Perturbation of parentally biased gene expression during interspecific hybridization

PLoS ONE

Volumn 10, Issue 2, 2015, Pages

  Burkart Waco, Diana ^a   Ngo, Kathie ^a   Lieberman, Meric ^a   Comai, Luca ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS ARENOSA; ARABIDOPSIS THALIANA; ARTICLE; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; GENOME IMPRINTING; HOMEODOMAIN GLABROUS 3 GENE; INTERSPECIFIC HYBRIDIZATION; NONHUMAN; PHERES1 GENE; PLANT GENE; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; CHIMERA; GENETICS; GROWTH, DEVELOPMENT AND AGING; HYBRIDIZATION; METABOLISM; PLANT SEED;

ARABIDOPSIS; ARABIDOPSIS ARENOSA; ARABIDOPSIS THALIANA;

ARABIDOPSIS PROTEIN; MADS DOMAIN PROTEIN; PHERES1 PROTEIN, ARABIDOPSIS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHIMERA; GENOMIC IMPRINTING; HYBRIDIZATION, GENETIC; MADS DOMAIN PROTEINS; SEEDS;

EID: 84923899588     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0117293     Document Type: Article

References (49)

1. Sharma DR, Kaur R, Kumar K (1996) Embryo rescue in plants-a review. Euphytica 89: 325-337.
2. Dilkes BP, Comai L (2004) A differential dosage hypothesis for parental effects in seed development. Plant Cell 16: 3174-3180. PMID: 15579806
3. Jullien PE, Kinoshita T, Ohad N, Berger F (2006) Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 18: 1360-1372. PMID: 16648367
4. Berger F, Chaudhury A (2009) Parental memories shape seeds. Trends Plant Sci 14: 550-556. doi: 10.1016/j.tplants.2009.08.003 PMID: 19748816
5. Adams S, Vinkenoog R, Spielman M, Dickinson HG, Scott RJ (2000) Parent-of-origin effects on seed development in Arabidopsis thaliana require DNA methylation. Development 127: 2493-2502. PMID: 10804189
6. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: 61-69. PMID: 17128275
7. Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y et al. (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124: 495-506. PMID: 16469697
8. Kohler C, Page DR, Gagliardini V, Grossniklaus U (2005) The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat Genet 37: 28-30. PMID: 15619622
9. Makarevich G, Villar CB, Erilova A, Kohler C (2008) Mechanism of PHERES1 imprinting in Arabidopsis. J Cell Sci 121: 906-912. doi: 10.1242/jcs.023077 PMID: 18303047
10. Gehring M, Missirian V, Henikoff S (2011) Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS One 6: e23687. doi: 10.1371/journal.pone.0023687 PMID: 21858209
11. Hsieh TF, Shin J, Uzawa R, Silva P, Cohen S et al. (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci U S A 108: 1755-1762. doi: 10.1073/pnas.1019273108 PMID: 21257907
12. Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C et al. (2011) High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm. PLoS Genet 7: e1002126. doi: 10.1371/journal. pgen.1002126 PMID: 21698132
13. Gehring M, Choi Y, Fischer RL (2004) Imprinting and seed development. Plant Cell 16 Suppl: S203-S213. PMID: 15010515
14. Barlow DP (2011) Genomic imprinting: a mammalian epigenetic discovery model. Annu Rev Genet 45: 379-403. doi: 10.1146/annurev-genet-110410-132459 PMID: 21942369
15. Kohler C, Weinhofer-Molisch I (2010) Mechanisms and evolution of genomic imprinting in plants. Heredity 105: 57-63. doi: 10.1038/hdy.2009.176 PMID: 19997125
16. Nodine MD, Bartel DP (2012) Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos. Nature 482: 94-97. doi: 10.1038/nature10756 PMID: 22266940
17. Del Toro-De Leon G, Garcia-Aguilar M, Gillmor CS (2014) Non-equivalent contributions of maternal and paternal genomes to early plant embryogenesis. Nature 514: 624-627. doi: 10.1038/nature13620 PMID: 25209660
18. Vielle-Calzada JP, Baskar R, Grossniklaus U (2000) Delayed activation of the paternal genome during seed development. Nature 404: 91-94. PMID: 10716449
19. Autran D, Baroux C, Raissig MT, Lenormand T, Wittig M et al. (2011) Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis. Cell 145: 707-719. doi: 10.1016/j. cell.2011.04.014 PMID: 21620136
20. Luo M, Taylor JM, Spriggs A, Zhang H, Wu X et al. (2011) A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet 7: e1002125. doi: 10. 1371/journal.pgen.1002125 PMID: 21731498
21. Jahnke S, Scholten S (2009) Epigenetic resetting of a gene imprinted in plant embryos. Curr Biol 19: 1677-1681. doi: 10.1016/j.cub.2009.08.053 PMID: 19781944
22. Haig D, WestobyM (1989) Parent-specific gene expression and the triploid endosperm. The American Naturalist 134: 147-155.
23. Hurst LD, McVean GT (1998) Do we understand the evolution of genomic imprinting? Curr Opin Genet Dev 8: 701-708. PMID: 9914201
24. Spencer HG, Clark AG (2014) Non-conflict theories for the evolution of genomic imprinting. Heredity (Edinb) 113: 112-118. doi: 10.1038/hdy.2013.129 PMID: 24398886
25. Beaudet AL, Jiang Y (2002) A rheostat model for a rapid and reversible form of imprinting-dependent evolution. Am J Hum Genet 70: 1389-1397. PMID: 11992247
26. Waters AJ, Bilinski P, Eichten SR, Vaughn MW, Ross-Ibarra J et al. (2013) Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species. Proc Natl Acad Sci U S A 110: 19639-19644. doi: 10.1073/pnas.1309182110 PMID: 24218619
27. Josefsson C, Dilkes B, Comai L (2006) Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol 16: 1322-1328. PMID: 16824920
28. Kohler C, Makarevich G (2006) Epigenetic mechanisms governing seed development in plants. EMBO Rep 7: 1223-1227. PMID: 17139298
29. Burkart-Waco D, Josefsson C, Dilkes BR, Kozloff N, Torjek O et al. (2011) Hybrid incompatibility in Arabidopsis is determined by a multi-locus genetic network. Plant Physiol
30. Paul W, Hodge R, Smartt S, Draper J, Scott R (1992) The isolation and characterisation of the tapetumspecific Arabidopsis thaliana A9 gene. Plant Mol Biol 19: 611-622. PMID: 1627774
31. Burkart-Waco D, Ngo K, Dilkes B, Josefsson C, Comai L (2013) Early disruption of maternal-zygotic interaction and activation of defense-like responses in Arabidopsis interspecific crosses. Plant Cell 25: 2037-2055. doi: 10.1105/tpc.112.108258 PMID: 23898028
32. Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH et al. (2000) Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell 12: 1551-1568. PMID: 11006331
33. Clauss MJ, Koch MA (2006) Poorly known relatives of Arabidopsis thaliana. Trends Plant Sci 11: 449-459. PMID: 16893672
34. Christodoulou DC, Gorham JM, Herman DS, Seidman JG (2011) Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Curr Protoc Mol Biol Chapter 4: Unit4.12. doi: 10.1002/0471142727.mb0412s94 PMID: 21472699
35. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi: 10.1093/bioinformatics/btp324 PMID: 19451168
36. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
37. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological) 289-300.
38. Huang DW, Sherman BT, Lempicki RA (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols 4: 44-57.
39. Anders S, HuberW(2010) Differential expression analysis for sequence count data. Genome Biol 11: R106. doi: 10.1186/gb-2010-11-10-r106 PMID: 20979621
40. Belmonte MF, Kirkbride RC, Stone SL, Pelletier JM, Bui AQ et al. (2013) Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proc Natl Acad Sci U S A 110: E435-E444. doi: 10.1073/pnas.1222061110 PMID: 23319655
41. Fitz Gerald JN, Hui PS, Berger F (2009) Polycomb group-dependent imprinting of the actin regulator AtFH5 regulates morphogenesis in Arabidopsis thaliana. Development 136: 3399-3404. doi: 10.1242/ dev.036921 PMID: 19783734
42. Shirzadi R, Andersen ED, Bjerkan KN, Gloeckle BM, Heese M et al. (2011) Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regulation of AGAMOUS-LIKE36. PLoS Genet 7: e1001303. doi: 10.1371/journal.pgen.1001303 PMID: 21379330
43. Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447-1451. doi: 10.1126/science.1171609 PMID: 19520961
44. Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X et al. (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303: 521-523. PMID: 14631047
45. Kradolfer D, Hennig L, Kohler C (2013) Increased maternal genome dosage bypasses the requirement of the FIS polycomb repressive complex 2 in Arabidopsis seed development. PLoS Genet 9: e1003163. doi: 10.1371/journal.pgen.1003163 PMID: 23326241
46. Gehring M (2013) Genomic imprinting: insights from plants. Annu Rev Genet 47: 187-208. doi: 10. 1146/annurev-genet-110711-155527 PMID: 24016190
47. Spillane C, Schmid KJ, Laoueille-Duprat S, Pien S, Escobar-Restrepo JM et al. (2007) Positive darwinian selection at the imprinted MEDEA locus in plants. Nature 448: 349-352. PMID: 17637669
48. Pignatta D, Erdmann RM, Scheer E, Picard CL, BellGWet al. (2014) Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. Elife 3: e03198. doi: 10.7554/eLife.03198 PMID: 24994762
49. Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14: 178-192. doi: 10.1093/bib/ bbs017 PMID: 22517427