Covering Your Bases: Inheritance of DNA Methylation in Plant Genomes

Molecular Plant - Tập 7 - Trang 472-480 - 2014
Chad E. Niederhuth1, Robert J. Schmitz1
1Department of Genetics, University of Georgia, Athens, GA 30602, USA

Tài liệu tham khảo

Ahmed, 2011, Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis, Nucleic Acids Res, 39, 6919, 10.1093/nar/gkr324 Becker, 2011, Spontaneous epigenetic variation in the Arabidopsis thaliana methylome, Nature, 480, 245, 10.1038/nature10555 Bender, 1995, Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis, Cell, 83, 725, 10.1016/0092-8674(95)90185-X Brink, 1956, A genetic change associated with the R locus in maize which is directed and potentially reversible, Genetics, 41, 872, 10.1093/genetics/41.6.872 Calarco, 2012, Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA, Cell, 151, 194, 10.1016/j.cell.2012.09.001 Chan, 2006, Two-step recruitment of RNA-directed DNA methylation to tandem repeats, PLoS Biol, 4, e363, 10.1371/journal.pbio.0040363 Coe, 1968, Heritable repression due to paramutation in maize, Science, 162, 925, 10.1126/science.162.3856.925 Cokus, 2008, Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature, 452, 215, 10.1038/nature06745 Coleman-Derr, 2012, Deposition of histone variant H2A.Z within gene bodies regulates responsive genes, PLoS Genet, 8, e1002988, 10.1371/journal.pgen.1002988 Colome-Tatche, 2012, Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation, Proc. Natl Acad. Sci. U S A, 109, 16240, 10.1073/pnas.1212955109 Cubas, 1999, An epigenetic mutation responsible for natural variation in floral symmetry, Nature, 401, 157, 10.1038/43657 Dowen, 2012, Widespread dynamic DNA methylation in response to biotic stress, Proc. Natl Acad. Sci. U S A, 10.1073/pnas.1209329109 Du, 2012, Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants, Cell, 151, 167, 10.1016/j.cell.2012.07.034 Durand, 2012, Rapid establishment of genetic incompatibility through natural epigenetic variation, Curr. Biol, 22, 326, 10.1016/j.cub.2011.12.054 Eichten, 2013, Epigenetic and genetic influences on DNA methylation variation in maize populations, Plant Cell, 25, 2783, 10.1105/tpc.113.114793 Eichten, 2012, Spreading of heterochromatin is limited to specific families of maize retrotransposons, PLoS Genet, 8, e1003127, 10.1371/journal.pgen.1003127 Eichten, 2011, Heritable epigenetic variation among maize inbreds, PLoS Genet, 7, e1002372, 10.1371/journal.pgen.1002372 Feng, 2010, Conservation and divergence of methylation patterning in plants and animals, Proc. Natl Acad. Sci. U S A, 107, 8689, 10.1073/pnas.1002720107 Finnegan, 1998, DNA methylation in plants, Annu. Rev. Plant Physiol. Plant Mol. Biol, 49, 223, 10.1146/annurev.arplant.49.1.223 Finnegan, 1996, Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development, Proc. Natl Acad. Sci. U S A, 93, 8449, 10.1073/pnas.93.16.8449 Hauben, 2009, Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield, Proc. Natl Acad. Sci. U S A, 106, 20109, 10.1073/pnas.0908755106 Hollick, 1995, Allelic interactions heritably alter the activity of a metastable maize pl allele, Genetics, 141, 709, 10.1093/genetics/141.2.709 Hollister, 2009, Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression, Genome Res, 19, 1419, 10.1101/gr.091678.109 Ibarra, 2012, Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes, Science, 337, 1360, 10.1126/science.1224839 Johannes, 2009, Assessing the impact of transgenerational epigenetic variation on complex traits, PLoS Genet, 5, e1000530, 10.1371/journal.pgen.1000530 Law, 2010, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat. Rev. Genet, 11, 204, 10.1038/nrg2719 Lister, 2009, Finding the fifth base: genome-wide sequencing of cytosine methylation, Genome Res, 19, 959, 10.1101/gr.083451.108 Lister, 2008, Highly integrated single-base resolution maps of the epigenome in Arabidopsis, Cell, 133, 523, 10.1016/j.cell.2008.03.029 Lister, 2009, Human DNA methylomes at base resolution show widespread epigenomic differences, Nature, 462, 315, 10.1038/nature08514 Liu, 2004, siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis, Genes Dev, 18, 2873, 10.1101/gad.1217304 Luff, 1999, An inverted repeat triggers cytosine methylation of identical sequences in Arabidopsis, Mol. Cell, 3, 505, 10.1016/S1097-2765(00)80478-5 Manning, 1999, Expression of FHIT in primary cultures of human epithelial ovarian tumors and malignant ovarian ascites, Mol. Carcinog, 24, 218, 10.1002/(SICI)1098-2744(199903)24:3<218::AID-MC8>3.0.CO;2-A Manning, 2006, A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening, Nat. Genet, 38, 948, 10.1038/ng1841 Mari-Ordonez, 2013, Reconstructing de novo silencing of an active plant retrotransposon, Nat. Genet, 45, 1029, 10.1038/ng.2703 Martin, 