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

PLoS ONE

Volumn 4, Issue 4, 2009, Pages

  Benachenhou, Farid ^a   Jern, Patric ^a,c   Oja, Merja ^b   Sperber, Göran ^a   Blikstad, Vidar ^a   Somervuo, Panu ^b   Kaski, Samuel ^b   Blomberg, Jonas ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF HELSINKI   (Finland)

^c TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ARTICLE; CHROMOSOME 19; CONSENSUS SEQUENCE; CONTROLLED STUDY; GENE MUTATION; GENETIC CONSERVATION; HIDDEN MARKOV MODEL; LONG TERMINAL REPEAT; MOUSE MAMMARY TUMOR ONCOVIRUS; NONHUMAN; OPEN READING FRAME; RETROVIRUS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; TATA BOX; TRANSCRIPTION INITIATION SITE; VIRAL GENETICS; VIRUS GENOME; ALGORITHM; ANIMAL; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; HUMAN; HUMAN GENOME; MOLECULAR GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; OPOSSUM;

GIARDIA; VERTEBRATA;

VIRUS DNA;

ALGORITHMS; ANIMALS; BASE SEQUENCE; DNA, VIRAL; GENE EXPRESSION REGULATION, VIRAL; GENOME, HUMAN; GENOME, VIRAL; HUMANS; MICE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; OPOSSUMS; RETROVIRIDAE; SENSITIVITY AND SPECIFICITY; TERMINAL REPEAT SEQUENCES;

EID: 65249167467     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005179     Document Type: Article

References (79)

