Pen Academic Publishing   |  ISSN: 2602-4810   |  e-ISSN: 2602-4535

International Journal of Innovative Approaches in Science Research 2017, Vol. 1(1) 47-56

Angiospermlerde Genomik Damgalama

Aslıhan Özbilen

pp. 47 - 56   |  DOI: https://doi.org/10.29329/ijiasr.2017.99.5   |  Manu. Number: MANU-1712-26-0005.R1

Published online: December 29, 2017  |   Number of Views: 87  |  Number of Download: 72


Abstract

Çiçekli bitkilerde embriyo ve embriyoyu besleyen endosperm dokusu çifte döllenme ile oluşur. Bu organizmalarda endosperm dokularında bazı genlerin yalnızca anneden gelen kopyalarının, bazılarının ise babadan gelen kopyalarının ifade olmasına genomik damgalama (damgalanma) denir. Genomik damgalama, epigenetik modifikasyonlar sonucu oluşur, anne alellerinin sessizleştirilmesinden genel olarak PRC2 kompleksi sorumluyken, baba alellerinin sessizleştirilmesinde PRC2 kompleksi veya metilasyon sorumludur. Bu epigenetik değişiklikler damgalama kontrol bölgeleri olarak bilinen DNA dizilerinde meydana gelir. Bu bölgelerin genomik damgalamaya uğrayacak gene olan uzaklıkları, o gene ait ana ya da baba alelinin ifade seviyesini belirler. Son zamanlarda, transkriptom ve metilom çalışmaları çeşitli bitki türlerinde 200’den fazla genomik damgalamaya uğrayan gen varlığını işaret etmiştir. Bu genlerin genomik damgalamaya uğradıkları, PCR yöntemleri ve mutasyonlar ile kanıtlanmıştır. Genomik damgalamaya uğrayan genlerin metiltransferaz aktivitesinden ligaz aktivitesine kadar çok çeşitli işlevleri bulunmaktadır. Ayrıca, bu genlerin yakınlarında transpozon elementleri keşfedilmiş olup, bu durum damgalamanın, transpozonların susturulması ile ilgili süreçler sonucunda ortaya çıktığını düşündürmektedir. Buna ek olarak, genomik damgalamaya uğrayan genlerin çoğunun genom duplikasyonu sonucu ortaya çıktığı düşünülmektedir. Bu genler, paraloglarına göre, daha hızlı değişim oranı göstermektedir. Genomik damgalama ebeveyn çatışma teorisi ile açıklanmaktadır. Bu teoriye göre baba genomu kaynakları yalnızca kendi döllerini destekleyecek şekilde düzenlerken, anne genomu tüm döllere eşit miktarda kaynak aktarır ve bu durum ebeveyn genomlar arasında bir anlaşmazlığa neden olur. Bu anlaşmazlık, alellerin köken aldıkları ebeveyne göre ifade edildiği genomik damgalama için bir temel oluşturabilir. Genomik damgalama için bazı bitkiler ortak mekanizmalar ile hareket ediyorken, bazı yakın türler oldukça farklı süreçler sergileyebilmektedirler. Bu nedenle, genomik damgalama sürecinin aydınlatılması için yeni çalışmalara ihtiyaç duyulmaktadır.

Keywords: Genomik damgalama, Endosperm, Epigenetik, DNA metilasyonu


How to Cite this Article?

APA 6th edition
Ozbilen, A. (2017). Angiospermlerde Genomik Damgalama. International Journal of Innovative Approaches in Science Research, 1(1), 47-56. doi: 10.29329/ijiasr.2017.99.5

Harvard
Ozbilen, A. (2017). Angiospermlerde Genomik Damgalama. International Journal of Innovative Approaches in Science Research, 1(1), pp. 47-56.

Chicago 16th edition
Ozbilen, Aslihan (2017). "Angiospermlerde Genomik Damgalama". International Journal of Innovative Approaches in Science Research 1 (1):47-56. doi:10.29329/ijiasr.2017.99.5.

