Spliceosomal small nuclear RNA genes in 11 insect genomes

  1. Stephen M. Mount1,2,5,
  2. Valer Gotea3,5,
  3. Chiao-Feng Lin3,
  4. Kristina Hernandez3, and
  5. Wojciech Makałowski3,4
  1. 1Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815, USA
  2. 2Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
  3. 3Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
  4. 4Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

  1. ↵5 These authors contributed equally to this work.

Abstract

The removal of introns from the primary transcripts of protein-coding genes is accomplished by the spliceosome, a large macromolecular complex of which small nuclear RNAs (snRNAs) are crucial components. Following the recent sequencing of the honeybee (Apis mellifera) genome, we used various computational methods, ranging from sequence similarity search to RNA secondary structure prediction, to search for putative snRNA genes (including their promoters) and to examine their pattern of conservation among 11 available insect genomes (A. mellifera, Tribolium castaneum, Bombyx mori, Anopheles gambiae, Aedes aegypti, and six Drosophila species). We identified candidates for all nine spliceosomal snRNA genes in all the analyzed genomes. All the species contain a similar number of snRNA genes, with the exception of A. aegypti, whose genome contains more U1, U2, and U5 genes, and A. mellifera, whose genome contains fewer U2 and U5 genes. We found that snRNA genes are generally more closely related to homologs within the same genus than to those in other genera. Promoter regions for all spliceosomal snRNA genes within each insect species share similar sequence motifs that are likely to correspond to the PSEA (proximal sequence element A), the binding site for snRNA activating protein complex, but these promoter elements vary in sequence among the five insect families surveyed here. In contrast to the other insect species investigated, Dipteran genomes are characterized by a rapid evolution (or loss) of components of the U12 spliceosome and a striking loss of U12-type introns.

Keywords

Footnotes

  • Reprint requests to: Wojciech Makalowski, 514 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA; e-mail: wojtek{at}psu.edu; fax: (814) 865-9366.

  • Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.259207.

    • Received August 8, 2006.
    • Accepted September 26, 2006.
« Previous | Next Article »Table of Contents

This Article

  1. Published in Advance November 9, 2006, doi: 10.1261/rna.259207 RNA 2007. 13: 5-14 Copyright © 2007 RNA Society

Current Issue

  1. December 2008, 14 (12)
  1. Current Issue
  1. Alert me to new issues of RNA