Эволюционный анализ длинных концевых повторов эндогенных ретровирусов генома человека
Диссертация
Целью данной работы является изучение последовательностей длинных концевых повторов (Long Terminal Repeat — LTR) эндогенных ретровирусов человека семейства HERV-K10 (HML-2), анализ их распределения в геноме человека и характеристика геномного окружения мест внедрения этих последовательностей. Выбор данного объекта исследования был продиктован широкой представленностью этих последовательностей… Читать ещё >
Содержание
- 1. Введение
- 2. Обзор литературы
- 2. 1. Краткая история изучения ретровирусов б
- 2. 2. Структура и жизненный цикл ретровирусов
- 2. 3. Ретроэлементы: происхождение, типы и структура
- 2. 4. Интеграция ретровирусов в геном клетки-хозяина
- 2. 5. Классификация ретровирусов
- 2. 6. Классификация HERV
- 2. 7. Биологическое значение ретроэлементов и эндогенных ретровирусов
- 2. 8. Длинные концевые повторы и их локализация в геноме
- 2. 9. Семейство HERV-K10 (HML-2)
- 3. Алгоритмы и методы
- 3. 1. Получение предварительной выборки последовательностейИР
- 3. 2. Классификация последовательностей
- 3. 3. Составление базы данных длинных концевых повторов
- 3. 4. Анализ геномного окружения
- 4. Результаты и обсуждение
- 4. 1. Распределение последовательностей LTR по хромосомам
- 4. 2. Распределение последовательностей в пределах каждой из хромосом
- 4. 3. Анализ геномного окружения
- 4. 3. 1. Сегменты по Гимза
- 4. 3. 2. Анализ локального GC-состава, характеризующего места локализации исследуемых последовательностей
- 4. 3. 3. Протяженные участки синтении геномов человека и
- 4. 3. 4. Частота однонуклеотидных полиморфизмов
Список литературы
- Льюин, Б. (1987) Гены. Мир
- Свердлов, Е.Д. (1999) Ретровирусные регуляторы экспрессии генов в геноме человека как возможные факторы его эволюции. Биоорг. Хим., т.25, 821−827
- Хесин, Р.Б. (1984) Непостоянство генома. Наука
- Хиль, П.П., Лебедев Ю. Б. и Свердлов Е.Д. (1997) Подсемейства длинных концевых повторов (LTR) человеческих эндогенных ретровирусов типа HERV-K. Доклады Академии наук, т.356, 833−837.
- Хиль, П.П., Лебедев Ю. Б. и Свердлов Е.Д. (1998) Длинный концевой повтор эндогенного ретровируса HERV-K в интроне гена ZNF91. Биоорганическая химия, т.24, 126−131.
- Akopov, S.B., Nikolaev, L.G., Khil, P.P., Lebedev, Y.B., and Sverdlov, E.D. (1998) Long terminal repeats of human endogenous retrovirus К family (HERV-K) specifically bind host cell nuclear proteins. FEBS Lett., v.421, 229−233
- Anderssen S, Sjottem E, Svineng G, Johansen T. «Comparative analyses of LTRs of the ERV-H family of primate-specific retrovirus-like elements isolated from marmoset, African green monkey, and man.» Virology, 1997 Jul 21−234(1):14−30
- Andersson, G., Svensson, A.-C., Setterblad, N., and Rask, L. (1998) Retroelements in the human MHC class II region. Trends in Genetics, v. 14, 109 115
- Andersson, M.-L., Lindeskog, M., Medstrand, P., Westley, В., May, F., and Blomberg, J. (1999) Diversity of human endogenous retrovirus class ll-like sequences. J. Gen. Virol., v.80, 255−260
- H.Baban, S., Freeman, J.D. and Mager, D.L. (1996) Transcripts from a novel human KRAB zinc finger gene contain spliced Alu and endogenous retroviral segments. Genomics, v.33, 463−72
- Baldo, A.M. and McClure, M.A. (1999) Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts. J. Virol., v.73, 7710−7721.
