Эволюционный анализ локусов генома приматов, содержащих гибридные эндогенные ретровирусные элементы семейств HERV-H/HERV-K
Диссертация
Любые исследования диспергированных повторов начинаются d идентификации их копий в геноме, выведения консенсусной последовательности с выделением подсемейств и подгрупп и установления филогенетических взаимосвязей между ними. На основании таких исследований, наряду с встречаемостью членов семейств ТЕ у различных организмов можно сделать выводы о времени и пути появления этих элементов в геноме… Читать ещё >
Содержание
- Роль повторяющейся геномной ДНК в эволюции живых организмов
- Мобильные элементы генома: паразиты или симбионты?
- Эндогенные ретровирусы и эволюция генома приматов. экспериментальная часть
- Материалы
- Оборудование и расходные материалы
- Среды и растворы
- Методы.¡
- Выделение ДНК рекомбинантных космид
- Рестрикция космидной ДНК
- Электрофорез в агарозном геле
- Гибридизация по Саузерну
- Очистка олигонуклеотидных праймеров
- Полимеразная цепная реакция
- Селективная РСЯ-амп.'шфикация с использованием эффекта РСИ-супрессии
- Выделение фрагментов ДНК из легкоплавкой агарозы
- Определение первичной структуры ДНК
- Выделение геномной ДНК.1. результаты экспериментов и их обсуждение
- Идентификация Н/К гибрида в локусе 19р12 генома человека
- Полногеномный поиск гибридных ретровирусных элементов НЕКУ-К/НЕ11У-Н семейств
- Характеристика и анализ последовательностей гибридных ретровирусных элементов
- Филогенетический анализ локусов, содержащих гибридные ретровирусные элементы
- Взаимная локализация гибридных ретровирусных элементов и известных или кандидатных генов
- Выводы
Список литературы
- Lander E.S. et al. «Initial sequencing and analysis of the human genome», Nature. 2001, 409:860−921
- Kidwell M.G., Lisch D. " Transposable elements as sources of variation in animals and plants. «, 1997, PNAS, 94(15):7704−11. I
- Deininger P.L., Batzer M.A., Hutchison C.A., III& Edgell M.H. „Master genes in mammalian repetitive DNA amplification“. Trends Genet, 1992, 8:307−311
- Jurka J. » Repeats in genomic DNA: mining and meaning."См/т О pin Struct Biol. 1998, 8(3):333−7 !
- Ohshima K., Hamada M., Terai Y., Okada N. «The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements.» Mol Cell Biol., 1996, 16(7):3756−64 j
- Jurka J. " Sequence patterns indicate an en2yinatic involvement in integration of mammalian retroposons", PNAS, 1997, 94, pp. 1872−1877. !
- Brosius. J «Genomes were forged by massive bombardments with retroelements and retrosequences.», Genetica, 1999−107(l-3):209−38.
- Spradling A.C., Stern D.M., Kiss I., Roote J., Laverty Т., Rubin G.M. «Gene disruptions using P transposable elements: an integral component of the Drosophila genome project.» PNAS, USA, 1995,92(24): 10 824−30.
- Ji H., Moore D.P., Blomberg M.A., Braitennan L.T., Voytas D.F., Natsoulis G., Boeke J.D. «Hotspots for unselected Tyl transposition events on yeast chromosome III are near tRNA genes and LTR sequences.» Cell, 1993, 73(5): 1007−18
- Jurka J. & Kapitonov V. «Sectorial mutagenesis by transposable elements». Genetica, 1999, 107: 239−248 j
- Rabinowicz P.D., Schutz K" Dedhia N" Yordan C" Parnell L.D., Stein L. j McCombie W.R., Martienssen R.A. «Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. „Nat Genet, 1999,23(3):305−8 j
- Bird A. „Does DNA methyilation control transposition of selfish elements in germ line?“, Trends Genet, 1997, 13(12):471−2
- Hartzog G.A., Wada T., Handa H“ Winston F. „Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II Saccharomyces cerevisiae.“ Genes Dev. 1998, 12(3):357−69
- Gdula D.A., Gerasimova T.I., Corces V.G."Genetic and molecular analysis of the gypsy chromatin insulator of Drosophila», PNAS, USA, 1996, 93(18):9378−83
- Martienssen R. «Transposons, DNA methylation and gene control.» Trends Genet, 1998, 14(7):263−4 i
- Kermekchiev M., Pettersson M., Matthias P., Schaffner W. «Every enhancer works with every promoter for all the combinations tested: could new regulatory pathways evolve by enhancer shuffling?» Gene Expr., 1991, 1(1):71−81.
- Kowalski P.E., Mager D.L. «A human endogenous retrovirus suppresses translation of an associated fusion transcript, PLA2L.», J Virol, 1998, 72(7):6164−8.
- Hansen J. D, McBlane J.F." Recombination-activating genes, transposition, and the lymphoid-specific combinatorial system: a common evolutionary connection.", Curr Top Microbiol Immunol., 2000−248:111−35.
- Sadofsky MJ." The RAG proteins in V (D)J recombination: more than just a nuclease.", Nucleic Acids Res, 2001 Apr 1−29(7): 1399−409
- Chu WM, Ballard R, Carpick BW, Williams BR, Schmid CW. «Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR „, Mol Cell Biol, 1998, 18(l):58−68 |
- Agrawal A., Eastman Q.M. & Schatz D.G. „Implications of transposition mediated by V (D) J-recombination proteins RAG1 and RAG2 for origins of antigen-specific immunity“, Nature, 1998, 394(6695):744−51″
- Rowold DJ, Herrera RJ. „Alu elements and the human genome.“, Genetica, 2000−108(l):57−72 j
- Thompson C. B. „New insights into V(D)J recombination and its role in the! evolution of the immune system.“ Immunity, 1995,3, 531−539 I
- Hakim I, Amariglio N, Grossman Z, Simoni-Brok F, Ohno S, Rechavi G. „The genome of the THE I human transposable repetitive elements is composed of a basic motif homologous to an ancestral immunoglobulin gene sequence“, PNAS, 1994, 91:7967−9
- Trabesinger-Ruef N., Jermann T., Zankel T., Durrant B., Frank G., Benner S.A. „Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function?“, FEBS Lett, 1996, 382(3):319−22.
- Koch, A.L. „Enzyme evolution: I. The importance of untranslatable intermediates.“ Genetics, 1972, 72:297−316.
- Ulloa-Aguirre A., Stanislaus D., Janovick J.A., Conn P.M. „Structure-activity relationships of G protein-coupled receptors“, Arch Med Res., 1999 Nov-Dec-30(6):420−35.
- Lundblad V. „Telomerase catalysis: A phylogenetically conserved reverse transcriptase“, PNAS, 1998, 95:8415−8416
- Eickbush T. H. “ Telomerase and Retrotransposons: Which Came First?», Science, 1997, 277(5328):911−2.
- Wolffe A.P. & Matzke M.A. «Epigenetics: regulation through repression», Science) 1999, 286(5439):481−6 —
- Lee JT, Jaenisch R."Long-range cis effects of ectopic X-inactivation centres on a mouse autosome.", Nature, 1997 Mar 20−386(6622):275−9.
