Imprinting in Plants and Its Underlying Mechanisms

Journal of Genetics and Genomics

Volumn 40, Issue 5, 2013, Pages 239-247

  Zhang, Hongyu ^a   Chaudhury, Abed ^b   Wu, Xianjun ^a  

^a SICHUAN AGRICULTURAL UNIVERSITY   (China)

^b NONE   (Bangladesh)

Author keywords

DNA methylation; Endosperm; Imprinting; Polycomb group; Small RNA

Indexed keywords

DNA METHYLTRANSFERASE 1; MICRORNA; POLYCOMB REPRESSIVE COMPLEX 2; SMALL INTERFERING RNA;

ALLELE; ANGIOSPERM; ARABIDOPSIS; DEMETHYLATION; DNA METHYLATION; EMBRYO DEVELOPMENT; ENDOSPERM; ENZYME ACTIVITY; EPIGENETICS; GENE ACTIVITY; GENE DOSAGE; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; GENE REPRESSION; GENE SEQUENCE; GENE SILENCING; GENOME IMPRINTING; HISTONE MODIFICATION; MAIZE; MALE GAMETOPHYTE; MONOCOT; NONHUMAN; PLACENTAL MAMMALS; REVIEW; RICE; TANDEM REPEAT; TRANSPOSON;

ARABIDOPSIS; EUTHERIA; LILIOPSIDA; MAGNOLIOPHYTA; ZEA MAYS;

EID: 84878149914     PISSN: 16738527     EISSN: 18735533     Source Type: Journal    
DOI: 10.1016/j.jgg.2013.04.003     Document Type: Review

References (53)

