Trans-chromosomal methylation

References

• Lippman ZB, Zamir D. Heterosis: revisiting the magic. Trends Genet 2007; 23:60 - 6; http://dx.doi.org/10.1016/j.tig.2006.12.006; PMID: 17188398
   PubMed Web of Science ®Google Scholar
• Hochholdinger F, Hoecker N. Towards the molecular basis of heterosis. Trends Plant Sci 2007; 12:427 - 32; http://dx.doi.org/10.1016/j.tplants.2007.08.005; PMID: 17720610
   PubMed Web of Science ®Google Scholar
• Birchler JA, Yao H, Chudalayandi S, Vaiman D, Veitia RA. Heterosis. Plant Cell 2010; 22:2105 - 12; http://dx.doi.org/10.1105/tpc.110.076133; PMID: 20622146
   PubMed Web of Science ®Google Scholar
• He GM, Zhu XP, Elling AA, Chen LB, Wang XF, Guo L, et al. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 2010; 22:17 - 33; http://dx.doi.org/10.1105/tpc.109.072041; PMID: 20086188
   PubMed Web of Science ®Google Scholar
• Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, et al. Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci U S A 2009; 106:17835 - 40; http://dx.doi.org/10.1073/pnas.0907003106; PMID: 19805056
   PubMed Web of Science ®Google Scholar
• Groszmann M, Greaves IK, Albertyn ZI, Scofield GN, Peacock WJ, Dennis ES. Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proc Natl Acad Sci U S A 2011; 108:2617 - 22; http://dx.doi.org/10.1073/pnas.1019217108; PMID: 21266545
   PubMed Web of Science ®Google Scholar
• Greaves IK, Groszmann M, Ying H, Taylor JM, Peacock WJ, Dennis ES. Trans chromosomal methylation in Arabidopsis hybrids. Proc Natl Acad Sci U S A 2012; 109:3570 - 5; http://dx.doi.org/10.1073/pnas.1201043109; PMID: 22331882
   PubMed Web of Science ®Google Scholar
• Shen H, He H, Li J, Chen W, Wang X, Guo L, et al. Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 2012; 24:875 - 92; http://dx.doi.org/10.1105/tpc.111.094870; PMID: 22438023
   PubMed Web of Science ®Google Scholar
• He X-J, Chen T, Zhu J-K. Regulation and function of DNA methylation in plants and animals. Cell Res 2011; 21:442 - 65; http://dx.doi.org/10.1038/cr.2011.23; PMID: 21321601
   PubMed Web of Science ®Google Scholar
• Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJM. Targets of RNA-directed DNA methylation. Curr Opin Plant Biol 2007; 10:512 - 9; http://dx.doi.org/10.1016/j.pbi.2007.06.007; PMID: 17702644
   PubMed Web of Science ®Google Scholar
• Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010; 11:204 - 20; http://dx.doi.org/10.1038/nrg2719; PMID: 20142834
   PubMed Web of Science ®Google Scholar
• Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008; 133:523 - 36; http://dx.doi.org/10.1016/j.cell.2008.03.029; PMID: 18423832
   PubMed Web of Science ®Google Scholar
• Cokus SJ, Feng SH, Zhang XY, Chen ZG, Merriman B, Haudenschild CD, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008; 452:215 - 9; http://dx.doi.org/10.1038/nature06745; PMID: 18278030
   PubMed Web of Science ®Google Scholar
• Soppe WJJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, et al. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 2000; 6:791 - 802; http://dx.doi.org/10.1016/S1097-2765(05)00090-0; PMID: 11090618
   PubMed Web of Science ®Google Scholar
• Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJJ, Koornneef M, et al. Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J 2007; 49:38 - 45; http://dx.doi.org/10.1111/j.1365-313X.2006.02936.x; PMID: 17144899
   PubMed Web of Science ®Google Scholar
• Cao XF, Jacobsen SE. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 2002; 12:1138 - 44; http://dx.doi.org/10.1016/S0960-9822(02)00925-9; PMID: 12121623
   PubMed Web of Science ®Google Scholar
• Chan SWL, Zhang X, Bernatavichute YV, Jacobsen SE. Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol 2006; 4:e363; http://dx.doi.org/10.1371/journal.pbio.0040363; PMID: 17105345
   PubMed Web of Science ®Google Scholar
• Chan SWL, Zilberman D, Xie ZX, Johansen LK, Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science 2004; 303:1336; http://dx.doi.org/10.1126/science.1095989; PMID: 14988555
   PubMed Web of Science ®Google Scholar
• Chandler VL. Paramutation’s properties and puzzles. Science 2010; 330:628 - 9; http://dx.doi.org/10.1126/science.1191044; PMID: 21030647
   PubMed Web of Science ®Google Scholar