- Brockdorff, N. «The role of Xist in X-inactivation.», Curr Opin Genet Dev, 1998, 8(3):328−33
- Lyon M.F. «LINE-1 elements and X chromosome inactivation: a function for „junk“ DNA?», PNAS, 2000, 97: 6248−9
- Bailey, J. A., Carrel, L., Chakravaiti, A. &Eichler, E. E. «From the cover: molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis.», PNAS, 2000, 97:6634−6639 i
- Graves, J. A. M., Disteche, C. M. & Toder, R. «Gene dosage in the evolution and function of mammalian sex chromosomes. „, Cytogenet. Cell Genet, 1998, 80:94 103
- Lahn, B. T. & Page, D. C. „Four evolutionary stratagies on the human X chromosome. Science, 1999, 286:964−967
- Shapiro J.A.. „Transposable elements as the key to a 21st century view of evolution.“, Genetica, 1999, 107(1−3): 171−9
- Deininger P.L., Batzer M.A. „Alu repeats and human disease.“, Mol Genet Metab, 1999, 67(3): 183−93
- McClintock B., „Intranuclear systems controlling gene action and mutation.“ Brookhaven Symp. Biol, 1956, 8:58−74
- McClintock, B. „The control of gene action in maize.“, Brookhaven Symp. Biol., 1965, 18:162−184
- Liu WM, Chu WM, Choudary PV, Schmid CW. „Cell stress and translation. inhibitors transiently increase the of mammalian SINE transcripts.“, Nucleic Acids Res, 1995 May 25−23(10): 1758−65
- Kapitonov V. & Jurka J. „MER53, a non-autonomous DNA transposon associated with a variety of functionally related defense genes in the human genome.“, 1998, DNA Sequence, 8: 277−288.
- Ryskov, A.P., P.L. Ivanov, D.A. Kramerov & G.P. Georgiev. „Universal orientation and 3 0 -terminal localization of repeated sequences in the B2 family of mRNA.“ Mol. Biol. Mosk., 1984, 18: 92−103.
- Hillis D. M. „SINEs of the perfect character.“ PNAS, 1999, 96:9979−9981
- Toda Y., Tomita M. „Alu elements as an aid in deciphering genome rearrangements.“ Gene, 1997, 205:173−176
- Jurka J. and Milosavljevic A. „Reconstruction and analysis of human Alu genes. „, J. Mol Evol., 1991, 32:105−121
- Wilkinson DA, Mager DL and Leong JAC. „Endogenous human retroviruses.“ p.465−535, in J.A.Levy (ed.), (1994), The Retroviridae, vol.3, Plenum Press, New York.
- Naldini L., Blomer U., Gage F.H., Trono D., Verma I.M. „Efficient transfer, integration, and sustained long-term expression of the transgene in adult rat brains injected with a lentiviral vector.“, PNAS, 1996, 93(21): 11 382−8.
- Tacke S.J., Kurth R, Denner J. „Porcine endogenous retroviruses inhibit human immune cell function: risk for xenotransplantation?“, Virology, 2000, 268(l):87−93.
- Lower R. „The pathogenic potential of endogenous retroviruses: facts and fantasies.“ Trends Microbiol., 1999, 7(9):350−6
- Krieg A.M., Gourley M.F., Perl A.“ Endogenous retroviruses: potential etiologic agents in autoimmunity.“, FASEBJ., 1992, 6(8):2537−44
- Fujinami R.S. and Libbey J.E. „Endogenous retroviruses: are they the cause of multiple sclerosis? „, Trends Microbiol, 1999, 7(7):263−264 !
- Lower R., Lower J., Kurth R. „The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences.“, PNAS. 1996, 93(11):5177−84
- Tristem M. „Identification and characterization of novel human endogenous families by phylogenetic screening of the human genome mapping database.“, J Virol, 2000 Apr-74(8):3715−30
- Li MD, Bronson DL, Lemke TD, Faras AJ. „Restricted expression of new HERV-K members in human teratocarcinoma cells.“ Virology, 1995, 208(2):733−41.
- Lower R, Boller K, Hasenmaier B, Korbmacher C, Muller-Lantzsch N, Lower jj Kurth R. „Identification of human endogenous retroviruses with complex m RNA expression and particle formation.“ Proc Nail Acad Sei USA, 1993, 90(10):4480−4.
- Leib-Mosch C., Seifarth W. „Evolution and biological significance of human retroelements.“, Virus Genes, 1996, 11(2−3): 133−45
- Patience C., Wilkinson D.A., Weiss R.A. “ Our retroviral heritage. „, Trends GenetJ 1997, 13(3): 116−20
- Seperack PK, Mercer JA, Strobel MC, Copeland NG, Jenkins NA. „Retroviral sequences located within an intron of the dilute gene alter dilute expression in a tissue-specific manner.“ EMBO J., 1995 May 15−14(10):2326−32.