References
  1. Baroux C., Gagliardini V., Page D.R., Grossniklaus U., 2006. Dynamic regulatory interactions of Polycomb group genes: MEDEA autoregulation is required for imprinted gene expression in Arabidopsis. Genes Dev, 20(9): 1081–6.
  2. Boavida L., Hernandez-Coronado M., Becker J., 2015. Setting the Stage for the Next Generation: Epigenetic Reprogramming During Sexual Plant Reproduction. In: Pontes O., Jin H. (eds) Nuclear Functions in Plant Transcription, Signaling and Development. Springer, New York, NY.
  3. Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., Goldberg R.B., Jacobsen S.E., Fischer R.L., 2002. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell, 110: 33-42.
  4. Costa L.M., Yuan J., Rouster J., Paul W., Dickinson H. ve Gutierrez-Marcos J.F., 2012. Maternal Control of Nutrient Allocation in Plant Seeds by Genomic Imprinting. Current Biology, 22(2): 160-165.
  5. Feil R., Berger F., 2007. Convergent Evolution of Genomic Imprinting in Plants and Mammals. Trends in Genetics, 23(4): 192-199.
  6. Fitz Gerald J.N., Hui P.S., Berger F., 2009. Polycomb Group-Dependent Imprinting of the Actin Regulator AtFH5 Regulates Morphogenesis in Arabidopsis thaliana. Development. 136: 3399-3404.
  7. Gehring M., Bubb K. L., Henikoff S., 2009. Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting. Science, 324: 1447-1451.
  8. Gehring M., Choi Y., Fischer R.L., 2004. Imprinting and Seed Development. The Plant Cell, 16: 203-213.
  9. Gehring M., Huh J.H., Hsieh T., Penterman J., Choi Y., Harada J.J., Goldberg R.B., Fischer R.L., 2006. DEMETER DNA Glycosylase Establishes MEDEA Polycomb Gene Self-Imprinting by Allele-Specific Demethylation. Cell, 124: 495-506.
  10. Gehring M., Missirian V., Henikoff S., 2011. Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds. PLoS ONE, 6 (8): e23687.
  11. Grossniklaus U., Vielle-Calzada J-P., Hoeppner M.A., Gagliano W.B., 1998. Maternal Control of Embryogenesis by MEDEA, a Polycomb Group Gene in Arabidopsis. Science, 28o: 446-450.
  12. Haig D., 2002. Genomic Imprinting and Kinship. Rutgers University Press, New Brunswick. 1-16.
  13. Haig D., Westoby M., 1989. Parent-specific gene expression and the triploid endosperm. American Naturalist, 134(1): 147-155
  14. Hatorangan M.R., Laenen B., Steige K., Slotte T., Köhler C., 2016. Rapid evolution of genomic imprinting in two species of the Brassicaceae. Plant Cell, 28:1815–27.
  15. Hsieh T., Shin J., Uzawa R., Silva P., Cohen S., Bauer M.J., Hashimoto M., Kirkbride R.C., Harada J.J., Zilberman D., Fischer R. L., 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Plant Biology, 108: 1755-1762.
  16. Hsieh T.F., Ibarra C.A., Silva P., Zemach A., Eshed-Williams L., Fischer R.L., Zilberman D., 2009. Genome-wide demethylation of Arabidopsis endosperm. Science, 324(5933): 1451–1454.
  17. Ikeda Y., 2012. Plant Imprinted Genes Identified by Genome-wide Approaches and Their Regulatory Mechanisms. Plant Cell Physiology, 53 (3): 809-816.
  18. Jahnke S., Scholten S., 2009. Epigenetic Resetting of a Gene Imprinted in Plant Embryos. Current Biology, 19: 1677-1681.
  19. Jeong C.W., Park G.T., Yun H., Hsieh T-F., Choi Y.D., Choi Y., Lee J.S., 2015. Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm. PLoS ONE, 10(2): e0117431. 