2009, A transposon-induced epigenetic change leads to sex determination in melon, Nature, 461, 1135, 10.1038/nature08498 Mathieu, 2007, Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation, Cell, 130, 851, 10.1016/j.cell.2007.07.007 Melquist, 1999, Arabidopsis PAI gene arrangements, cytosine methylation and expression, Genetics, 153, 401, 10.1093/genetics/153.1.401 Mirouze, 2012, Loss of DNA methylation affects the recombination landscape in Arabidopsis, Proc. Natl Acad. Sci. U S A, 109, 5880, 10.1073/pnas.1120841109 Ossowski, 2010, The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana, Science, 327, 92, 10.1126/science.1180677 Patterson, 1993, Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize b regulatory gene, Genetics, 135, 881, 10.1093/genetics/135.3.881 Regulski, 2013, The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA, Genome Res, 10.1101/gr.153510.112 Reinders, 2009, Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes, Genes Dev, 23, 939, 10.1101/gad.524609 Richards, 2006, Inherited epigenetic variation: revisiting soft inheritance, Nat. Rev. Genet, 7, 395, 10.1038/nrg1834 Richards, 2009, Quantitative epigenetics: DNA sequence variation need not apply, Genes Dev, 23, 1601, 10.1101/gad.1824909 Ronemus, 1996, Demethylation-induced developmental pleiotropy in Arabidopsis, Science, 273, 654, 10.1126/science.273.5275.654 Roux, 2011, Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature, Genetics, 188, 1015, 10.1534/genetics.111.128744 Schmitz, 2012, Epigenetic and epigenomic variation in Arabidopsis thaliana, Trends Plant Sci, 17, 149, 10.1016/j.tplants.2012.01.001 Schmitz, 2011, High-throughput approaches for plant epigenomic studies, Curr. Opin. Plant Biol, 14, 130, 10.1016/j.pbi.2011.03.010 Schmitz, 2013, Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population, Genome Res, 23, 1663, 10.1101/gr.152538.112 Schmitz, 2011, Transgenerational epigenetic instability is a source of novel methylation variants, Science, 334, 369, 10.1126/science.1212959 Schmitz, 2013, Patterns of population epigenomic diversity, Nature, 495, 193, 10.1038/nature11968 Schmutz, 2010, Genome sequence of the palaeopolyploid soybean, Nature, 463, 178, 10.1038/nature08670 Shaw, 2000, Spontaneous mutational effects on reproductive traits of Arabidopsis thaliana, Genetics, 155, 369, 10.1093/genetics/155.1.369 Sidorenko, 2001, Transgene-induced silencing identifies sequences involved in the establishment of paramutation of the maize p1 gene, Plant Cell, 13, 319, 10.1105/tpc.13.2.319 Silveira, 2013, Extensive natural epigenetic variation at a originated gene, PLoS Genet, 9, e1003437, 10.1371/journal.pgen.1003437 Slotkin, 2009, Epigenetic reprogramming and small RNA silencing of transposable elements in pollen, Cell, 136, 461, 10.1016/j.cell.2008.12.038 Springer, 2013, Epigenetics and crop improvement, Trends Genet, 29, 241, 10.1016/j.tig.2012.10.009 Stroud, 2013, Plants regenerated from tissue culture contain stable epigenome changes in rice, Elife, 2, e00354, 10.7554/eLife.00354 Stroud, 2013, Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome, Cell, 152, 352, 10.1016/j.cell.2012.10.054 Takuno, 2013, Gene body methylation is conserved between plant orthologs and is of evolutionary consequence, Proc. Natl Acad. Sci. U S A, 110, 1797, 10.1073/pnas.1215380110 Teixeira, 2009, A role for RNAi in the selective correction of DNA methylation defects, Science, 323, 1600, 10.1126/science.1165313 Thompson, 1999, Molecular and genetic characterization of a novel pleiotropic tomato-ripening mutant, Plant Physiol, 120, 383, 10.1104/pp.120.2.383 Vaughn, 2007, Epigenetic natural variation in Arabidopsis thaliana, PLoS Biol, 5, e174, 10.1371/journal.pbio.0050174 Vongs, 1993, Arabidopsis thaliana DNA methylation mutants, Science, 260, 1926, 10.1126/science.8316832 Walker, 1998, Paramutation of the r1 locus of maize is associated with increased cytosine methylation, Genetics, 148, 1973, 10.1093/genetics/148.4.1973 Weigel, 2012, Epialleles in plant evolution, Genome Biol, 13, 249, 10.1186/gb-2012-13-10-249 Woo, 2007, VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization, Genes Dev, 21, 267, 10.1101/gad.1512007 Zemach, 2013, The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin, Cell, 153, 193, 10.1016/j.cell.2013.02.033 Zemach, 2010, Genome-wide evolutionary analysis of eukaryotic DNA methylation, Science, 328, 916, 10.1126/science.1186366 Zhang, 2006, Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis, Cell, 126, 1189, 10.1016/j.cell.2006.08.003 Zhong, 2013, Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening, Nat. Biotechnol, 31, 154, 10.1038/nbt.2462 Zilberman, 2006, Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription, Nat. Genet, 39, 61, 10.1038/ng1929