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AMNE:(Microbiology in the medical area)
 

Sökning: AMNE:(Microbiology in the medical area) > Evolutionary Conser...

  • Benachenhou, Farid (författare)

Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data

  • E-artikel/E-kapitelEngelska2009

Förlag, utgivningsår, omfång ...

  • Public Library of Science (PLoS)2009

Nummerbeteckningar

  • LIBRIS-ID:22278078
  • http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-119767uri
  • urn:nbn:se:uu:diva-119767urn
  • 10.1371/journal.pone.0005179doi

Kompletterande språkuppgifter

  • Språk:engelska

Ingår i deldatabas

Anmärkningar

  • Published
  • gratis
  • BACKGROUND: Retroviral LTRs, paired or single, influence the transcription of both retroviral and non-retroviral genomic sequences. Vertebrate genomes contain many thousand endogenous retroviruses (ERVs) and their LTRs. Single LTRs are difficult to detect from genomic sequences without recourse to repetitiveness or presence in a proviral structure. Understanding of LTR structure increases understanding of LTR function, and of functional genomics. Here we develop models of orthoretroviral LTRs useful for detection in genomes and for structural analysis. PRINCIPAL FINDINGS: Although mutated, ERV LTRs are more numerous and diverse than exogenous retroviral (XRV) LTRs. Hidden Markov models (HMMs), and alignments based on them, were created for HML- (human MMTV-like), general-beta-, gamma- and lentiretroviruslike LTRs, plus a general-vertebrate LTR model. Training sets were XRV LTRs and RepBase LTR consensuses. The HML HMM was most sensitive and detected 87% of the HML LTRs in human chromosome 19 at 96% specificity. By combining all HMMs with a low cutoff, for screening, 71% of all LTRs found by RepeatMasker in chromosome 19 were found. HMM consensus sequences had a conserved modular LTR structure. Target site duplications (TG-CA), TATA (occasionally absent), an AATAAA box and a T-rich region were prominent features. Most of the conservation was located in, or adjacent to, R and U5, with evidence for stem loops. Several of the long HML LTRs contained long ORFs inserted after the second A rich module. HMM consensus alignment allowed comparison of functional features like transcriptional start sites (sense and antisense) between XRVs and ERVs. CONCLUSION: The modular conserved and redundant orthoretroviral LTR structure with three A-rich regions is reminiscent of structurally relaxed Giardia promoters. The five HMMs provided a novel broad range, repeat-independent, ab initio LTR detection, with prospects for greater generalisation, and insight into LTR structure, which may aid development of LTR-targeted pharmaceuticals.

Ämnesord och genrebeteckningar

Biuppslag (personer, institutioner, konferenser, titlar ...)

  • Jern, Patric (författare)
  • Oja, Merja (författare)
  • Sperber, Göran (författare)
  • Blikstad, Vidar (författare)
  • Somervuo, Panu (författare)
  • Kaski, Samuel (författare)
  • Blomberg, Jonas (författare)
  • Uppsala universitetMedicinska och farmaceutiska vetenskapsområdet (utgivare)
  • Uppsala universitetMedicinska och farmaceutiska vetenskapsområdet (utgivare)
  • Uppsala universitetMedicinska och farmaceutiska vetenskapsområdet (utgivare)
  • Blomberg (medarbetare)
  • Sperber (medarbetare)
  • Blomberg (medarbetare)
  • Blomberg (medarbetare)

Sammanhörande titlar

  • Del av/supplement till:channel record
  • Ingår i:VärdpublikationPLos ONE4:4, e51791932-6203

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  • PLos ONE (Sök värdpublikationen i LIBRIS)

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