1. Baroux C., Gagliardini V., Page D.R., Grossniklaus U. Dynamic regulatory interactions of Polycomb group genes: MEDEA auto regulation is required for imprinted gene expression in Arabidopsis. Genes Dev. 2006, 20:1081-1086.
2. Belmonte M.F., Kirkbride R.C., Stone S.L., Pelletier J.M., Bui A.Q., Yeung E.C., Hashimoto M., Fei J., Harada C.M., Munoz M.D., Le B.H., Drews G.N., Brady S.M., Goldberg R.B., Harada J.J. Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proc. Natl. Acad. Sci. USA 2013, 110:E435-E444.
3. Berger F., Vu T.M., Li J., Chen B. Hypothesis: selection of imprinted genes is driven by silencing deleterious gene activity in somatic tissues. Cold Spring Harbor Symposia on Quantitative Biology 2013, (Epub ahead of print).
4. Bird A. Perceptions of epigenetics. Nature 2007, 447:396-398.
5. Calarco J.P., Borges F., Donoghue M.T., Van Ex F., Jullien P.E., Lopes T., Gardner R., Berger F., Feijo J.A., Becker J.D., Martienssen J.A. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 2012, 151:194-205.
6. Chaudhury A.M., Luo M., Miller C., Craig S., Dennis E.S., Peacock W.J. Fertilization-independent seed development in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 1997, 94:4223-4228.
7. Chen G., Wang C., Shi T. Overview of available methods for diverse RNA-Seq data analyses. Sci. China Life Sci. 2011, 54:1121-1128.
8. Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., Goldberg R.B., Jacobsen S.E., Fischer R.L. DEMETER, a DNA glycosidase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 2002, 110:33-42.
9. Dilkes B.P., Comai L. A differential dosage hypothesis for parental effects in seed development. Plant Cell 2004, 16:3174-3180.
10. Feil R., Berger F. Convergent evolution of genomic imprinting in plants and mammals. Trends Genet. 2007, 23:192-199.
11. Feng S.H., Cokus S.J., Zhang X.Y., Chen P.Y., Bostick M., Goll M.G., Hetzel J., Jain J., Strauss S.H., Halpem M.E., Ukomadu C., Sadler K.C., Paradhan S., Pellegrini M., Jacobsen S.E. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl. Acad. Sci. USA 2010, 107:8689-8694.
12. Gehring M., Missirian V., Henikoff S. Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS ONE 2011, 6:e23687.
13. Gehring M., Huh J.H., Hsieh T.F., Penterman J., Choi Y., Harada J.J., Goldberg R.B., Fischer R.L. DEMETER DNA glycosylase establishes MEDEA Polycomb gene self-imprinting by allele-specific demethylation. Cell 2006, 124:495-506.
14. Gehring M., Bubb K.L., Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009, 324:1447-1451.
15. Gutierrez-Marcos J.F., Costa L.M., Dal Pra M., Scholten S., Kranz E., Perez P., Dickinson H.G. Epigenetic asymmetry of imprinted genes in plant gametes. Nat. Genet. 2006, 38:876-878.
16. Haig D., Westoby M. Parent specific gene expression and the triploid endosperm. Am. Nat. 1989, 134:147-155.
17. Haun W.J., Springer N.M. Maternal and paternal alleles exhibit differential histone methylation and acetylation at maize imprinted genes. Plant J. 2008, 56:903-912.
18. Hennig L., Derkacheva M. Diversity of Polycomb group complexes in plants: same rules, different players?. Trends Genet. 2009, 25:414-423.
19. Hsieh T.F., Shin J., Uzawa R., Silva P., Cohen S., Bauer M.J., Hashimoto M., Kirkbride R.C., Harada J.J., Zilberman D., Fischer R.L. Regulation of imprinted gene expression in Arabidopsis endosperm. Proc. Natl. Acad. Sci. USA 2011, 108:1755-1762.
20. Hsieh T.F., Ibarra, Silva P., Zemach A., Eshed W.L., Fischer R.L., Zilberman D. Genome-wide demethylation of Arabidopsis endosperm. Science 2009, 324:1451-1454.
21. Ibarra, Feng X.Q., Schoft V.K., Hsieh T.F., Uzawa R., Rodrigues J.A., Zemach A., Chumak N., Machlicova A., Nishimura T., Rojas D., Fischer R., Tamaru H., Zilberman D. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 2012, 337:1360-1364.
22. Ikeda Y., Kinoshita Y., Susaki D., Ikeda Y., Iwano M., Takayama S., Higashiyama T., Kakutan T., Kinoshieta T. HMG domain containing SSRP1 is required for DNA demethylation and genomic imprinting in Arabidopsis. Dev. Cell 2011, 21:589-596.
23. Jahnke S., Scholten S. Epigenetic resetting of a gene imprinted in plant embryos. Curr. Biol. 2009, 19:1677-1681.
24. Jullien P.E., Kinoshita T., Ohad N., Berger F. Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 2006, 18:1360-1372.
25. Jullien P.E., Mosquna A., Ingouff M., Sakata T., Ohad N., Berger F. Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol. 2008, 6:e194.
26. Jullien P.E., Katz A., Oliva M., Ohad N., Berger F. Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr. Biol. 2006, 16:486-492.