- Sverdlov E.D. “ Perpetually mobile footprints of ancient infections in human genome. „, FEES Lett., 1998, 428(1−2): 1−6 1
- Ting CN, Rosenberg MP, Snow CM, Samuelson LC, Meisler MH. „Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene.“ Genes Dev., 1992 Aug-6(8): 1457−65.
- Tiedge H, Chen W, Brosius J.“ Primary structure, neural-specific expression, and dendritic location of human BC200 RNA.“, JNeurosci, 1993 Jun-13(6):2382−90
- Brosius J. „RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements.“ Gene, 1999 Sep 30−238(1):115−34.
- Knossl M, Lower R, Lower J. „Expression of the human endogenous retrovirus HTDV/HERV-K is enhanced by cellular transcription factor YY1.“ J Virol., 1999 Feb-73(2): 1254−61.
- Goodchild NL, Wilkinson DA, Mager DL. „A human endogenous long terminal repeat provides a polyadenylation signal to a novel, alternatively spliced transcript in normal placenta.“ Gene, 1992 Nov 16- 121(2):287−94.i i
- Ono M, Kawakami M, Ushikubo H. „Stimulation of expression of the humari endogenous retrovirus genome by female steroid hormones in human breast cancer cell line T47D.“ J Virol., 1987 Jun-61(6):2059−62.
- Kapitonov V. V., Jurka J. “ The long terminal repeat of an endogenous retrovirus induces alternative splicing and encodes an additional carboxy-terminal sequence iri the human leptin receptor. „, J. Mol. Evol., 1999, 48(2): 248−51.
- Mager D. L., Hunter D. G., Schertzer M., Freeman J. D.“ Endogenous retroviruses provide the primary polyadenylation signal for two new human genes (HHLA2 and HHLA3).“, Genomics, 1999, 59(3):255−63.
- Schulte A.M., Lai S» Kurtz A., Czubayko F., Riegel A.T., Wellstein A. «Human trophoblast and choriocarcinoma expression of the growth factor pleiotrophin attributable to germ-line insertion of an endogenous retrovirus.», PNAS, 1996- 93(25): 14 759−64
- Harris J.R. " Placental endogenous retrovirus (ERV): structural, functional, and evolutionary significance. «, Bioessays, 1998, 20(4):307−16
- Boyd M.T., Bax C.M., Bax B.E., Bloxam D.L., Weiss R.A. „The humanjendogenous retrovirus ERV-3 is upregulated in differentiating placental trophoblast cells. „, Virology, 1993, 196(2):905−9
- Schommer S, Sauter M, Krausslich HG, Best B, Mueller-Lantzsch Ni „Characterization of the human endogenous retrovirus К proteinase.“ J Gen Virol., 1996 Feb-77 (Pt 2):375−9. J
- Mi S., Lee X., Li X., Veldman G.M., Finnerty H“ Racie L“ LaVallie E» Tang X.Y., Edouard P., Howes S., Keith J.C. Jr., McCoy J.M. «Syncytin is a captive retroviral envelope protein involved in human placental moiphogenesis. „, Nature, 2000, 403:785−789
- Berkhout B., Jebbink M., Zsiros J. “ Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus. J Virol., 1999, 73(3):2365−2375
- Shih A., Coutavas E.E., Rush M.G. » Evolutionary implications of primate endogenous retroviruses. «, Virology, 1991, 182(2):495−502
- Mariani-Costantini R, Horn TM, Callahan R. „Ancestry of a human endogenous retrovirus family.“ J Virol, 1989 Nov-63(l l):4982−5.i
- Faff 0., Murray A.B., Schmidt J., Leib-Mosch C» Erfle V., Hehlmann R. «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, 1992, 73 (Pt 5): 1087−97
- Sverdlov E.D. » Retroviruses and primate evolution. «, BioEssccys, 2000, 22:161−171
- Lebedev Y.B., Belonovitch O.S., Zybrova N.V., Khil P.P., Kurdyukovj