  20. Jiang H., Kohler C., 2012. Evolution, function, and regulation of genomic imprinting in plant seed development. J Exp Bot, 63(13): 4713–22.
  21. Jullien P.E., Katz A., Oliva M., Ohad N., Berger F., 2006(a). Polycomb Group Complexes Self-Regulate Imprinting of the Polycomb Group Gene MEDEA in Arabidopsis. Current Biology, 16: 486-492.
  22. Jullien P.E., Kinoshita T., Ohad N., Berger F., 2006(b). Maintenance of DNA Methylation during the Arabidopsis Life Cycle Is Essential for Parental Imprinting. The Plant Cell, 18: 1360-1372.
  23. Kermicle J.L., 1970. Dependence of the R-Mottled Aleurone Phenotype in Maize on Mode of Sexual Transmission. Genetics, 66: 69-85.
  24. Kinoshita T., Miura A., Choi Y., Kinoshita Y., Cao X., Jacobsen E.S., Robert L.F., Kakutani T., 2004. One-Way Control of FWA Imprinting in Arabidopsis Endosperm by DNA Methylation. Science, 303: 521.
  25. Kinoshita T., Yadegari R., Harada J.J., Goldberg R.B., Fischer R.L., 1999. Imprinting of the MEDEA Polycomb Gene in the Arabidopsis Endosperm. The Plant Cell, 11: 1945-1952.
  26. Klosinska M., Picard C.L., Gehring M., 2016. Conserved imprinting associated with unique epigenetic signatures in the Arabidopsis genus. Nature Plants, 2:16145.
  27. Kohler C., Weinhofer-Molisch I., 2010. Mechanisms and evolution of genomic imprinting in plants. Heredity. 105(1): 57–63.
  28. Köhler C., Page D.R., Gagliardini V., Grossniklaus U., 2005. The Arabidopsis thaliana MEDEA Polycomb Group Protein Controls Expression of PHERES1 by Parental Imprinting. Nature Genetics, 37: 28-30.
  29. Kradolfer D., Wolff P., Jiang H., Siretskiy A., Köhler. C., 2013. An imprinted gene underlies postzygotic reproductive isolation in Arabidopsis thaliana. Dev Cell, 26: 525-535.
  30. Luo M., Bilodeau P., Koltunow A., Dennis E.S., Peacock W.J., Chaudhury A.M., 1999. Genes controlling fertilization-independent seed development in Arabidopsis thaliana. Proc. Natl. Acad. Sci., 96: 296–301.
  31. Luo M., Taylor J.M., Spriggs A., Zhang H., Wu X., Russell S., Singh M., Koltunow A., 2011. A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm. PLoS Genetics, 7 (6): e1002125.
  32. McCrath J., Solter D., 1984. Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell, 37:179-83.
  33. Park K., Kim M.Y., Vickers M., Park J.S., Hyun Y., Okamoto T., Zilberman D., Fischer R.L., Feng X., Choi Y., Scholtene S., (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proc Natl Acad Sci USA, 113:15138–43.
  34. Qiu Y., Liu S.L., Adams K.L, 2014. Frequent Changes in Expression Profile and Accelerated Sequence Evolution of Duplicated Imprinted Genes in Arabidopsis. Genome Biology and Evolution, 6(7): 1830–1842.
  35. Reik W., Walter J., 2011. Genomic imprinting: parental in fluence on the genome. Nat Rev Genet, 2: 21–32.
  36. Satyaki P.R.V., Gehring M., 2017. DNA methylation and imprinting in plants: machinery and mechanisms. Crit Rev Biochem Mol Biol, 52(2): 163-75.
  37. Schoft V.K., Chumak N., Choi Y., Hannon M., Garcia-Aguilar M., Machlicova A., Slusarz L., Masiolek M., Park J.S., Park G.T., Fischer R.L., Tamaru H., 2011. Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte. Proc Natl Acad Sci USA, 108: 8042–7.
