Original Research ARTICLE

Front. Genet., 05 October 2011 | http://dx.doi.org/10.3389/fgene.2011.00069

Molecular evolution of the non-coding eosinophil granule ontogeny transcript

Dominic Rose1* and Peter F. Stadler2,3,4,5,6,7
  • 1 Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
  • 2 Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
  • 3 Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
  • 4 Fraunhofer Institut für Zelltherapie und Immunologie, Leipzig, Germany
  • 5 Department of Theoretical Chemistry, University of Vienna, Wien, Austria
  • 6 Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
  • 7 Santa Fe Institute, Santa Fe, NM, USA

Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs). The evolutionary history of mlncRNAs is still largely uncharted territory. In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT), an experimentally confirmed representative of an abundant class of totally intronic non-coding transcripts (TINs). EGOT is located antisense to an intron of the ITPR1 gene. We computationally identify putative EGOT orthologs in the genomes of 32 different amniotes, including orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans, as well as putative candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyze patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, may be present throughout the placental mammals, but most likely dates back even further. We demonstrate here for the first time that the whole EGOT locus is highly structured, containing several evolutionary conserved, and thermodynamic stable secondary structures. Our analyses allow us to postulate novel functional roles of a hitherto poorly understood region at the intron of EGO-B which is highly conserved at the sequence level. The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element.

Keywords: EGO, EGO-A, EGO-B, EGOT, long non-coding RNA, lncRNA, mlncRNA, evolution

Citation: Rose D and Stadler PF (2011) Molecular evolution of the non-coding eosinophil granule ontogeny transcript. Front. Gene. 2:69. doi: 10.3389/fgene.2011.00069

Received: 01 June 2011; Accepted: 16 September 2011;
Published online: 05 October 2011.

Edited by:

Helder I. Nakaya, Emory University, USA

Reviewed by:

Helder I. Nakaya, Emory University, USA
Fei Li, Nanjing Agricultural University, China
Paulo De Paiva Rosa Amaral, The University of Queensland, Australia

Copyright: © 2011 Rose and Stadler. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with.

*Correspondence: Dominic Rose, Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany. e-mail: dominic@informatik.uni-freiburg.de