- Benit, L., Lallemand, J.-B., Casella, J.-F., Philippe, H., and Heidmann, T. (1999) ERV-L elements: a family of endogenous retrovirus-like elements active throughout the evolution of mammals. J. Virol., v.73, 3301−3308
- Bieda, K., Hoffmann, A., and Boiler, K. (2001)Phenotypic heterogeneity of human endogenous retrovirus particles produced by teratocarcinoma cell lines. J. Gen. Virol., v.82, 591−596
- Bonner, T.I., O’Connell, C., and Cohen, M. (1982) Cloned endogenous retroviral sequences from human DNA. PNAS USA, v.79, 4709−4713
- Boiler, K., Konig, M., Sauter M., Mueller-Lantzsch N., Lower, R., Lower J., and Kurth, R. (1993) Evidence that HERV-K is endogenous retrovirus sequence that codes for the human teratocarcinoma-derived retrovirus HTDV. Virology, v. 196, 349−353
- Casau, A.E., Vaughan, J.E., Guillermina, L., and Levine, A. (1999) Germ cell expression of an isolated human endogenous retroviral long terminal repeat of the HERV-K/HTDV family in transgenic mice. J. Virol., v.73, 9976−9983
- Christy, R.J. and Huang, R.C. (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., v.8, 1093−1102
- Cianciolo, G.J., Copeland, T.D., Oroszlan, S. and Snyderman, R. (1985) Inhibition of lymphocyte proliferation by a synthetic peptide homologous to retroviral envelope proteins. Science, v.230, 453−455
- Clay O, Bernardi G. (2002) Isochores: dream or reality? Trends Biotechnol, v.20(6), 237
- Conrad, В., Weissmahr, R.N., Boni, J., Arcari, R., Schupbach, J., and Mach, B. (1997) A Human endogenous retroviral superantigen as candidate autoimmune gene in type I diabetes. Cell, v.90, 303−313
- DeLuca, C., Kwon, H., Lin, R., Wainberg, M., and Hiscott, J. (1999) NF-kB activation and HIV-1 induced apoptosis. Cytokine and GF Rev., v.10, 235−253
- Eisfeld, K., Candau, R., Truss, M. and Beato, M. (1997) Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1. Nucl. Acids Res., v.25, 3733−3742
- Felsenstein, J. (1993) PHYLIP version 3.5c. Distributed by the author. Based program in Felsenstein, J. (1989) PHYLIP Phylogeny Inference Package. Cladistics, v.5, 164−166.
- Feuchter, A. and Mager, D. (1990) Functional heterogeneity of a large family of human LTR-like promoters and enhancers. Nucl. Acids Res., v. 18, 1261−1270
- Friesen, P. D" Rice, W. C" Miller, D. W" and Miller, L. K. (1986) Bidirectional transcription from a solo long terminal repeat of the retrotransposon TED: symmetrical RNA start sites. Mol. Cell. Biol., v.6, 1599−1607
- Gotzinger, N., Sauter. M., Roemer, K., and Mueller-Lantzsch, N. (1996) Regulation of endogenous retrovirus-K Gag expression in teratocarcinoma cell lines and human tumours. J. Gen. Virol., v.77, 2983−2990
- Guntaka, R.V. (1993) Transcription termination and polyadenylation in retroviruses. Microbiol. Rev., v.57, 511−521
- Harris, J. R. (1998) Placental endogenous retrovirus (ERV): structural, functional, and evolutionary significance. Bioessays 20, 307−316
- Herniou, E., Martin, J., Miller, K., Cook, J., Wilkinson, M., and Tristem, M. (1998) Retroviral diversity and distribution in vertebrates. J.Virol., v.12, 5955−5966
- Hohenadl, C., Leib-Mosch, C., Hehlmann, R. and Erfle, V. (1996) Biological significance of human endogenous retroviral sequences. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol., v. 13, Suppl.1, 268−273
- Hull, R. (2001) Classifying reverse transcribing elements: a proposal and a challenge to the ICTV. Virology Division News, v. 146, 2255−2261
- Indraccolo, S., Gunzburg, W. H., Leib-Mosch, C., Erfle, V., and Salmons, B. (1995) Identification of three human sequences with viral superantigen-specific primers. Mamm. Genome, v.6, 339−44
- International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, v.409, 860−921
- Johnson W.E. and Coffin J.M. «Constructing primate phylogenies from ancient retrovirus sequences.», PNAS, 1999, 96(18): 10 254−60
- Jurka, J. (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. PNAS USA, v.94, 1872−1877
- Kidwell M.G. and Lisch D. «Transposable elements as sources of variation in animals and plants.», 1997, PNAS, 94(15):7704−11.
