Изучение механизмов ограничения активности энхансеров D. melanogaster тема диссертации и автореферата по ВАК РФ 03.01.07, кандидат биологических наук Давыдова, Анна Игоревна

  • Давыдова, Анна Игоревна
  • кандидат биологических науккандидат биологических наук
  • 2011, Москва
  • Специальность ВАК РФ03.01.07
  • Количество страниц 100
Давыдова, Анна Игоревна. Изучение механизмов ограничения активности энхансеров D. melanogaster: дис. кандидат биологических наук: 03.01.07 - Молекулярная генетика. Москва. 2011. 100 с.

Введение диссертации (часть автореферата) на тему «Изучение механизмов ограничения активности энхансеров D. melanogaster»

Актуальность проблемы.8

Цель и задачи исследования.10

Научная новизна и практическая ценность работы.11

Апробация работы.11

Публикации.12

Похожие диссертационные работы по специальности «Молекулярная генетика», 03.01.07 шифр ВАК

Заключение диссертации по теме «Молекулярная генетика», Давыдова, Анна Игоревна

выводы

1) Показано, что некодирующая транскрипция негативно влияет на активность энхансеров генов white и yellow.

2) Продемонстрировано, что терминаторы транскрипции стабилизируют функционирование энхансеров генов white и yellow в составе трансгенов.

3) Установлено, что 1А2- и Wari-инсуляторы функционально взаимодействуют с промоторами разных классов.

4) Выяснено, что обогащение белков CP 190 и Mod(mdg4)-67.2 на промоторе гена even-skipped зависит от присутствия 1 А2-инсулятора в трансгене.

Список литературы диссертационного исследования кандидат биологических наук Давыдова, Анна Игоревна, 2011 год

1. Ashe HL, Monks J, Wijgerde M, Fräser P, Proudfoot NJ. (1997) Intergenic transcription and transinduction of the human beta-globin locus. Genes Dev. ll(19):2494-509.

2. Barski A, Cuddapah S, Cui K, Roh TY, Schönes DE, Wang Z, Wei G, Chepelev I, Zhao K. (2007) High-resolution profiling of histone methylations in the human genome. Cell.l29(4):823-37.

3. Bartkuhn M, Renkawitz R. (2008) Long range chromatin interactions involved in gene regulation. Biochim Biophys Acta. 1783(11):2161-6.

4. Bartolomei MS, Zemel S, Tilghman SM. (1991) Parental imprinting of the mouse H19 gene. Nature. 351(6322):153-5.

5. Bertone P, Stole V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science. 306(5705):2242-6.

6. Birney E, Stamatoyannopoulos JA, Dutta A, Guigö R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS et all. (2007) ENCODE Project Consortium. Nature. 447(7146):799-816.

7. Blanton J, Gaszner M, Schedl P. Protein:protein interactions and the pairing of boundary elements in vivo. Genes Dev. 2003 Mar l;17(5):664-75.

8. Brand AH, Perrimon N. (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development. 118(2):401-15.

9. Brasset E, and Vaury C. (2005) Insulators are fundamental components of the eukaryotic genomes. Heredity. 94: 571-576.

10. Bushey AM, Dorman ER, Corces VG (2008) Chromatin insulators: regulatory mechanisms and epigenetic inheritance. Mol. Cell. 32:1-9

11. Butler JE, Kadonaga JT. (2001) Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 15(19):2515-9.

12. Butler JE, Kadonaga JT. (2002) The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev. 16(20):2583-92.

13. Cai H, and Shen P. (2001) Effects on eis arrangement of chromatin insulators on enhancer-blocking activity. Science. 291: 493-495.

14. Capelson M, Corces VG. (2006) SUMO conjugation attenuates the activity of the gypsy chromatin insulator. EMBO J. 25(9): 1906-14.

15. Capelson M. and Corces V. (2005) The ubiquitin ligase dTopors directs the nuclear organization of a chromatin insulator. Mol. Cell. 20: 105-116.