• Stam M, Belele C, Dorweiler JE, Chandler VL. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev 2002; 16:1906 - 18; http://dx.doi.org/10.1101/gad.1006702; PMID: 12154122
   PubMed Web of Science ®Google Scholar
• Haring M, Bader R, Louwers M, Schwabe A, van Driel R, Stam M. The role of DNA methylation, nucleosome occupancy and histone modifications in paramutation. Plant J 2010; 63:366 - 78; http://dx.doi.org/10.1111/j.1365-313X.2010.04245.x; PMID: 20444233
   PubMed Web of Science ®Google Scholar
• Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, et al. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 2006; 442:295 - 8; http://dx.doi.org/10.1038/nature04884; PMID: 16855589
   PubMed Web of Science ®Google Scholar
• Arteaga-Vazquez M, Sidorenko L, Rabanal FA, Shrivistava R, Nobuta K, Green PJ, et al. RNA-mediated trans-communication can establish paramutation at the b1 locus in maize. Proc Natl Acad Sci U S A 2010; 107:12986 - 91; http://dx.doi.org/10.1073/pnas.1007972107; PMID: 20616013
   PubMed Web of Science ®Google Scholar
• Reinders J, Wulff BBH, Mirouze M, Marí-Ordóñez A, Dapp M, Rozhon W, et al. Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 2009; 23:939 - 50; http://dx.doi.org/10.1101/gad.524609; PMID: 19390088
   PubMed Web of Science ®Google Scholar
• Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, et al. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 2009; 5:e1000530; http://dx.doi.org/10.1371/journal.pgen.1000530; PMID: 19557164
   PubMed Web of Science ®Google Scholar
• Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, et al. A role for RNAi in the selective correction of DNA methylation defects. Science 2009; 323:1600 - 4; http://dx.doi.org/10.1126/science.1165313; PMID: 19179494
   PubMed Web of Science ®Google Scholar
• Tarutani Y, Shiba H, Iwano M, Kakizaki T, Suzuki G, Watanabe M, et al. Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility. Nature 2010; 466:983 - 6; http://dx.doi.org/10.1038/nature09308; PMID: 20725042
   PubMed Web of Science ®Google Scholar
• Luff B, Pawlowski L, Bender J. An inverted repeat triggers cytosine methylation of identical sequences in Arabidopsis. Mol Cell 1999; 3:505 - 11; http://dx.doi.org/10.1016/S1097-2765(00)80478-5; PMID: 10230403
   PubMed Web of Science ®Google Scholar
• Enke RA, Dong Z, Bender J. Small RNAs prevent transcription-coupled loss of histone H3 lysine 9 methylation in Arabidopsis thaliana. PLoS Genet 2011; 7:e1002350; http://dx.doi.org/10.1371/journal.pgen.1002350; PMID: 22046144
   PubMed Web of Science ®Google Scholar
• Groszmann M, Greaves IK, Albert N, Fujimoto R, Helliwell CA, Dennis ES, et al. Epigenetics in plants-vernalisation and hybrid vigour. Biochim Biophys Acta 2011; 1809:427 - 37; PMID: 21459171
   PubMed Web of Science ®Google Scholar
• Sasaki TKA, Kobayashi A, Saze H, Kakutani T. RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1. Plant J 2012; 70:750 - 8; http://dx.doi.org/10.1111/j.1365-313X.2012.04911.x; PMID: 22269081
   PubMed Web of Science ®Google Scholar
• Zhang XY, Yazaki J, Sundaresan A, Cokus S, Chan SWL, Chen HM, et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 2006; 126:1189 - 201; http://dx.doi.org/10.1016/j.cell.2006.08.003; PMID: 16949657
   PubMed Web of Science ®Google Scholar
• Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 2007; 39:61 - 9; http://dx.doi.org/10.1038/ng1929; PMID: 17128275
   PubMed Web of Science ®Google Scholar
• Pilu R. Paramutation: just a curiosity or fine tuning of gene expression in the next generation?. Curr Genomics 2011; 12:298 - 306; http://dx.doi.org/10.2174/138920211795860099; PMID: 22131875
   PubMed Web of Science ®Google Scholar
• Daxinger L, Whitelaw E. Transgenerational epigenetic inheritance: more questions than answers. Genome Res 2010; 20:1623 - 8; http://dx.doi.org/10.1101/gr.106138.110; PMID: 21041414
   PubMed Web of Science ®Google Scholar
• Ferguson-Smith AC. Genomic imprinting: the emergence of an epigenetic paradigm. Nat Rev Genet 2011; 12:565 - 75; http://dx.doi.org/10.1038/nrg3032; PMID: 21765458
   PubMed Web of Science ®Google Scholar
• Watanabe T, Tomizawa S-i, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, et al. Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science 2011; 332:848 - 52; http://dx.doi.org/10.1126/science.1203919; PMID: 21566194
   PubMed Web of Science ®Google Scholar