- Kingsman, S.M. and Kingsman, A.J. (1996) The regulation of human immunodeficiency virus type-1 gene expression. Eur. J. Biochem., v.240, 491 507
- Knossl, M., Lower, R., and Lower, J. (1999) Expression of the human endogenous retrovirus HTDV/HERV-K Is enhanced by cellular transcription factor YY1. J.Virol., v.73, 1254−1261
- Kongsuwan, K., Allen, J., and Adams, J.M. (1989) Expression of Hox-2.4 homeobox gene directed by proviral insertion in a myeloid leukemia. Nucl. Acids Res., v.17, 1881−1892
- Kowalski, P.E. and Mager, D.L. (1998) A human endogenous retrovirus suppresses translation of an associated fusion transcript, PLA2L. J. Virol., v.72, 6164−6168
- Lander, E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature, v.409, 860−921
- Lebedev, Y. В., Volik, S. V., Obradovic, D., Ermolaeva, O. D., Ashworth, L. K., Lennon, G. G. and Sverdlov, E. D. (1995) Physical mapping of sequenceshomologous to an endogenous retrovirus LTR on human chromosome 19. Mol. Gen. Genet., v.247, 742−748
- Leib-Mosch, C., Bachmann, M., Brack-Werner, R., Werner, Т., Erfle, V., and Hehlmann, R. (1992) Expression and biological sugnificance of human endogenous retroviral sequences. Leukemia, v.6, Suppl.3, 72−75
- Leib-Mosch, C. and Seifarth, W. (1996) Evolution and biological significance of human retroelements. Virus Genes, v.11, 133−145
- Lindeskog M (1999) Doctoral Dissertation. Transcription, splicing and genetic structure within the human endogenous retroviral HERV-H family.
- Linial, M. (2000) Why aren’t foamy viruses pathogenic? Trends in Microbiology, v.8.6, 284−289
- Lower, R., Lower, J., and Kurth, R. (1996) The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. PNAS USA, v.93, 5177−5184
- Lower, R. (1999) The pathogenic potential of endogenous retroviruses: facts and fantasies. Trends in Microbiology, v.7.9, 350−356
- Mager, D.L. and Freeman, J.D. (1995) HERV-H endogenous retroviruses: presence in the New World branch but amplification in the Old World primate lineage. Virology, v.213, 395−404
- Mager, D.L., Hunter, D.G., Schertzer, M., and Freeman, J.D. (1999) Endogenous retroviruses provide the primary polyadenylation signal for two new human genes (HHLA2 and HHLA3). Genomics, v.59, 255−263
- Mariani-Costantini R, Horn TM, Callahan R. «Ancestry of a human endogenous retrovirus family.» J Virol., 1989 Nov-63(11):4982−5
- Martin, J., Herniou, E., Cook, J., O’Neill, R.W., and Tristem, M. (1997) Human endogenous retrovirus type l-related viruses have an apparently widespread distribution within vertebrates. J. Virol., v.71, 437−443
- Martin, M.A., Bryan, Т., Rasheed, S., and Khan, A.S. (1981) Identification and cloning of endogenous retroviral sequences present in human DNA. PNAS USA, v.78, 4892−4896
- Mayer, W.E., O’hUigin, C" and Klein, J. (1993) Resolution of the HLA-DRB6 puzzle: a case of grafting a de novo-generated exon on an existing gene. PNAS USA, v.90, 10 720−10 724
- Medstrand, P. and Mager, D.L. (1998) Human-specific integrations of the HERV-K endogenous retrovirus family. J. Virol., v.72, 9782−9787
- Medstrand, P., Mager, D.L., Yin, H., Dietrich, U., and Blomberg, J. (1997) Structure and genomic organization of a novel human endogenous retrovirus family: HERV-K (HML-6). J. Gen. Virol., v.78, 1731−1744
- Qin, W., Golovkina, T.V., Peng, Т., Nepomnaschy, I., Buggiano, V., Piazzon, I., and Ross, S.R. (1999) Mammary gland expression of mouse mammary tumorvirus is regulated by a novel element in he long terminal repeat. J. Virol., v.73, 368−376
- Ramakrishman, C., Robins, D.M. Steroid hormone responsiveness of a family of closely related mouse proviral elements. Mammalian Genome, v.8, 811−817 (1997).
- Reus, K., Mayer, J., Sauter, M., Zischler, H., Muller-Lantzsch, N., and Meese, E. (2001)HERV-K (OLD): ancestor sequences of the Human Endogenous Retrovirus family HERV-K (HML-2). J. Virol., v.75, 8917−8926
- Ruddell, A. (1995) Transcription regulatory elements of the avian retroviral long terminal repeat. Virology, v.206, 1−7
- Rynditch, A.V., S. Zoubak, L. Tsyba, N. Tryapitsina-Guley, and G. Bernardi (1998) The regional integration of retroviral sequences into the mosaic genomes of mammals. Gene, v.222, 1−16
- Stoye, J. (2001) Endogenous retrovirus: still active after all these years? Current Biology, v.11 R914-R916
- Strazzullo, M., Majello, В., Lania, L., and La Mantia, G. (1994) Mutational analysis of the human endogenous ERV9 proviruses promoter region. Virology, v.200, 686−695
- Strazzullo, M., Parisi, Т., Di Cristofano, A., Rocchi, M., La Mantia, G. (1998) Characterization and genomic mapping of chimeric ERV9 endogenous retroviruses-host gene transcripts. Gene, v.206, 77−83
- Sverdlov, E.D. (1998) Perpetually mobile footprints of ancient infections in human genome. FEBS Letters, v.428, 1−6
- Sverdlov, E.D. (2000) Retroviruses and primate evolution. Bioessays, v.22, 161 171
- Temin, H.M. (1971) The protovirus hypothesis: speculations on the significance of RNA-directed DNA synthesis for normal development and for carcinogenesis. J. Natl. Cancer Inst., v.46, 3−7
- Thomas, M.J. and Seto, E. (1999) Unlocking the mechanisms of transcription factor YY1: are chromatin modifying enzymes the key? Gene, v.236, 197−208
- Tonjes, R.R., Czauderna, F., and Kurth, R. (1999) Genome-wide screening, cloning, chromosomal assignment, and expression of full-length human endogenous retrovirus type K. J. Virol., v.73, 9187−9195
- Tristem, M. (2000) Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database. J Virol., v.74, 3715−3730
- Turner, G., Barbulescu, M., Su, M., Jensen-Seaman, M.I., Kidd, K.K., Lenz, J. Insertional polymorphisms of full-length endogenous retroviruses in humans. Current Biology, v.11, 1531−1535 (2001).
- Urnovitz, H.B. and Murphy, W.H. (1996) Human endogenous retroviruses: nature, occurrence, and clinical implications in human disease. Clin. Microbiol. Rev., v.9, 72−99
- Wilkinson, D.A., Mager, D.L., and Leong, J.C. (1994) Endogenous human retroviruses. In The Retroviridae, v.3, 465−535. Edited by J. A. Levy. New York, N. Y.: Plenum Press
- Yoder, J.A., Walsh, C.P., and Bestor, Т.Н. (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet., v. 13, 335−340
- Zhou, H., Rainey, J., Wong, S.-K., and Coffin, J.M. (2001) Substrate sequence selection by retroviral integrase. J. Virol., v.75, 1359−1370
- Zoubak S, Clay O, Bernardi G. (1996) The gene distribution of the human genome. Gene, v. 174, 95−102