Automated characterization of potentially active retroid agents in the human genome

Genomics

Volumn 85, Issue 4, 2005, Pages 512-523

  McClure, Marcella A ^a   Richardson, Hugh S ^a   Clinton, Rochelle A ^a   Hepp, Crystal M ^a   Crowther, Brad A ^a   Donaldson, Eric F ^b  

^a MONTANA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Endogenous retroviruses; Genome Parsing Suite software; Repetitive elements; Retroid; Retroposons; Retrotransposons

Indexed keywords

RNA DIRECTED DNA POLYMERASE;

ARTICLE; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC COMPLEMENTATION; HUMAN; HUMAN GENOME; MUTAGENESIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RIBOSOMAL FRAMESHIFTING; STATISTICAL SIGNIFICANCE; STOP CODON;

EID: 15244354523     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ygeno.2004.12.006     Document Type: Article

References (58)

1. J.L. Blond An envelope glycoprotein of the human endogenous retrovirus HERV-W is expressed in the human placenta and fuses cells expressing the type D mammalian retrovirus receptor J. Virol. 74 2000 3321 3329
2. S. Mi Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis Nature 403 2000 785 789
3. F. Mallet The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology Proc. Natl. Acad. Sci. USA 101 2004 1731 1766
4. L.C. Samuelson, K. Wiebauer, D.L. Gumcio, and M.H. Meisler Expression of the human amylase genes: recent origin of a salivary amylase promoter from an actin pseudogene Nucleic Acids Res. 16 1988 8261 8276
5. Z. Yang, D. Boffelli, N. Boonmark, K. Schwartz, and R. Lawn Apolipoprotein(a) gene enhancer resides within a LINE element J. Biol. Chem. 273 1998 891 897
6. P. Medstrand, J.R. Landry, and D.L. Mager Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans J. Biol. Chem. 276 2001 1896 1903
7. M.L. Pardue, O.N. Danilevskaya, K. Lowenhaupt, F. Slot, and K.L. Traverse Drosophila telomeres: new views on chromosome evolution Trends Genet. 12 1996 572 583
8. J.K. Moore, and J.E. Haber Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks Nature 383 1996 645 646
9. D. Kordis, and F. Gubensek Unusual horizontal transfer of a LINE element between distant vertebrate classes Proc. Natl. Acad. Sci. USA 95 1998 10704 10709
10. E.M. Ostertag, J.L. Goodier, Y. Zhang, and H.H. Kazazian Jr. SVA elements are nonautonomous retrotransposons that cause disease in humans Am. J. Hum. Genet. 73 2003 1444 1451
11. K. Yoshida, A. Nakamura, M. Yazaki, S. Ikeda, and S. Takeda Insertional mutation by transposable element, L1, in the DMD gene results in X-linked dilated cardiomyopathy Hum. Mol. Genet. 7 1998 1129 1132
12. K. Kobayashi An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy Nature 394 1998 388 392
13. C. Meischl, M. Boer, A. Ahlin, and D. Roos A new exon created by intronic insertion of a rearranged LINE-1 element as the cause of chronic granulomatous disease Eur. J. Hum. Genet. 8 2000 697 703
14. Y. Segal LINE-1 elements at the sites of molecular rearrangements in Alport syndrome-diffuse leiomyomatosis Am. J. Hum. Genet. 64 1999 62 69
15. C. Seidl An endogenous retroviral long terminal repeat at the HLA-DQB1 gene locus confers susceptibility to rheumatoid arthritis Hum. Immunol. 60 1999 63 68
16. C. Magistrelli Polymorphic genotypes of the HRES-1 human endogenous retrovirus locus correlate with systemic lupus erythematosus and autoreactivity Immunogenetics 49 1999 829 834
17. H. Karlsson Retroviral RNA identified in the cerebrospinal fluids and brains of individuals with schizophrenia Proc. Natl. Acad. Sci. USA 98 2001 4634 4639
18. M.A. McClure Evolution of retroposons by acquisition or deletion of retrovirus-like genes Mol. Biol. Evol. 8 1991 835 856
19. M.S. Johnson, M.A. McClure, D.F. Feng, J. Gray, and R.F. Doolittle Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes Proc. Natl. Acad. Sci. USA 83 1986 7648 7652
20. R.F. Doolittle, D.-F. Feng, M.S. Johnson, and M.A. McClure Origins and evolutionary relationships of retroviruses Q. Rev. Biol. 64 1989 1 30
21. L.A. Kohlstaedt, J. Wang, J.M. Friedman, P.A. Rice, and T.A. Steitz Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor Science 256 1992 1783 1790
22. H.M. Temin Reverse transcription in the eukaryotic genome: retroviruses, pararetroviruses, retrotransposons, and retrotranscripts Mol. Biol. Evol. 2 1985 455 468
23. H.M. Temin Retrons in bacteria Nature 339 1989 252 255
24. R. Hull Classifying reverse transcribing elements: a proposal and a challenge to the ICTV, International Committee on Taxonomy of Viruses Arch. Virol. 146 2001 2255 2261