- S.G., Vinogradova T.V., Hunsmann G» Sverdlov E.D. «Differences in HERV-K LTR insertions in orthologous loci of humans and great apes. «, Gene, 2000, 247(l-2):265−77
- Medstrand P., Mager D.L. «Human-specific integrations of the HERV-K endogenous retrovirus family.», J Virol, 1998, 72(12):9782−7
- Kim H.S., Wadekar R.V., Takenaka 0., Hyun B.H., Crow T.J. «Phylogenetic analysis of a retroposon family in african great apes. «, J Mol Evol, 1999, 49(5):699−702 j
- Barbulescu M., Turner G., Seaman M.I., Deinard A.S., Kidd K.K., Lenz J. » Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans. «, C. urr Biol, 1999, 9(16):861−8
- Mayer J., Sauter M., Racz A., Scherer D., Mueller-Lantzsch N., Meese E. «An almost-intact human endogenous retrovirus K on human chromosome 7. «, Nat Genei, 1999, 21(3):257−8
- Tonjes R.R., Czauderna F., Kurth R. » Genome-wide screening, cloning, chromosomal assignment, and expression of full-length endogenous retrovirus type К. J Virol, 1999, 73(11):9187−95
- Britten RJ. «Mobile elements inserted in the distant past have taken on important functions.» Gene, 1997 Dec 31 -205(l-2): 177−82.
- Britten RJ. «DNA sequence insertion and evolutionary variation in gene regulation.» Proc Natl Acad Sci USA, 1996 Sep 3−93(18):9374−7. '
- Britten RJ. «Cases of ancient mobile element DNA insertions that now affect gene regulation.» Mol Phylogenet Evol., 1996 Feb-5(1): 13−7. j
- 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(l):14−30.
- Лапук A.B., Лебедев Ю. Б. и Свердлов Е.Д. «Структура гибридного! человеческого эндогенного ретровируса HERV-K/HERV-H и его эволюция в геноме приматов.», Докл. Акад. Наук, 2000, 373(1−6): 150−2 |
- Johnson W.E., Coffin J.M. » Constructing primate phylogenies from ancient retrovirus sequences. PNAS, 1999, 96(18): 10 254−60
- Conrad B., Weissmahr R.N., Boni J., Arcari R., Schupbach J., Mach B. » human endogenous retroviral superantigen as candidate autoimmune gene in type diabetes.», Cell, 1997, 90(2):303−13
- Carrano, A.V., de Jong, P.J., Branscomb, E» Slezak, T. and Watkins, B. WJ (1989) «Constructing chromosome- and region-specific cosmid maps of the human genome.» Genome, v. 31, 1059−1065.
- Jurka J, Klonowski P, Trifonov EN. «Mammalian retroposons integrate at kinkable DNA sites.» JBiomol Struct Dyn., 1998 Feb- 15(4):717−21.
- Scherdin U, Rhodes K, Breindl M. Transcriptionally active genome regions are preferred targets for retrovirus integration. J Virol. 1990 Feb-64(2):907−12.
- Rynditch AV, Zoubak S, Tsyba L, Tryapitsina-Guley N, Bemardi G «The regional integration of retroviral sequences into the mosaic genomes of mammals.» Gene, 1998 Nov 5−222(1): 1−16.
- Shih CC, Stoye JP, Coffin JM. «Highly preferred targets for retrovirus integration.» Cell, 1988 May 20−53(4):531 -7. 1
- Vijaya S, Steffen DL, Robinson HL. «Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin.» J Virol, 1986 Nov-60(2):683−92.
- Bor YC, Miller MD, Bushman FD, Orgel LE. «Target-sequence preferences of HIV-1 integration complexes in vitro.» Virology, 1996 Aug l-222(l):283−8.
- Paul AL, Ferl RJ «Higher-order chromatin structure: looping long molecules.» Plant Mol Biol., 1999 Dec-41(6):713−20.
- Belmont AS, Dietzel S, Nye AC, Strukov YG, Tumbar T «Large-scale chromatin structure and function.» Carr Opin Cell Biol., 1999 Jun- 11 (3):307−11.
