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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 lenti HMM.A. Weblogo for a Viterbi alignment of the lentiviral LTR training set (“lenti”). Conventions are as in Fig 1. Conserved lentiviral landmarks (nef termination, TFBS and other characteristics of the proximal promoter), TATA and AATAAA boxes with their surroundings, TAR, the GT/CT rich stretch and a U5 portion which binds to integrase, are visible. B. RU5 of the HIV-1 hxb2 RNA sequence analysed with the lenti HMM. The conservation (upper case) of the crown and 3′ half of the tar stem loop, AATAAA and polyadenylation sites is shown.
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pone-0005179-g004: Outcome of the lenti HMM.A. Weblogo for a Viterbi alignment of the lentiviral LTR training set (“lenti”). Conventions are as in Fig 1. Conserved lentiviral landmarks (nef termination, TFBS and other characteristics of the proximal promoter), TATA and AATAAA boxes with their surroundings, TAR, the GT/CT rich stretch and a U5 portion which binds to integrase, are visible. B. RU5 of the HIV-1 hxb2 RNA sequence analysed with the lenti HMM. The conservation (upper case) of the crown and 3′ half of the tar stem loop, AATAAA and polyadenylation sites is shown.

Mentions: The lenti HMM scored highly with all lentiviral LTRs. The structure of the lentivirus LTRs is qualitatively similar to that of the gammaretroviruslike LTRs. The most notable features of the 190 nt consensus (see weblogo Fig 4a) are a TATA-box detected by MOTIF at position 44–58 and an AATAAA-box at position 118–123. When the HIV hxb2 sequence was run with the lenti HMM, only a few landmarks before TATA proved to be conserved. From 5′to 3′, two of three Sp1 repeats (SP1_1 and SP1_2), as well as a “CCC” stretch, both part of the proximal promoter were conserved. Accordingly, when the consensus sequences were analysed with MOTIF, a conserved GC box element was detected at position 18–31. The GC-box is an upstream promoter element recognised by the transcription factor Sp1. MFOLD on the consensus predicted two stable stem-loops in the R-region, one corresponding to the tar loop at position 67–95, where in HIV1 the loop apex is at 68–73 (CTGGGA), and the remaining residues constituting the downstream part of the stem; they form base-pairs with inserts that can not be seen in the consensus. The second stem-loop comprises the region at position 97–142 with the AATAAA motif in the loop (Fig 4b; cf Fig S6). A GT-rich area is also found at position 136–164. Several of these lentiviral conserved features were are also found in a study [7] which used different bioinformatical methods, and a less diverse sequence set.


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 lenti HMM.A. Weblogo for a Viterbi alignment of the lentiviral LTR training set (“lenti”). Conventions are as in Fig 1. Conserved lentiviral landmarks (nef termination, TFBS and other characteristics of the proximal promoter), TATA and AATAAA boxes with their surroundings, TAR, the GT/CT rich stretch and a U5 portion which binds to integrase, are visible. B. RU5 of the HIV-1 hxb2 RNA sequence analysed with the lenti HMM. The conservation (upper case) of the crown and 3′ half of the tar stem loop, AATAAA and polyadenylation sites is shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0005179-g004: Outcome of the lenti HMM.A. Weblogo for a Viterbi alignment of the lentiviral LTR training set (“lenti”). Conventions are as in Fig 1. Conserved lentiviral landmarks (nef termination, TFBS and other characteristics of the proximal promoter), TATA and AATAAA boxes with their surroundings, TAR, the GT/CT rich stretch and a U5 portion which binds to integrase, are visible. B. RU5 of the HIV-1 hxb2 RNA sequence analysed with the lenti HMM. The conservation (upper case) of the crown and 3′ half of the tar stem loop, AATAAA and polyadenylation sites is shown.
Mentions: The lenti HMM scored highly with all lentiviral LTRs. The structure of the lentivirus LTRs is qualitatively similar to that of the gammaretroviruslike LTRs. The most notable features of the 190 nt consensus (see weblogo Fig 4a) are a TATA-box detected by MOTIF at position 44–58 and an AATAAA-box at position 118–123. When the HIV hxb2 sequence was run with the lenti HMM, only a few landmarks before TATA proved to be conserved. From 5′to 3′, two of three Sp1 repeats (SP1_1 and SP1_2), as well as a “CCC” stretch, both part of the proximal promoter were conserved. Accordingly, when the consensus sequences were analysed with MOTIF, a conserved GC box element was detected at position 18–31. The GC-box is an upstream promoter element recognised by the transcription factor Sp1. MFOLD on the consensus predicted two stable stem-loops in the R-region, one corresponding to the tar loop at position 67–95, where in HIV1 the loop apex is at 68–73 (CTGGGA), and the remaining residues constituting the downstream part of the stem; they form base-pairs with inserts that can not be seen in the consensus. The second stem-loop comprises the region at position 97–142 with the AATAAA motif in the loop (Fig 4b; cf Fig S6). A GT-rich area is also found at position 136–164. Several of these lentiviral conserved features were are also found in a study [7] which used different bioinformatical methods, and a less diverse sequence set.

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