1. Jern P, Sperber GO, Blomberg J (2005) Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology 2: 50.
2. Katzourakis A, Tristem M, Pybus OG, Gifford RJ (2007) Discovery and analysis of the first endogenous lentivirus. Proc Natl Acad Sci U S A 104: 6261-6265.
3. Leib-Mosch C, Seifarth W, Schön U (2005) Influence of Human Endogenous Retroviruses on Cellular Gene Expression. Retroviruses and Primate Genome Evolution: Landes Bioscience.
4. Mager DL, Medstrand P (2003) Retroviral repeat sequences. Nature encyclopedia of the human genome. London, UK: Nature publishing group.
5. Quandt K, Frech K, Karas H, Wingender E, Werner T (1995) MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res 23: 4878-4884.
6. Blusch JH, Haltmeier M, Frech K, Sander I, Leib-Mosch C, et al. (1997) Identification of endogenous retroviral sequences based on modular organization: proviral structure at the SSAV1 locus. Genomics 43: 52-61.
7. Frech K, Brack-Werner R, Werner T (1996) Common modular structure of lentivirus LTRs. Virology 224: 256-267.
8. Frech K, Danescu-Mayer J, Werner T (1997) A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter. J Mol Biol 270: 674-687.
9. McCarthy EM, McDonald JF (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362-367.
10. Xu Z, Wang H (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35: W265-268.
11. Rho M, Choi JH, Kim S, Lynch M, Tang H (2007) De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics 8: 90.
12. Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, et al. (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 1: 166-175.
13. Kalyanaraman A, Aluru S (2006) Efficient algorithms and software for detection of full-length LTR retrotransposons. J Bioinform Comput Biol 4: 197-216.
14. Ellinghaus D, Kurtz S, Willhoeft U (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9: 18.
15. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
16. Bao Z, Eddy SR (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12: 1269-1276.
17. Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21 Suppl 1: i351-358.
18. Edgar RC, Myers EW (2005) PILER: identification and classification of genomic repeats. Bioinformatics 21 Suppl 1: i152-158.
19. Caspi A, Pachter L (2006) Identification of transposable elements using multiple alignments of related genomes. Genome Res 16: 260-270.
20. Sperber GO, Airola T, Jern P, Blomberg J (2007) Automated recognition of retroviral sequences in genomic data RetroTector(C). Nucleic Acids Res.
21. La Mantia G, Majello B, Di Cristofano A, Strazzullo M, Minchiotti G, et al. (1992) Identification of regulatory elements within the minimal promoter region of the human endogenous ERV9 proviruses: accurate transcription initiation is controlled by an Inr-like element. Nucleic Acids Res 20: 4129-4136.
22. Sjottem E, Anderssen S, Johansen T (1996) The promoter activity of long terminal repeats of the HERV-H family of human retrovirus-like elements is critically dependent on Sp1 family proteins interacting with a GC/GT box located immediately 3′ to the TATA box. J Virol 70: 188-198.
23. Anderssen S, Sjottem E, Svineng G, Johansen T (1997) Comparative analyses of LTRs of the ERV-H family of primate-specific retrovirus-like elements isolated from marmoset, African green monkey, and man. Virology 234: 14-30.
24. Colgan DF, Manley JL (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev 11: 2755-2766.
25. Guntaka RV (1993) Transcription termination and polyadenylation in retroviruses. Microbiol Rev 57: 511-521.
26. Andersson ML, Lindeskog M, Medstrand P, Westley B, May F, et al. (1999) Diversity of human endogenous retrovirus class II-like sequences. J Gen Virol 80 (Pt 1): 255-260.
27. Baust C, Seifarth W, Germaier H, Hehlmann R, Leib-Mosch C (2000) HERV-K-T47D-Related long terminal repeats mediate polyadenylation of cellular transcripts. Genomics 66: 98-103.
28. Ahmed YF, Gilmartin GM, Hanly SM, Nevins JR, Greene WC (1991) The HTLV-I Rex response element mediates a novel form of mRNA polyadenylation. Cell 64: 727-737.
29. Coffin J, Hughes S, Varmus H (1997) Tat, the Trans-activator of HIV. Retroviruses: Cold Spring Harbor Laboratory Press. pp 225-230.
30. Trubetskoy AM, Okenquist SA, Lenz J (1999) R region sequences in the long terminal repeat of a murine retrovirus specifically increase expression of unspliced RNAs. J Virol 73: 3477-3483.
31. Cupelli L, Okenquist SA, Trubetskoy A, Lenz J (1998) The secondary structure of the R region of a murine leukemia virus is important for stimulation of long terminal repeat-driven gene expression. J Virol 72: 7807-7814.
32. Cupelli LA, Lenz J (1991) Transcriptional initiation and postinitiation effects of murine leukemia virus long terminal repeat R-region sequences. J Virol 65: 6961-6968.
33. Pierce J, Fee BE, Toohey MG, Peterson DO (1993) A mouse mammary tumor virus promoter element near the transcription initiation site. J Virol 67: 415-424.
34. Kovalskaya E, Buzdin A, Gogvadze E, Vinogradova T, Sverdlov E (2006) Functional human endogenous retroviral LTR transcription start sites are located between the R and U5 regions. Virology 346: 373-378.
35. Briquet S, Vaquero C (2002) Immunolocalization studies of an antisense protein in HIV-1-infected cells and viral particles. Virology 292: 177-184.
36. Cavanagh MH, Landry S, Audet B, Arpin-Andre C, Hivin P, et al. (2006) HTLV-I antisense transcripts initiating in the 3′LTR are alternatively spliced and polyadenylated. Retrovirology 3: 15.
37. Dunn CA, Romanish MT, Gutierrez LE, van de Lagemaat LN, Mager DL (2006) Transcription of two human genes from a bidirectional endogenous retrovirus promoter. Gene 366: 335-342.
38. Leupin O, Attanasio C, Marguerat S, Tapernoux M, Antonarakis SE, et al. (2005) Transcriptional activation by bidirectional RNA polymerase II elongation over a silent promoter. EMBO Rep 6: 956-960.