16. Capelson M. and Corces V.G. (2004) Boundary elements and nuclear organization. Biol. Cell. 96: 617-629.

17. Carthew RW, Sontheimer EJ. (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell. 136(4):642-55.

18. Chopra V.S., Cande J., Hong J.W., Levine M. (2009) Stalled Hox promoters as chromosomal boundaries. Genes Dev. 23(13):1505-1509.

19. Clemson CM, McNeil JA, Willard HF, Lawrence JB. (1996) XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol. 132(3):259-75.

20. Conte C, Dastugue B, and Vaury C. (2002a) Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes. Mol. Cell Biol. 22: 1767-1777.

21. Conte C, Dastugue B, Vaury C. (2002b) Promoter competition as a mechanism of transcriptional interference mediated by retrotransposons. EMBO J. 21:39083916

22. Core LJ, Waterfall JJ, Lis JT. (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 322(5909): 1845-8.

23. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 8(5):el000384.

24. Deng X, Koya SK, Kong Y, Meller VH. (2009) Coordinated regulation of heterochromatic genes in Drosophila melanogaster males. Genetics. 182(2):481-91.

25. Ernst P, Wang J, Huang M, Goodman RH, Korsmeyer SJ. (2001) MLL and CREB bind cooperatively to the nuclear coactivator CREB-binding protein. Mol Cell Biol. 21(7):2249-58.

26. Erokhin MM, Georgiev PG, Chetverina DA. (2010) Effects of functional interactions between nonhomologous insulators Wari and Su(Hw). Genetika. 46(1): 18-25.

27. Gaszner M, and Felsenfeld G. (2006) Insulators: Exploiting transcriptional and epigenetic mechanisms. Nat. Rev. Genet. 7: 703-713.

28. Gerasimova TI, Corces VG. (1998) Polycomb and Trithorax group proteins mediate the function of a chromatin insulator. Cell 92: 511-521.

29. Geyer PK, Clark I. (2002) Protecting against promiscuity: the regulatory role of insulators. Cell Mol Life Sci. 59(12):2112-27.

30. Geyer PK. (1997) The role of insulator elements in defining domains of gene expression. Curr Opin Genet Dev. 7(2):242-8.

31. Golovnin A, Birukova I, Romanova O, Silicheva M, Parshikov A, Savitskaya E, Pirrotta, V and Georgiev P. (2003) An endogenous Su(Hw) insulator separates the yellow gene from the Achaete-scute gene complex in Drosophila. Development 130: 3249-3258.

32. Golovnin A, Melnikova L, Volkov I, Kostuchenko M, Galkin AV, Georgiev P. (2008) 'Insulator bodies' are aggregates of proteins but not of insulators. EMBO Rep. 9:440-445.

33. Golovnin A., Melnick E., Mazur A., Georgiev P. (2005)-Drosophila Su(Hw) insulator can stimulate transcription of a weakened yellow promoter over a distance. Genetics. 170(3):133-1142.

34. Hallikas O; Palin K, Sinjushina N, Rautiainen R, Partanen J, Ukkonen E, Taipale J. (2006) Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell. 124(l):47-59.

35. He H.H., Meyer C.A., Shin H:, Bailey S.T., Wei G., Wang Q., Zhang Y., Xu K., Ni M., Lupien M., Mieczkowski P., Lieb J.D:, Zhao K., Brown M:, Liu X.S. (2010) Nucleosome dynamics define transcriptional enhancers. Nat Genet. 42(4):343-7.

36. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Ban-era LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE,

37. Ren B. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 39(3):311-8.

38. Hogga I, Karch F. (2002) Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing. Development. 129(21):4915-22.

39. Jack J, Dorsett D, Delotto Y, Liu S. (1991) Expression of the cut locus in the Drosophila wing margin is required for cell type specification and is regulated by a distant enhancer. Development. 113(3):735-47.

40. Jin C, Felsenfeld G. (2007) Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev. 21 (12): 1519-29.

41. Knezetic JA, Felsenfeld G. (1989) Identification and characterization of a chicken alpha-globin enhancer. Mol Cell Biol. 9(3):893-901.

42. Kong, S., Bohl, D., Li, C., and Tuan, D. (2007) Transcription of the HS2 enhancer toward a cis-linked gene is independent of the orientation, position, and distance of the enhancer relative to the gene. Mol. Cell. Biol. 17, 3955-3965

43. Kravchenko E., Savitskaya E., Kravchuk O. et al. (2005) Pairing between gypsy insulators facilitates the enhancer action in trans throughout the Drosophila genome. Mol. Cell Biol. 25(21): 9283-9291.

44. Kuhn EJ, Hart CM, Geyer PK. (2004) Studies of the role of the Drosophila scs and scs1 insulators in defining boundaries of a chromosome puff. Mol Cell Biol. 24(4): 1470-1480.

45. Kuhn, E.J., and Geyer, P.K. (2003) Genomic insulators: Connecting properties to mechanism. Curr. Opin. Cell Biol. 15: 259-265

46. Kurshakova M, Maksimenko O, Golovnin A, Pulina M, Georgieva S, Georgiev P, Krasnov A. (2007) Evolutionarily conserved E(y)2/Susl protein is essential forthe barrier activity of Su(Hw)-dependent insulators in Drosophila. Mol Cell. 27:332-338.

47. Kyrchanova O, Chetverina D, Maksimenko O, Kullyev A, Georgiev P. (2008) Orientation-dependent interaction between Drosophila insulators is a property of this class of regulatory elements. Nucleic Acids Res. 36:7019-7028.

48. Kyrchanova O, Toshchakov S, Podstreshnaya Y, Parshikov A, Georgiev P. (2008b) Functional interaction between the Fab-7 and Fab-8 boundaries and the upstream promoter region in the Drosophila Abd-B gene. Mol Cell Biol. 28(12):4188-95.

49. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K. (2001) Initial sequencing and analysis of the human genome. Nature. 409(6822): 860-921.

50. Ling J, Baibakov B, Pi W, Emerson BM, Tuan D. (2005) The HS2 enhancer of the beta-globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis-linked globin promoter. J Mol Biol. 350(5):883-96.

51. Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R. (2006) Interchromosomal interactions and olfactory receptor choice. Cell. 126(2):403-13.

52. Mahmoudi T, Katsani KR, Verrijzer CP. (2002) GAGA can mediate enhancer function in trans by linking two separate DNA molecules. EMBO J. 21(7): 177581.

53. Majumder P, Cai HN. (2003) The functional analysis of insulator interactions in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 100: 5223-5228.

54. Maksimenko OG, Georgiev PG. (2007) A study of the structure of 1A2 insulator of Drosophila melanogaster. Dokl Biochem Biophys. 416:252-5.

55. Matsui M, Sharma K, Cooke C, Wakimoto BT, Rasool M, Hay worth M, Hylton CA, Tomkiel JE. (2011) Nuclear Structure and Chromosome Segregation in Drosophila Male Meiosis Depends on the Ubiquitin Ligase dTopors. Genetics. 2011 Sep 6. Epub ahead of print.

56. Melnikova L, Kostuchenko M, Silicheva M, Georgiev P. (2008) Drosophila gypsy insulator and yellow enhancers regulate activity of yellow promoter through the same regulatory element. Chromosoma. 117(2): 137-45.

57. Muravyova E, Golovnin A, Gracheva E, Parshikov A, Belenkaya T, Pirrotta V and Georgiev P. (2001) Loss of insulator activity by paired Su(Hw) chromatin insulators. Science 291: 495-498.

58. Narlikar L, Ovcharenko I. (2009) Identifying regulatory elements in eukaryotic genomes. BriefFunct Genomic Proteomic. 8(4):215-30.

59. Nègre N., Brown C.D., Shah P.K. et al. (2010) A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 6:el000814.

60. Pai C, Lei C, Ghosh D, Corces V. (2004) The centrosomal protein CP 190 is a component of the gypsy chromatin insulator. Mol. Cell. 16: 737-748.

