark, hagfish, and amphioxus genomes. All of the newly described SINE families have a common central domain that is also shared by zebrafish SINE3, and we collectively name them the DeuSINE (Deuterostomia SINE) superfamily. Notably, of the ∼1000 still identifiable copies of AmnSINE1 in the human genome, 105 correspond to loci phylogenetically highly conserved among mammalian orthologs. The conservation is strongest over the central domain. Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality.

Footnotes

  • 3 Corresponding author.

    3 E-mail nokada{at}bio.titech.ac.jp; fax 81-45-924-5835.

  • [Supplemental material is available online at www.genome.org.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.5255506

    • Received October 11, 2005.
    • Accepted April 18, 2006.
  • Freely available online through the Genome Research Open Access option.

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