Epigenetic regulation and functional exaptation of transposable elements in higher plants

Current Opinion in Plant Biology - Tập 21 - Trang 83-88 - 2014
Xiekui Cui1, Xiaofeng Cao1
1State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

Tài liệu tham khảo

Lisch, 2013, How important are transposons for plant evolution?, Nat Rev Genet, 14, 49, 10.1038/nrg3374 Rebollo, 2012, Transposable elements: an abundant and natural source of regulatory sequences for host genes, Annu Rev Genet, 46, 21, 10.1146/annurev-genet-110711-155621 Mc, 1951, Chromosome organization and genic expression, Cold Spring Harb Symp Quant Biol, 16, 13, 10.1101/SQB.1951.016.01.004 McClintock, 1956, Controlling elements and the gene, Cold Spring Harb Symp Quant Biol, 21, 197, 10.1101/SQB.1956.021.01.017 Feschotte, 2002, Plant transposable elements: where genetics meets genomics, Nat Rev Genet, 3, 329, 10.1038/nrg793 Doolittle, 1980, Selfish genes, the phenotype paradigm and genome evolution, Nature, 284, 601, 10.1038/284601a0 Orgel, 1980, Selfish DNA: the ultimate parasite, Nature, 284, 604, 10.1038/284604a0 Bennetzen, 2014, The contributions of transposable elements to the structure, function, and evolution of plant genomes, Annu Rev Plant Biol, 10.1146/annurev-arplant-050213-035811 Schnable, 2009, The B73 maize genome: complexity, diversity, and dynamics, Science, 326, 1112, 10.1126/science.1178534 2005, International Rice Genome Sequencing P: the map-based sequence of the rice genome, Nature, 436, 793, 10.1038/nature03895 Gore, 2009, A first-generation haplotype map of maize, Science, 326, 1115, 10.1126/science.1177837 Lisch, 2009, Epigenetic regulation of transposable elements in plants, Annu Rev Plant Biol, 60, 43, 10.1146/annurev.arplant.59.032607.092744 Xie, 2004, Genetic and functional diversification of small RNA pathways in plants, PLoS Biol, 2, e104, 10.1371/journal.pbio.0020104 Law, 2010, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat Rev Genet, 11, 204, 10.1038/nrg2719 Zhong, 2014, Molecular mechanism of action of plant DRM de novo DNA methyltransferases, Cell, 157, 1050, 10.1016/j.cell.2014.03.056 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 Jeddeloh, 1999, Maintenance of genomic methylation requires a SWI2/SNF2-like protein, Nat Genet, 22, 94, 10.1038/8803 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 Inagaki, 2010, Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome, EMBO J, 29, 3496, 10.1038/emboj.2010.227 Johnson, 2007, The SRA methyl-cytosine-binding domain links DNA and histone methylation, Curr Biol, 17, 379, 10.1016/j.cub.2007.01.009 Slotkin, 2009, Epigenetic reprogramming and small RNA silencing of transposable elements in pollen, Cell, 136, 461, 10.1016/j.cell.2008.12.038 Creasey, 2014, miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis, Nature, 508, 411, 10.1038/nature13069 Song, 2012, Roles of DCL4 and DCL3b in rice phased small RNA biogenesis, Plant J, 69, 462, 10.1111/j.1365-313X.2011.04805.x Song, 2012, Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development, Plant J, 71, 378 Gehring, 2009, Extensive demethylation of repetitive elements during seed development underlies gene imprinting, Science, 324, 1447, 10.1126/science.1171609 Hsieh, 2009, Genome-wide demethylation of Arabidopsis endosperm, Science, 324, 1451, 10.1126/science.1172417 Miura, 2001, Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis, Nature, 411, 212, 10.1038/35075612 Tsukahara, 2009, Bursts of retrotransposition reproduced in Arabidopsis, Nature, 461, 423, 10.1038/nature08351 Johannes, 2009, Assessing the impact of transgenerational epigenetic variation on complex traits, PLoS Genet, 5, e1000530, 10.1371/journal.pgen.1000530 Reinders, 2009, Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes, Genes