Publications - Published papers

Please find below publications of our group. Currently, we list 500 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript

Dominic Rose, Peter F. Stadler

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Frontiers in Genetics, 2:69. Epub 2011 Oct 5

Abstract


<p>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.</p> <p>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 identified EGOT orthologs in the genomes of 32 different amniotes. We compiled 25 reliable orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans but also provide seven putative EGOT candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyse patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, is 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. It contains several evolutionary conserved and thermodynamic stable secondary structures.</p> <p>Moreover, we characterize and unravel novel functional roles of a hitherto poorly understood region that shows the highest sequence conservation at the EGOT locus. It is located within the intron of EGO-B. We show that it contains both a novel ITPR1 exon but also conserved RNA secondary structures together with a conserved TATA-like promoter element which is indicative of an independent regulatory element.</p>

Keywords


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

Note


doi 10.3389/fgene.2011.00069