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Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data.

Benachenhou F, Jern P, Oja M, Sperber G, Blikstad V, Somervuo P, Kaski S, Blomberg J - PLoS ONE (2009)

Bottom Line: By combining all HMMs with a low cutoff, for screening, 71% of all LTRs found by RepeatMasker in chromosome 19 were found.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Sciences, Section of Virology, Uppsala University, Uppsala, Sweden.

ABSTRACT

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.

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Outcome of the gamma HMM.A. Weblogo for a Viterbi alignment of the gamma training set (“gamma”). Conventions are as in Fig 1. B. MLV RU5 (MLMCG) RNA analysed with the gamma HMM and MFOLD. Match state positions are in upper case. R boundaries [43], [56], [57], [58], TATA box and AATAAA are shown. A partially conserved predicted stem loop early in R [31] is also shown.
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pone-0005179-g003: Outcome of the gamma HMM.A. Weblogo for a Viterbi alignment of the gamma training set (“gamma”). Conventions are as in Fig 1. B. MLV RU5 (MLMCG) RNA analysed with the gamma HMM and MFOLD. Match state positions are in upper case. R boundaries [43], [56], [57], [58], TATA box and AATAAA are shown. A partially conserved predicted stem loop early in R [31] is also shown.

Mentions: A 109 nt consensus sequence was derived from the gamma LTR HMM. Transcription factor binding sites were sought with the MOTIF program. The consensus contains non-contiguous match states but this was taken into account by looking back at the Viterbi alignment of the training set. Only MOTIF matches which were contiguous were taken into account. The Viterbi alignment was visualised as a sequence logo (see Fig 3a). At position 87–101, a T-rich element is apparent. There is a clear AATAAA motif at position 69–74. Unlike HML LTRs, the distance between this box and the T-rich region is within the normal range (30–70 nt) [24]. Between them there are conserved A:s at position 85–86, probably poly(A) sites. For HERV-H, these putative poly(A) sites have been confirmed experimentally [56]. MOTIF predicts one TATA box at position 13–22 but another one is clear at position 27–32 (also found in the SuperViterbi alignment, see below). The second TATA box agrees well with experiments, for example in the case of gammaretroviruses (i.e. MLV and its relatives [57]), HERV-H [43] and HERV-I [58]. As mentioned in the introduction, ERV9 lacks a functional TATA box but has an AATAAA 28 nt upstream of the established transcription start site [21], which is Inr dependent. The transcription start site for HERV-H corresponds to GC/G at position 41–42 [43]. A conserved CCAAT-box between the TATA-boxes was also detected by MOTIF. The CCAAT-box is an upstream enhancer/promoter elements, common in vertebrate genes, recognised by the transcription factor NF-Y. It is located upstream of the TATA-box [59]. The found structure is consistent with the mammalian C-type LTR model of [6]. That model had a conserved hairpin loop in the R-region, also found in the MLV LTR (Fig 3b) by MFOLD (Fig S4). The gamma HMM consensus (Fig S5) also displays a shorter version of it. As in the HML case conserved G:s at position 41–45 bind to (less) conserved C(T):s at position 51–55 with the tip of the loop at position 47–49. This stem-loop has been studied in great detail for the MLV LTR [30], [31], [32] where it has been found important for RNA processing. As seen in fig 3b there are two other loops predicted in the R-U5 region of MLV.


Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data.

Benachenhou F, Jern P, Oja M, Sperber G, Blikstad V, Somervuo P, Kaski S, Blomberg J - PLoS ONE (2009)

Outcome of the gamma HMM.A. Weblogo for a Viterbi alignment of the gamma training set (“gamma”). Conventions are as in Fig 1. B. MLV RU5 (MLMCG) RNA analysed with the gamma HMM and MFOLD. Match state positions are in upper case. R boundaries [43], [56], [57], [58], TATA box and AATAAA are shown. A partially conserved predicted stem loop early in R [31] is also shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2664473&req=5

pone-0005179-g003: Outcome of the gamma HMM.A. Weblogo for a Viterbi alignment of the gamma training set (“gamma”). Conventions are as in Fig 1. B. MLV RU5 (MLMCG) RNA analysed with the gamma HMM and MFOLD. Match state positions are in upper case. R boundaries [43], [56], [57], [58], TATA box and AATAAA are shown. A partially conserved predicted stem loop early in R [31] is also shown.
Mentions: A 109 nt consensus sequence was derived from the gamma LTR HMM. Transcription factor binding sites were sought with the MOTIF program. The consensus contains non-contiguous match states but this was taken into account by looking back at the Viterbi alignment of the training set. Only MOTIF matches which were contiguous were taken into account. The Viterbi alignment was visualised as a sequence logo (see Fig 3a). At position 87–101, a T-rich element is apparent. There is a clear AATAAA motif at position 69–74. Unlike HML LTRs, the distance between this box and the T-rich region is within the normal range (30–70 nt) [24]. Between them there are conserved A:s at position 85–86, probably poly(A) sites. For HERV-H, these putative poly(A) sites have been confirmed experimentally [56]. MOTIF predicts one TATA box at position 13–22 but another one is clear at position 27–32 (also found in the SuperViterbi alignment, see below). The second TATA box agrees well with experiments, for example in the case of gammaretroviruses (i.e. MLV and its relatives [57]), HERV-H [43] and HERV-I [58]. As mentioned in the introduction, ERV9 lacks a functional TATA box but has an AATAAA 28 nt upstream of the established transcription start site [21], which is Inr dependent. The transcription start site for HERV-H corresponds to GC/G at position 41–42 [43]. A conserved CCAAT-box between the TATA-boxes was also detected by MOTIF. The CCAAT-box is an upstream enhancer/promoter elements, common in vertebrate genes, recognised by the transcription factor NF-Y. It is located upstream of the TATA-box [59]. The found structure is consistent with the mammalian C-type LTR model of [6]. That model had a conserved hairpin loop in the R-region, also found in the MLV LTR (Fig 3b) by MFOLD (Fig S4). The gamma HMM consensus (Fig S5) also displays a shorter version of it. As in the HML case conserved G:s at position 41–45 bind to (less) conserved C(T):s at position 51–55 with the tip of the loop at position 47–49. This stem-loop has been studied in great detail for the MLV LTR [30], [31], [32] where it has been found important for RNA processing. As seen in fig 3b there are two other loops predicted in the R-U5 region of MLV.

Bottom Line: By combining all HMMs with a low cutoff, for screening, 71% of all LTRs found by RepeatMasker in chromosome 19 were found.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Sciences, Section of Virology, Uppsala University, Uppsala, Sweden.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus