Conserved imprinting associated with unique epigenetic signatures in the Arabidopsis genus

Nature Plants

Volumn 2, Issue 10, 2016, Pages

  Klosinska, Maja ^a   Picard, Colette L ^a,b   Gehring, Mary ^a,b  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; DNA METHYLATION; ENDOSPERM; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; GENOME IMPRINTING; MOLECULAR EVOLUTION;

ARABIDOPSIS; DNA METHYLATION; ENDOSPERM; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; GENOMIC IMPRINTING;

EID: 84990206476     PISSN: None     EISSN: 20550278     Source Type: Journal    
DOI: 10.1038/nplants.2016.145     Document Type: Article

References (30)

1. Gehring, M. Genomic imprinting: insights from plants. Annu. Rev. Genet. 47, 187-208 (2013).
2. Haig, D. and Westoby, M. Parent-specific gene expression and the triploid endosperm. Am. Nat. 134, 147-155 (1989).
3. Hsieh, T.-F. et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proc. Natl Acad. Sci. USA 108, 1755-1762 (2011).
4. Wolff, P. et al. High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm. PLoS Genet. 7, e1002126 (2011).
5. Gehring, M., Missirian, V. and Henikoff, S. Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS ONE 6, e23687 (2011).
6. Pignatta, D. et al. Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. eLife e03198 (2014).
7. Luo, M. et al. A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet. 7, e1002125 (2011).
8. Waters, A. J. et al. Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 23, 4221-4233 (2012).
9. Xin, M. et al. Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development. Plant Cell 25, 3212-3227 (2013).
10. Zhang, M. et al. Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc. Natl Acad. Sci. USA 108, 20042-20047 (2011).
11. Zhang, M. et al. Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize. Genome Res. 24, 167-176 (2014).
12. Moreno-Romero, J., Jiang, H., Santos-Gonzalez, J. and Kohler, C. Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm. EMBO J. 35, 1298-1311 (2016).
13. Patten, M. M. et al. The evolution of genomic imprinting: theories, predictions and empirical tests. Heredity 113, 119-128 (2014).
14. Waters, A. J. et al. 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 (2013).
15. Berger, F., Vu, T. M., Li, J. and Chen, B. Hypothesis: selection of imprinted genes is driven by silencing deleterious gene activity in somatic tissues. Cold Spring Harb. Symp. Quant. Biol. 77, 23-29 (2012).
16. Kawashima, T. and Berger, F. Epigenetic reprogramming in plant sexual reproduction. Nat. Rev. Genet. 15, 613-624 (2014).
17. Beilstein, M. A., Nagalingum, N. S., Clements, M. D., Manchester, S. R. and Mathews, S. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 107, 18724-18728 (2010).
18. Morison, I. M. and Reeve, A. E. A catalogue of imprinted genes and parent-oforigin effects in humans and animals. Hum. Mol. Genet. 7, 1599-1609 (1998).
19. Danilevskaya, O. N. et al. Duplicated fie genes in maize: expression pattern and imprinting suggest distinct functions. Plant Cell 15, 425-438 (2003).
20. Matzke, M. A. and Mosher, R. A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15, 394-408 (2014).
21. Gehring, M., Bubb, K. L. and Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447-1451 (2009).
22. Ibarra, C. A. et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360-1364 (2012).
23. Du, J. et al. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151, 167-180 (2012).
24. Saze, H., Shiraishi, A., Miura, A. and Kakutani, T. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 319, 462-465 (2008).
25. Rigal, M., Kevei, Z., Pelissier, T. and Mathieu, O. DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns. EMBO J. 31, 2981-2993 (2012).
26. Schatlowski, N. et al. Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis. Plant Cell 26, 3556-3568 (2014).
27. Deleris, A. et al. Loss of the DNA methyltransferase MET1 induces H3K9 hypermethylation at PcG target genes and redistribution of H3K27 trimethylation to transposons in Arabidopsis thaliana. PLoS Genet. 8, e1003062 (2012).
28. Hu, T. T. et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476-481 (2011).
29. Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
30. Krueger, F. and Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572 (2011).