- Gu Y, Nakamura T, Alder H, Prasad R, Canaani O, Cimino G, Croce CM, Canaani E. «The t (4-ll) chromosome translocation of human acute leukemias fuses the ALL-1 gene, related to Drosophila trithorax, to the AF-4 gene.» Cell, 1992 Nov 13−71(4):701−8.
- Domer PH, Fakharzadeh SS, Chen CS, Jockel J, Johansen L, Silverman GA, Kersey JH, Korsmeyer SJ. «Acute mixed-lineage leukemia t (4-ll)(q21-q23) generates an MLL-AF4 fusion product.» Proc Natl Acad Sei U S A, 1993 Aug 15−90(16):7884−8.
- Tkachuk DC, Kohler S, Cleary ML. «Involvement of a homolog of Drosophila trithorax by llq23 chromosomal translocations in acute leukemias.» Cell, 1992 Nov 13−71(4):691−700.i
- Lu D, Yunis JJ. «Cloning, expression and localization of an RNA helicase gene from a human lymphoid cell line with chromosomal breakpoint llq23.3.» Nucleic Acids Res., 1992 Apr 25−20(8): 1967−72.
- Ishihara R, Taketani S, Sasai-Takedatsu M, Kino M, Tokunaga R, Kobayashi Y. «Molecular cloning, sequencing and expression of cDNA encoding human trehalase.» Gene, 1997 Nov 20−202(l-2):69−74.
- Eichler EE, Hoffman SM, Adamson A A, Gordon LA, McCready P, Lamerdin JE, Mohrenweiser HW. «Complex beta-satellite repeat structures and the expansion of the zinc finger gene cluster in 19pl2.» Genome Res., 1998 Aug-8(8):791−808.
- Bellefroid EJ, Poncelet DA, Lecocq PJ, Revelant 0, Martial JA. «The evolutionarily conserved Kruppel-associated box domain defines a subfamily of eukaryotic multifingered proteins.» Proc Natl Acad Sci U S A, 1991 May 1−88(9):3608−12. |
- Ashworth LK, Batzer MA, Brandriff B, Branscomb E, de Jong P, Garcia E.
- Games JA, Gordon LA, Lamerdin JE, Lennon G, Mohrenweiser H, Olsen AS, Slezakj
- T and Carrano AV. «An integrated metric physical map of human chromosome 19.» Nature Genet., 1995, v. 11, 422−427. |
- Fuscoe, J.C., Clark, L.M., Van Dilla, M.A. «Construction of fifteen human chromosome-specific DNA libraries from flow-purified chromosomes.» Cytogenei Cell Genet., 1986, 43(l-2):79−86.
- Lukyanov, K.A., Matz, M.V., Bogdanova, E.A., Gurskaya, N.G. and Lukyanov,
- S.A. «Molecule by molecule PCR amplification of complex DNA mixtures for directisequencing: an approach to in vitro cloning.» Nucleic Acids Res., 1996, v. 24, 21 942 195.
- Ellis N, Yen P, Neiswanger K, Shapiro LJ, Goodfellow PN. «Evolution of the pseudoautosomal boundary in Old World monkeys and great apes.» Cell, 1990 Nov 30−63(5):977−86. |
- Weller PA, Critcher R, Goodfellow PN, German J, Ellis NA. «The human Y chromosome homologue of XG: transcription of a naturally truncated gene.» Hunl Mol Genet., 1995 May-4(5):859−68.
- Bernardi G. «Isochores and the evolutionaiy genomics of vertebrates.» Gene, 2000 Jan 4−241(1):3−17.
- Page R.D.M and Holmes E.C. (1998). Molecular evolution: a phylogenetic approach. Blackwell Science, Oxford1. БЛАГОДАРНОСТИ
- Но все усилия были бы тщетны, если бы я не имела абсолютную поддержку во всех своих замыслах, которую мне подарила моя семья родители Ядвига Ивановна и Виктор Александрович Лапук. Я безмерно им благодарна — моим самым первым учителям и наставникам. j
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