25. M.A. McClure The retroid agents: disease, function, and evolution Origin and evolution of viruses 1999 Academic Press London 163 195
26. A.F. Smit Interspersed repeats and other mementos of transposable elements in mammalian genomes Curr. Opin. Genet. Dev. 9 1999 657 663
27. E.S. Lander Initial sequencing and analysis of the human genome Nature 409 2001 860 921
28. J.C. Venter The sequence of the human genome Science 291 2001 1304 1351
29. A.F.A. Smit, P. Green, http://ftp.genome.washington.edu/RM/RepeatMasker. html, 2002.
30. A. Perl Detection and cloning of new HTLV-related endogenous sequences in man Nucleic Acids Res. 17 1989 6841 6854
31. M.A. Martin, T. Bryan, S. Rasheed, and A.S. Khan Identification and cloning of endogenous retroviral sequences present in human DNA Proc. Natl. Acad. Sci. USA 78 1981 4892 4896
32. B. Liu Identification of a proviral structure in human breast cancer Cancer Res. 61 2001 1754 1759
33. O. Faff Retrovirus-like particles from the human T47D cell line are related to mouse mammary tumour virus and are of human endogenous origin J. Gen. Virol. 73 Pt 5 1992 1087 1097
34. J.V. Moran High frequency retrotransposition in cultured mammalian cells Cell 1996 917 927
35. D.M. Sassaman Many human L1 elements are capable of retrotransposition Nat. Genet. 16 1997 37 43
36. M.A. McClure, M.S. Johnson, D.F. Feng, and R.F. Doolittle Sequence comparisons of retroviral proteins: relative rates of change and general phylogeny Proc. Natl. Acad. Sci. USA 85 1988 2469 2473
37. W.R. Gish, http://blast.wustl.edu, 1996-2002.
38. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome Nature 431 2004 931 945
39. O. Poch, B.M. Blumberg, L. Bougueleret, and N. Tordo Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains J. Gen. Virol. 71 1990 1153 1162
40. M. Tristem Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database J. Virol. 74 2000 3715 3730
41. W. Seifarth HERV-IP-T47D, a novel type C-related human endogenous retroviral sequence derived from T47D particles AIDS Res. Hum. Retroviruses 16 2000 471 480
42. K. Banki Human T-cell lymphotropic virus (HTLV)-related endogenous sequence, HRES-1, encodes a 28-kDa protein: a possible autoantigen for HTLV-I gag-reactive autoantibodies Proc. Natl. Acad. Sci. USA 89 1992 1939 1943
43. B. Brouha Hot L1s account for the bulk of retrotransposition in the human population Proc. Natl. Acad. Sci. USA 100 2003 5280 5285
44. P.V. Baranov, R.F. Gesteland, and J.F. Atkins Recoding: translational bifurcations in gene expression Gene 286 2002 187 201
45. E.B. ten Dam, P.W. Verlaan, and C.W. Pleij Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: loop lengths and stability of the stem regions RNA 1 1995 146 154
46. R.F. Gesteland, and J.F. Atkins Recoding: dynamic reprogramming of translation Annu. Rev. Biochem. 65 1996 741 768
47. C.A. Theimer, and D.P. Giedroc Equilibrium unfolding pathway of an H-type RNA pseudoknot which promotes programmed -1 ribosomal frameshifting J. Mol. Biol. 289 1999 1283 1299
48. D. Dulude, M. Baril, and L. Brakier-Gingras Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1 Nucleic Acids Res. 30 2002 5094 5102
49. J. Paces HERVd: the Human Endogenous RetroViruses Database: update Nucleic Acids Res. 32 2004 D50 (database issue)
50. K. Hata, and Y. Sakaki Identification of critical CpG sites for repression of L1 transcription by DNA methylation Gene 189 1997 227 234
51. W. Wei Human L1 retrotransposition: cis preference versus trans complementation Mol. Cell. Biol. 21 2001 1429 1439
52. R. Belshaw Long-term reinfection of the human genome by endogenous retroviruses Proc. Natl. Acad. Sci. USA 101 2004 4894 4899
53. W.J. Kent The human genome browser at UCSC Genome Res. 12 2002 996 1006
54. S.F. Altschul Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
55. M.O. Dayhoff, R.M. Schwartz, and B.C. Orcutt A model of evolutionary change in proteins Atlas of protein sequence and structure vol. 5 1978 National Biomedical Research Foundation 345 352
56. M.A. McClure, and J. Kowalski The effects of ordered-series-of-motifs anchoring and sub-class modeling on the generation of HMMs representing highly divergent protein sequences Proc. Pac. Symp. Biocomput. 1999 162 170
57. M.A. McClure, and R. Raman Parameterization studies of Hidden Markov Models representing highly divergent protein sequences 28th Annual Hawaii International Conference on System Sciences, Kihei, HA 1995 184
58. M.A. McClure, J. Hudak, and J. Kowalski Low identity, low similarity protein sequences: independent modeling of the ordered-series-of-motifs and motif-intervening-regions Genome Inform. Ser. Workshop Genome Inform. 9 1998 183 192