[1] |
MITA P, BOEKE J D. How retrotransposons shape genome regulation [J]. Curr Opin Genet Dev, 2016, 37: 90 − 100. |
[2] |
FINNEGAN D J. Eukaryotic transposable elements and genome evolution [J]. Trends Genet, 1989, 5(4): 103 − 107. |
[3] |
WICKER T, SABOT F, HUA-VAN A, et al. A unified classification system for eukaryotic transposable elements [J]. Nat Rev Genet, 2007, 8(12): 973 − 982. |
[4] |
SCHULMAN A H. Retrotransposon replication in plants [J]. Curr Opin Virol, 2013, 3(6): 604 − 614. |
[5] |
OROZCO-ARIAS S, ISAZA G, GUYOT R. Retrotransposons in plant genomes: structure, identification, and classification through bioinformatics and machine learning [J]. Int J Mol Sci, 2019, 20(15): 3837. doi: 10.3390/ijms20153837. |
[6] |
GONZALEZ J, PETROV D A. Evolution of genome content: population dynamics of transposable elements in flies and humans[C]//ANISIMOVA M. Evolutionary Genomics. Methods in Molecular Biology (Methods and Protocols), vol 855. Totowa: Humana Press, 2012: 361 − 383. |
[7] |
de KONING A P J, GU Wanjun, CASTOE T A, et al. Repetitive elements may comprise over two-thirds of the human genome[J]. PLoS Genet, 2011, 7(12): e1002384. doi: 10.1371/journal.pgen.1002384. |
[8] |
SAVAGE A L, SCHUMANN G G, BREEN G, et al. Retrotransposons in the development and progression of amyotrophic lateral sclerosis [J]. J Neurol Neurosurg Psychiatry, 2019, 90(3): 284 − 293. |
[9] |
LANDER E S, LINTON L M, BIRREN B, et al. Initial sequencing and analysis of the human genome [J]. Nature, 2001, 409(6822): 860 − 921. |
[10] |
YANG Fang, WANG P J. Multiple LINEs of retrotransposon silencing mechanisms in the mammalian germline [J]. Semin Cell Dev Biol, 2016, 59: 118 − 125. |
[11] |
CHOULET F, WICKER T, RUSTENHOLZ C, et al. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces [J]. Plant Cell, 2010, 22(6): 1686 − 1701. |
[12] |
SONG Xianwei, CAO Xiaofeng. Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice [J]. Curr Opin Plant Biol, 2017, 36: 111 − 118. |
[13] |
SASAKI T. The map-based sequence of the rice genome [J]. Nature, 2005, 436(7052): 793 − 800. |
[14] |
JIAO Yinping, PELUSO P, SHI Jinghua, et al. Improved maize reference genome with single-molecule technologies [J]. Nature, 2017, 546(7659): 524 − 527. |
[15] |
SCHNABLE P S, WARE D, FULTON R S, et al. The B73 maize genome: complexity, diversity, and dynamics [J]. Science, 2009, 326(5956): 1112 − 1115. |
[16] |
ENNOS R A, CLEGG M T. Flower color variation in the morning glory, Ipomoea purpurea [J]. J Hered, 1983, 74(4): 247 − 250. |
[17] |
BUTELLI E, LICCIARDELLO C, ZHANG Yang, et al. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges [J]. Plant Cell, 2012, 24(3): 1242 − 1255. |
[18] |
LISCH D. How important are transposons for plant evolution? [J]. Nat Rev Genet, 2013, 14(1): 49 − 61. |
[19] |
BENOIT M, DROST H G, CATONI M, et al. Environmental and epigenetic regulation of Rider retrotransposons in tomato[J]. PLoS Genet, 2019, 15(9): e1008370. doi: 10.1371/journal.pgen.1008370. |
[20] |
SANCHEZ D H, GAUBERT H, YANG Weibing. Evidence of developmental escape from transcriptional gene silencing in MESSI retrotransposons [J]. New Phytol, 2019, 223(2): 950 − 964. |
[21] |
KUBOTA S, ISHIKAWA T, KAWATA K, et al. Retrotransposons manipulating mammalian skeletal development in chondrocytes[J]. Int J Mol Sci, 2020, 21(5): 1564. doi: 10.3390/ijms21051564. |
[22] |
BUNDO M, TOYOSHIMA M, OKADA Y, et al. Increased l1 retrotransposition in the neuronal genome in schizophrenia [J]. Neuron, 2014, 81(2): 306 − 313. |
[23] |
陈文充, 贾宁, 董昂, 等. 山核桃甲基化敏感扩增多态体系的建立与甲基化初步分析[J]. 浙江农林大学学报, 2019, 36(3): 468 − 478.