27. Jullien P.E., Susaki D., Yelagandula R., Higashiyama T., Berger F. DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana. Curr. Biol. 2012, 22:1825-1830.
28. Kermicle J.L. Dependence of the R-mottled aleurone phenotype in maize on the mode of sexual transmission. Genetics 1970, 66:69-85.
29. Kinoshita Y., Saze H., Kinoshita T., Miura A., Soppe W.J.J., Koornneef M., Kakutani T. Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J. 2007, 49:38-45.
30. Kinoshita T. Reproductive barrier and genomic imprinting in the endosperm of flowering plants. Genes Genet. Syst. 2007, 82:177-186.
31. Kinoshita T., Miura A., Choi Y., Kinoshita Y., Cao X.F., Jacosen S.E., Fischer R.L., Kakutan T. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 2004, 303:521-523.
32. Kinoshita T., Yadegari R., Harada J.J., Goldberg R.B., Fischer R.L. Imprinting of the MEDEA Polycomb gene in the Arabidopsis endosperm. Plant Cell 1999, 11:1945-1952.
33. Kohler C., Page D.R., Gagliardini V., Grossniklaus U. The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat. Genet. 2005, 37:28-30.
34. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010, 11:204-220.
35. Luo M., Bilodeau P., Dennis E.S., Peacock W.J., Chaudhury A. Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds. Proc. Natl. Acad. Sci. USA 2000, 97:10637-10642.
36. Luo M., Taylor J.M., Spriggs A., Zhang H.Y., Wu X.J., Russell S., Singh M., Koltunow A. A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet. 2011, 7:e1002125.
37. Luo M., Platten D., Chaudhury A., Peacock W., Dennis E.S. Expression, imprinting, and evolution of rice homologs of the Polycomb group genes. Mol. Plant 2009, 2:711-723.
38. Makarevich G., Villar C.B., Erilova A., Köhler C. Mechanism of PHERES1 imprinting in Arabidopsis. J. Cell Sci. 2008, 121:906-912.
39. Mosher R.A., Melnyk C.W., Kelly K.A., Dunn R.M., Studholme D.J., Baulcombe D.C. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 2009, 460:283-286.
40. Raissig M.T., Baroux C., Grossniklaus U. Regulation and flexibility of genomic imprinting during seed development. Plant Cell 2011, 23:16-26.
41. Schatlowski N., Köhler C. Tearing down barriers: understanding the molecular mechanisms of interploidy hybridizations. J. Exp. Bot. 2012, 63:6059-6067.
42. Schuettengruber B., Cavalli G. Recruitment of Polycomb group complexes and their role in the dynamic regulation of cell fate choice. Development 2009, 136:3531-3542.
43. Scott R.J., Spielman M., Bailey J., Dickinson H.G. Parent-of-origin effects on seed development in Arabidopsis thaliana. Development 1998, 125:3329-3341.
44. Slotkin R.K., Vaughn M., Borges F., Tanurdzic M., Becker J.D., Feijo J.A., Martienssen R.A. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 2009, 136:461-472.
45. Tiwari S., Schulz R., Ikeda Y., Dytham L., Bravo J., Mathers L., Spielman M., Guzman P., Oakey R.J., Kinoshita T., Scott R.J. MATERNALLY EXPRESSED PAB C-TERMINAL, a novel imprinted gene in Arabidopsis, encodes the conserved C-terminal domain of polyadenylate binding proteins. Plant Cell 2008, 20:2387-2398.
46. Villar C.B., Erilova A., Makarevich G., Trösch R., Kohler C. Control of PHERES1 imprinting in Arabidopsis by direct tandem repeats. Mol. Plant 2009, 2:654-660.
47. Waters A.J., Makarevitcha I., Eichtena S.R., Swanson-Wagnera R.A., Yeh Ch.T., Xu W., Schnabl P.S., Vaughn M.W., Gehring M., Springer N.M. Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 2011, 23:4221-4233.
48. Weinhofer I., Hehenberger E., Roszak P., Hennig L., Köhler C. H3K27me3 profiling of the endosperm implies exclusion of polycombgroup protein targeting by DNA methylation. PLoS Genet. 2010, 6:e1001152.
49. Wolff, Weinhofer I., Seguin J., Roszak P., Beisel C., Donoghue M.T.A., Spillane C., Nordborg M., Rehmsmeter M., Kohler C. High-resolution analysis of parent-of origin allelic expression in the Arabidopsis endosperm. PLoS Genet. 2011, 7:e1002126.
50. Wolf J.B., Hager R. A maternal-offspring coadaptation theory for the evolution of genomic imprinting. PLoS Biol. 2006, 4:e380.
51. Zemach A., Kim M.Y., Silva P., Rodrigues J.A., Dotson B., Brooks M.D., Zilberman D. Local DNA hypomethylation activates genes in rice endosperm. Proc. Natl. Acad. Sci. USA 2010, 107:18729-18734.
52. Zhang L.G., Cheng Z.J., Qin R.Z., Qiu Y., Wang J.L., Cui X.K., Gu L.F., Zhang X., Guo X.P., Wang D., Jiang L., Wu C.Y., Wang H.Y., Cao X.F., Wan J.M. Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice. Plant Cell 2012, 4:4407-4421.
53. Zhang M., Zhao H.N., Xie S.J., Chen J., Xu Y.Y., Wang K.K., Zhao H.M., Guan H.Y., Hu X.J., Song W.B., Lai J.S. Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc. Natl. Acad. Sci. USA 2011, 108:20042-20047.