Imprinting meets genomics: New insights and new challenges

Current Opinion in Plant Biology

Volumn 15, Issue 5, 2012, Pages 530-535

  Pignatta, Daniela ^a   Gehring, Mary ^a  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYCOMB GROUP PROTEIN; VEGETABLE PROTEIN;

ALLELE; DNA METHYLATION; GENE EXPRESSION REGULATION; GENETICS; GENOME IMPRINTING; GENOMICS; METABOLISM; PLANT; REPRODUCTION; REVIEW;

ALLELES; DNA METHYLATION; GENE EXPRESSION REGULATION, PLANT; GENOMIC IMPRINTING; GENOMICS; PLANT PROTEINS; PLANTS; POLYCOMB-GROUP PROTEINS; REPRODUCTION;

DICOTYLEDONEAE; LILIOPSIDA;

EID: 84869502648     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2012.09.004     Document Type: Review

References (36)

1. Huh J.H., Bauer M.J., Hsieh T.F., Fischer R.L. Cellular programming of plant gene imprinting. Cell 2008, 132:735-744.
2. Kermicle J.L. Dependence of the R-mottled aleurone phenotype in maize on mode of sexual transmission. Genetics 1970, 66:69-85.
3. Barlow D.P. Genomic imprinting: a mammalian epigenetic discovery model. Annu Rev Genet 2011, 45:379-403.
4. Gehring M., Missirian V., Henikoff S. Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS ONE 2011, 6:e23687.
5. 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.
6. Wolff P., Weinhofer I., Seguin J., Roszak P., Beisel C., Donoghue M.T., Spillane C., Nordborg M., Rehmsmeier M., Kohler C. High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm. PLoS Genet 2011, 7:e1002126.
7. Waters A.J., Makarevitch I., Eichten S.R., Swanson-Wagner R.A., Yeh C.T., Xu W., Schnable 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.
8. Zhang M., Zhao H., Xie S., Chen J., Xu Y., Wang K., Guan H., Hu X., Jiao Y., Song W., Lai J. Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc Natl Acad Sci USA 2011, 108:20042-20047.
9. Luo M., Taylor J.M., Spriggs A., Zhang H., Wu X., 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.
10. Fontanillas P., Landry C.R., Wittkopp P.J., Russ C., Gruber J.D., Nusbaum C., Hartl D.L. Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol Ecol 2010, 19(Suppl 1):212-227.
11. Degner J.F., Marioni J.C., Pai A.A., Pickrell J.K., Nkadori E., Gilad Y., Pritchard J.K. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 2009, 25:3207-3212.
12. Haig D. Genomic imprinting and kinship: how good is the evidence?. Annu Rev Genet 2004, 38:553-585.
13. Dilkes B.P., Comai L. A differential dosage hypothesis for parental effects in seed development. Plant Cell 2004, 16:3174-3180.
14. Babak T., Deveale B., Armour C., Raymond C., Cleary M.A., van der Kooy D., Johnson J.M., Lim L.P. Global survey of genomic imprinting by transcriptome sequencing. Curr Biol 2008, 18:1735-1741.
15. Gregg C., Zhang J., Weissbourd B., Luo S., Schroth G.P., Haig D., Dulac C. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 2010, 329:643-648.
16. Wang X., Sun Q., McGrath S.D., Mardis E.R., Soloway P.D., Clark A.G. Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE 2008, 3:e3839.
17. Deveale B., van der Kooy D., Babak T. Critical evaluation of imprinted gene expression by RNA-seq: a new perspective. PLoS Genet 2012, 8:e1002600.
18. Wang X., Soloway P.D., Clark A.G. A survey for novel imprinted genes in the mouse placenta by mRNA-seq. Genetics 2011, 189:109-122.
19. Costa L.M., Yuan J., Rouster J., Paul W., Dickinson H., Gutierrez-Marcos J.F. Maternal control of nutrient allocation in plant seeds by genomic imprinting. Curr Biol 2012, 22:160-165.
20. Wolf J.B., Hager R. A maternal-offspring coadaptation theory for the evolution of genomic imprinting. PLoS Biol 2006, 4:e380.
21. Zhu J.K. Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 2009, 43:143-166.
22. Gehring M., Bubb K.L., Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science (New York, NY) 2009, 324:1447-1451.
23. 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.
24. Ikeda Y., Kinoshita Y., Susaki D., Iwano M., Takayama S., Higashiyama T., Kakutani T., Kinoshita T. HMG domain containing SSRP1 is required for DNA demethylation and genomic imprinting in Arabidopsis. Dev Cell 2011, 21:589-596.
25. Weinhofer I., Hehenberger E., Roszak P., Hennig L., Kohler C. H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet 2010, 6:e1001152.
26. Roszak P., Kohler C. Polycomb group proteins are required to couple seed coat initiation to fertilization. Proc Natl Acad Sci USA 2011, 108:20826-20831.
27. Heo J.B., Sung S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 2011, 331:76-79.
28. Kinoshita T., Miura A., Choi Y., Kinoshita Y., Cao X., Jacobsen S.E., Fischer R.L., Kakutani T. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 2004, 303:521-523.
29. Zhang X., Borevitz J.O. Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics 2009, 182:943-954.
30. Springer N.M., Stupar R.M. Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 2007, 19:2391-2402.
31. He G., Zhu X., Elling A.A., Chen L., Wang X., Guo L., Liang M., He H., Zhang H., Chen F., et al. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 2010, 22:17-33.
32. Nodine M.D., Bartel D.P. Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos. Nature 2012, 482:94-97.
33. Autran D., Baroux C., Raissig M.T., Lenormand T., Wittig M., Grob S., Steimer A., Barann M., Klostermeier U.C., Leblanc O., et al. Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis. Cell 2011, 145:707-719.
34. Bayer M., Nawy T., Giglione C., Galli M., Meinnel T., Lukowitz W. Paternal control of embryonic patterning in Arabidopsis thaliana. Science 2009, 323:1485-1488.
35. Jahnke S., Scholten S. Epigenetic resetting of a gene imprinted in plant embryos. Curr Biol 2009, 19:1677-1681.
36. Hale C.J., Jacobsen S.E. Plant biology: Equal-parenting policy. Nature 2012, 482:42-44.