  38. Surani M. A., 2001. Reprogramming of Genome Function Through Epigenetic Inheritance. Nature, 414: 122-128.
  39. Surani M.A., Barton S.C., Norris M.L., 1984. Development of reconstituted eggs suggests imprinting of the genome during gametogenesis. Nature, 308:548-50.
  40. Tiwari S., Schulz R., Ikeda Y., Dytham L., Bravo J., Mathers L., Spielman M., Guzman P., Oakey R.J., Kinoshita T., Scott R.J., 2008. MATERNALLY EXPRESSED PAB C-TERMINAL, a Novel Imprinted Gene in Arabidopsis, Encodes the Conserved C-Terminal Domain of Polyadenylate Binding Proteins. The Plant Cell, 20: 2387-2398.
  41. Vinkenoog R., Spielman M., Adams S., Dickinson H.G., Scott R.J., 2002. Genomic Imprinting in Plants. Methods in Molecular Biology, 181:327-370.
  42. Walter J., Paulsen M., 2003. The potential role of gene duplications in the evolution of imprinting mechanisms. Hum Mol Genet, 12: 215–220.
  43. Waters A.J., Bilinski P., Eichten S.R., Vaughn M.W., Ross-Ibbara J., Gehring M., Springer N.M., 2013. Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species. Proc Natl Acad Sci USA, 110:19639–19644.
  44. Wilkins J.F., Haig D., 2003. What good is genomic imprinting: the function of parent-specific gene expression. Nature Reviews Genetics, 4: 359–368.
  45. Wolff P., Weinhofer I., Seguin J., Roszak P., Beisel C., Donoghue M.T.A., Spillane C., Nordborg M., Rehmsmeier M., Köhler C., 2011. High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm. PLoS Genet 7(6): e1002126. 
  46. Wollmann H., Berger F., 2012. Epigenetic Reprogramming During Plant Reproduction and Seed Development. Current Opinion in Plant Biology, 15: 63-69.
  47. Wöhrmann H.J., Gagliardini V., Raissig M.T., Wehrle W., Arand J., Schmidt A., Tierling S., Page D.R., Schöb H., Walter J., Grossniklaus U., 2012. Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus. Genes Dev., 26(16): 1837–50.
  48. Xiao W., Gehring M., Choi Y., Margossian L., Pu H., Harada J.J., Goldberg R.B., Pennell R.I., Fischer R.L., 2003. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell, 5(6): 891–901.
  49. Xu W., Dai M., Li F., Liu A., 2014. Genomic imprinting, metyhlation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean. Nucleic Acids Res., 42: 6987–6998.
  50. Zemach A., Kim M.Y., Silva P., Rodrigues J.A., Dotson B., Brooks M.D., Zilberman D., 2010. Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci USA, 107: 18729–18734.
  51. Zhang M., Xie S., Dong X., Zhao X., Zeng B., Chen J., Li H., Yang W., Zhao H., Wang G., Chen Z., Sun S., Hauck A., Jin W., Lai J., 2014. Genome-wide high resolution parental-specific DNA and histone metyhlation maps uncover patterns of imprinting regulation in maize. Genome Res., 24: 167-76.
  52. Zhang M., Zhao H., Xie S., Chen J., Xu Y., Wang K., Zhao H., Guan H., Hu X., Jiao Y., Song W., Lai J., 2011. Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc Natl Acad Sci USA, 108: 20042–20047.
  53. Zhang, M., Li, N., He, W., Zhang, H., Yang, W., Liu, B., 2016. Genome-Wide  Screen  of  Genes  Imprinted   in   Sorghum   Endosperm   and   the   Roles   of   Allelic   Differential   Cytosine   Methylation. Plant J., 85(3): 424-436.