39. Ludwig LB, Ambrus JL Jr, Krawczyk KA, Sharma S, Brooks S, et al. (2006) Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products. Retrovirology 3: 80.
40. Zhang Z, Kim E, Martineau D (1999) Functional characterization of a piscine retroviral promoter. J Gen Virol 80 (Pt 12): 3065-3072.
41. Domansky AN, Kopantzev EP, Snezhkov EV, Lebedev YB, Leib-Mosch C, et al. (2000) Solitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region. FEBS Lett 472: 191-195.
42. Christy RJ, Huang RC (1988) Functional analysis of the long terminal repeats of intracisternal A-particle genes: sequences within the U3 region determine both the efficiency and direction of promoter activity. Mol Cell Biol 8: 1093-1102.
43. Feuchter A, Mager D (1990) Functional heterogeneity of a large family of human LTR-like promoters and enhancers. Nucleic Acids Res 18: 1261-1270.
44. Rabiner L (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 77: 257-286.
45. Barton N, Briggs D, Eisen J, Goldstein D, Patel N (2007) Evolution: Cold Spring Harbor Laboratory Press.
46. Futuyma D (2005) Evolution. Sunderland, MA 01375: Sinauer. 603 p.
47. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, et al. (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351.
48. Durbin R, Eddy SR, Krogh A, Mitchison GJ (1998) Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge, UK: Cambridge University Press.
49. Blikstad V, Benachenhou F, Sperber GO, Blomberg J (2008) Endogenous retroviruses : Evolution of human endogenous retroviral sequences: a conceptual account. Cell Mol Life Sci 65: 3348-3365.
50. Andersson AC, Yun Z, Sperber GO, Larsson E, Blomberg J (2005) ERV3 and related sequences in humans: structure and RNA expression. J Virol 79: 9270-9284.
51. Oja M, Sperber GO, Blomberg J, Kaski S (2005) Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups. Int J Neural Syst 15: 163-179.
52. Jern P, Sperber GO, Ahlsen G, Blomberg J (2005) Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H. J Virol 79: 6325-6337.
53. Jern P, Sperber GO, Blomberg J (2004) Definition and variation of human endogenous retrovirus H. Virology 327: 93-110.
54. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.
55. Seifarth W, Baust C, Murr A, Skladny H, Krieg-Schneider F, et al. (1998) Proviral structure, chromosomal location, and expression of HERV-K-T47D, a novel human endogenous retrovirus derived from T47D particles. J Virol 72: 8384-8391.
56. Mager DL (1989) Polyadenylation function and sequence variability of the long terminal repeats of the human endogenous retrovirus-like family RTVL-H. Virology 173: 591-599.
57. Chen HR, Barker WC (1984) Nucleotide Sequences of the retroviral long terminal repeats and their adjacent regions. Nucleic Acids Research 12: 1767-1778.
58. Chang NT, Yang WK, Huang HC, Yeh KW, Wu CW (2006) The transcriptional activity of HERV-I LTR is negatively regulated by its cis-elements and wild type p53 tumor suppressor protein. J Biomed Sci.
59. Bucher P (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol 212: 563-578.
60. Coffin JM, Hughes SH, Varmus HE, eds (1997) Retroviruses. New York: Cold Spring Harbor Laboratory Press.
61. Karlin S (2005) Statistical signals in bioinformatics. Proc Natl Acad Sci U S A 102: 13355-13362.
62. Elisaphenko EA, Kolesnikov NN, Shevchenko AI, Rogozin IB, Nesterova TB, et al. (2008) A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. PLoS ONE 3: e2521.
63. Nesterova TB, Popova BC, Cobb BS, Norton S, Senner CE, et al. (2008) Dicer regulates Xist promoter methylation in ES cells indirectly through transcriptional control of Dnmt3a. Epigenetics Chromatin 1: 2.
64. Teodorovic S, Walls CD, Elmendorf HG (2007) Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome. Nucleic Acids Res 35: 2544-2553.
65. Coffin J, Hughes S, Varmus H (1997) Appendix 2. Retroviruses: Cold Spring Harbor Laboratory Press. pp 776-777.
66. Armour JA, Wong Z, Wilson V, Royle NJ, Jeffreys AJ (1989) Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements. Nucleic Acids Res 17: 4925-4935.
67. Kelly RG (1994) Similar origins of two mouse minisatellites within transposon-like LTRs. Genomics 24: 509-515.
68. Tek AL, Song J, Macas J, Jiang J (2005) Sobo, a recently amplified satellite repeat of potato, and its implications for the origin of tandemly repeated sequences. Genetics 170: 1231-1238.
69. Wolgamot G, Miller AD (1999) Replication of Mus dunni endogenous retrovirus depends on promoter activation followed by enhancer multimerization. J Virol 73: 9803-9809.
70. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D (1994) Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 235: 1501-1531.
71. Krogh A, Mitchison G (1995) Maximum entropy weighting of aligned sequences of proteins or DNA. Proc Int Conf Intell Syst Mol Biol 3: 215-221.
72. Brand M (1999) Structure Learning in Conditional Probability Models via an Entropic Prior and Parameter Extinction. Neural Comp 11: 1155-1182.
73. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
74. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5: 150-163.
75. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
76. Hall T (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
77. Zuker M, Mathews D, Turner D (1999) Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide in RNA biochemistry and biotechnology. Barciszewski JaC, BFC, ed. Kluwer Academic Publishers.
78. Heinemeyer T, Chen X, Karas H, Kel AE, Kel OV, et al. (1999) Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res 27: 318-322.
79. Lavrentieva I, Khil P, Vinogradova T, Akhmedov A, Lapuk A, et al. (1998) Subfamilies and nearest-neighbour dendrogram for the LTRs of human endogenous retroviruses HERV-K mapped on human chromosome 19: physical neighbourhood does not correlate with identity level. Hum Genet 102: 107-116.