61. Parnell TJ, Geyer PK. (2000) Differences in insulator properties revealed by enhancer blocking assays on episomes. EMBO J. 19(21):5864-74.

62. Parnell TJ, Viering MM, Skjesol A, Helou C, Kuhn EJ and Geyer PK. (2003) An endogenous suppressor of hairy-wing insulator separates regulatory domains in Drosophila. Proc. Natl. Acad. Sci. 100: 13436-13441.

63. Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau JC, Ferrier P, Spicuglia S. (2011) H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J. doi: 10.103 8/emboj.2011.295.

64. Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, Hirose S, Jaynes JB, Brock HW, Mazo A. (2006) Transcription of bxd noncoding RNÀs promoted1 by trithorax represses Ubx in cis by transcriptional interference. Cell. 127(6): 120921.

65. Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH. (2008) RNA exosome depletion reveals transcription upstream of active human promoters. Science. 322(5909):1851-4.

66. Ptashne M. (1986) Gene regulation by proteins acting nearby and at a distance. Nature. 322(6081):697-701.

67. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 470(7333):279-83.

68. Rodin S, Georgiev P. (2005) Handling three regulatory elements in one transgene: Combined use of cre-lox, FLP-FRT, and I-Scel recombination systems. Biotechniques 39: 871—876.

69. Sandmann T, Jakobsen JS, Furlong EE. (2006) ChlP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. NatProtoc. l(6):2839-55.

70. Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G. (2007) Genome regulation by polycomb and trithorax proteins. Cell. 128(4):735-45.

71. Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA. (2008) Divergent transcription from active promoters. Science. 2008 322(5909): 1849-51.

72. Stamatoyannopoulos G. (2005) Control of globin gene expression during development and erythroid differentiation. Exp Hematol. 33(3):259-71.

73. Talbert PB, Henikoff S. (2010) Histone variants-ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol. 11(4):264-75.

74. Tie F, Banerjee R, Stratton CA, Prasad-Sinha J, Stepanik V, Zlobin A, Diaz M0, Scacheri PC, Harte PJ. (2009) CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development. 136(18):3131-41.

75. Tuan D, Kong S, Hu K. (1992) Transcription of the hypersensitive site HS2 enhancer in erythroid cells. Proc Natl Acad Sci USA. 89(23): 11219-23.

76. Valenzuela L, Kamakaka RT. (2006) Chromatin insulators. Annu. Rev. Genet. 40: 107-138. .

77. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 10(4):252-63.

78. Vazquez J, Schedl P. (2000) Deletion of an insulator element by the mutation facet-strawberry in Drosophila melanogaster. Genetics. 155: 1297—1311.

79. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. (2009) ChlP-seq accurately predicts tissue-specific activity of enhancers. Nature. 457(7231):854-8.

80. Wallace J.A., Felsenfeld G. (2007) We gather together: insulators and genome organization. Curr. Opin. Genet. Dev. 17(5):400^Ю7.

81. Wang Z, Zang C, Rosenfeld JA, Schönes DE, Barski A, Cuddapah S, Cui К, Roh TY, Peng W, Zhang MQ, Zhao К. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 40(7):897-903.

82. Wei W, Pelechano V, Järvelin AI, Steinmetz LM. (2011) Functional consequences of bidirectional promoters. Trends Genet. 27(7):267-76.

83. West AG and Fraser P. (2005) Remote control of gene transcription. Hum. Mol. Genet. 14: 101-111.

84. Wu C, Bingham PM, LivakKJ, Holmgren R; Elgin SC. (1979) The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence. Cell. 16(4):797-806.

85. Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature. 457(7232): 1033-7.

86. Zhao H, Dean A. (2005) Organizing the genome: enhancers and insulators. Biochem Cell Biol. 83:516-524.

87. Zhou J, Barolo S, Szymanski P, Levine M. (1996) The Fab-7 element of the bithorax complex attenuates enhancer-promoter interactions in the Drosophila embryo. Genes Dev. 10: 3195-3201.

88. Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE. (2009)-Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature. 462(7269):65-70.