Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT
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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2011-10-01
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| Series: | Frontiers in Genetics |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00069/full |
| _version_ | 1811323697845239808 |
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| author | Dominic eRose Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler |
| author_facet | Dominic eRose Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler |
| author_sort | Dominic eRose |
| collection | DOAJ |
| description | 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, analyse 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 demonstrat 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. |
| first_indexed | 2024-04-13T13:59:56Z |
| format | Article |
| id | doaj.art-7f6e7787dbc149d994eb0314c7d7fce5 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T13:59:56Z |
| publishDate | 2011-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-7f6e7787dbc149d994eb0314c7d7fce52022-12-22T02:44:04ZengFrontiers Media S.A.Frontiers in Genetics1664-80212011-10-01210.3389/fgene.2011.0006912040Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOTDominic eRose0Peter F. Stadler1Peter F. Stadler2Peter F. Stadler3Peter F. Stadler4Peter F. Stadler5Peter F. Stadler6University of FreiburgUniversity of LeipzigMPI MISFraunhofer Institut für Zelltherapie und ImmunologieUniversity of ViennaUniversity of CopenhagenSanta Fe InstituteEukaryotic 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, analyse 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 demonstrat 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.http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00069/fullevolutionlong non-coding RNAlncRNAEGOEGO-AEGO-B |
| spellingShingle | Dominic eRose Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler Peter F. Stadler Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT Frontiers in Genetics evolution long non-coding RNA lncRNA EGO EGO-A EGO-B |
| title | Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT |
| title_full | Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT |
| title_fullStr | Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT |
| title_full_unstemmed | Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT |
| title_short | Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT |
| title_sort | molecular evolution of the non coding eosinophil granule ontogeny transcript egot |
| topic | evolution long non-coding RNA lncRNA EGO EGO-A EGO-B |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00069/full |
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