Dev, 23, 939, 10.1101/gad.524609 Mirouze, 2009, Selective epigenetic control of retrotransposition in Arabidopsis, Nature, 461, 427, 10.1038/nature08328 Mari-Ordonez, 2013, Reconstructing de novo silencing of an active plant retrotransposon, Nat Genet, 45, 1029, 10.1038/ng.2703 Reinders, 2013, Parent-of-origin control of transgenerational retrotransposon proliferation in Arabidopsis, EMBO Rep, 14, 823, 10.1038/embor.2013.95 Tsukahara, 2012, Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata, Genes Dev, 26, 705, 10.1101/gad.183871.111 Ding, 2007, SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice, Plant Cell, 19, 9, 10.1105/tpc.106.048124 La, 2011, A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice, Proc Natl Acad Sci U S A, 108, 15498, 10.1073/pnas.1112704108 Cui, 2013, Control of transposon activity by a histone H3K4 demethylase in rice, Proc Natl Acad Sci U S A, 110, 1953, 10.1073/pnas.1217020110 Baubec, 2014, Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis, EMBO Rep, 15, 446, 10.1002/embr.201337915 Grandbastien, 2004, Stress activation and genomic impact of plant retrotransposons, J Soc Biol, 198, 425, 10.1051/jbio/2004198040425 Pecinka, 2010, Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis, Plant Cell, 22, 3118, 10.1105/tpc.110.078493 Tittel-Elmer, 2010, Stress-induced activation of heterochromatic transcription, PLoS Genet, 6, e1001175, 10.1371/journal.pgen.1001175 Ito, 2011, An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress, Nature, 472, 115, 10.1038/nature09861 Wang, 2010, Mutations in retrotransposon AtCOPIA4 compromises resistance to Hyaloperonospora parasitica in Arabidopsis thaliana, Genet Mol Biol, 33, 135, 10.1590/S1415-47572009005000099 Jiang, 2004, Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs), Curr Opin Plant Biol, 7, 115, 10.1016/j.pbi.2004.01.004 Jiang, 2003, An active DNA transposon family in rice, Nature, 421, 163, 10.1038/nature01214 Kikuchi, 2003, The plant MITE mPing is mobilized in anther culture, Nature, 421, 167, 10.1038/nature01218 Nakazaki, 2003, Mobilization of a transposon in the rice genome, Nature, 421, 170, 10.1038/nature01219 Naito, 2006, Dramatic amplification of a rice transposable element during recent domestication, Proc Natl Acad Sci U S A, 103, 17620, 10.1073/pnas.0605421103 Naito, 2009, Unexpected consequences of a sudden and massive transposon amplification on rice gene expression, Nature, 461, 1130, 10.1038/nature08479 Studer, 2011, Identification of a functional transposon insertion in the maize domestication gene tb1, Nat Genet, 43, 1160, 10.1038/ng.942 Yang, 2013, CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize, Proc Natl Acad Sci U S A, 110, 16969, 10.1073/pnas.1310949110 Eichten, 2012, Spreading of heterochromatin is limited to specific families of maize retrotransposons, PLoS Genet, 8, e1003127, 10.1371/journal.pgen.1003127 Gent, 2013, CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize, Genome Res, 23, 628, 10.1101/gr.146985.112 Tsuchiya, 2013, An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication, Proc Natl Acad Sci U S A, 110, E3535, 10.1073/pnas.1312545110 McCue, 2012, Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA, PLoS Genet, 8, e1002474, 10.1371/journal.pgen.1002474 Nosaka, 2012, Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice, PLoS Genet, 8, e1002953, 10.1371/journal.pgen.1002953 Wei, 2014, Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice, Proc Natl Acad Sci U S A, 111, 3877, 10.1073/pnas.1318131111 Cortijo, 2014, Mapping the epigenetic basis of complex traits, Science, 343, 1145, 10.1126/science.1248127 Schmitz, 2014, Genetics. The secret garden-epigenetic alleles underlie complex traits, Science, 343, 1082, 10.1126/science.1251864