CHEN Wenchong, JIA Ning, DONG Ang, et al. A protocol for methylation-sensitive amplified polymorphism markers and its application to a methylation analysis in Carya cathayensis [J]. J Zhejiang A&F Univ, 2019, 36(3): 468 − 478. |
[24] |
HANCKS D C, KAZAZIAN H H. Roles for retrotransposon insertions in human disease[J]. Mob DNA, 2016, 7: 9. doi: 10.1186/s13100-016-0065-9. |
[25] |
SCOTT E C, GARDNER E J, MASOOD A, et al. A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer [J]. Genome Res, 2016, 26(6): 745 − 755. |
[26] |
MAO Hude, WANG Hongwei, LIU Shengxue, et al. A transposable element in a NAC gene is associated with drought tolerance in maize seedlings [J]. Nat Commun, 2015, 6(1): 1 − 13. |
[27] |
MOLARO A, MALIK H S. Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline [J]. Curr Opin Genet Dev, 2016, 37: 51 − 58. |
[28] |
CHOI Y J, LIN C P, RISSO D, et al. Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells [J]. Science, 2017, 355(6325): eaag1927. doi: 10.1126/science.aag1927. |
[29] |
HUTCHISON C A, MERRYMAN C, SUN Lijie, et al. Polar effects of transposon insertion into a minimal bacterial genome [J]. J Bacteriol, 2019, 201(19): e00185-19. doi: 10.1128/JB.00185-19. |
[30] |
FURNER I J, MATZKE M. Methylation and demethylation of the Arabidopsis genome [J]. Curr Opin Plant Biol, 2011, 14(2): 137 − 141. |
[31] |
DENIZ Ö, FROST J M, BRANCO M R. Author correction: regulation of transposable elements by DNA modifications [J]. Nat Rev Genet, 2019, 20(7): 432 − 432. |
[32] |
CHAN S W L, HENDERSON I R, JACOBSEN S E. Gardening the genome: DNA methylation in Arabidopsis thaliana [J]. Nat Rev Genet, 2005, 6(5): 351 − 360. |
[33] |
GIRARD A, HANNON G J. Conserved themes in small-RNA-mediated transposon control [J]. Trends Cell Biol, 2008, 18(3): 136 − 148. |
[34] |
LI Qing, GENT J I, ZYNDA G, et al. RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome [J]. Proc Natl Acad Sci, 2015, 112(47): 14728 − 14733. |
[35] |
JÖNSSON M E, BRATTÅS P L, GUSTAFSSON C, et al. Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors [J]. Nat Commun, 2019, 10: 3182. doi: 10.1038/s41467-019-11150-8. |
[36] |
LIU Nian, LEE C H, SWIGUT T, et al. Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators [J]. Nature, 2018, 553(7687): 228 − 232. |
[37] |
CUI Xiekui, JIN Ping, CUI Xia, et al. Control of transposon activity by a histone H3K4 demethylase in rice [J]. Proc Natl Acad Sci, 2013, 110(5): 1953 − 1958. |
[38] |
WANG Dafang, ZHANG Jianbo, ZUO Tao, et al. Small RNA-mediated De Novo silencing of Ac/Ds transposons is initiated by alternative transposition in maize [J]. Genetics, 2020, 215(2): 393 − 406. |
[39] |
CAPPUCCI U, NORO F, CASALE A M, et al. The Hsp70 chaperone is a major player in stress-induced transposable element activation [J]. Proc Natl Acad Sci, 2019, 116(36): 17943 − 17950. |
[40] |
BARTHOLOMEW B. Regulating the chromatin landscape: structural and mechanistic perspectives [J]. Annu Rev Biochem, 2014, 83: 671 − 696. |
[41] |
HORVÁTH V, MERENCIANO M, GONZÁLEZ J. Revisiting the relationship between transposable elements and the eukaryotic stress response [J]. Trends Genet, 2017, 33(11): 832 − 841. |
[42] |
JIE Yang, YUAN Lianyu, YEN M R, et al. SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis [J]. Plant J, 2019, 102(4): 809 − 822. |
[43] |
陈昂. 毛竹微型反向重复转座子(MITEs)鉴定及对宿主基因表达的影响[D]. 杭州: 浙江农林大学, 2016.
CHEN Ang. Identification of Miniature Inverted Repeat Transposable Elements (MITEs) from Phyllostachys edulis and Their Effects on Host Gene Expression[D]. Hangzhou: Zhejiang A&F University, 2016. |
[44] |
ZHOU Mingbing, LIANG Linlin, HÄNNINEN H. A transposition-active Phyllostachys edulis long terminal repeat (LTR) retrotransposon [J]. J Plant Res, 2018, 131(2): 203 − 210. |
[45] |
WANG Zhengming, BAULCOMBE D C. Transposon age and non-CG methylation [J]. Nat Commun, 2020, 11: 1221. doi: 10.1038/s41467-020-14995-6. |
[46] |
ZHANG Huiming, LANG Zhaobo, ZHU Jiankang. Dynamics and function of DNA methylation in plants [J]. Nat Rev Mol Cell Biol, 2018, 19(8): 489 − 506. |
[47] |
KIM M Y, ZILBERMAN D. DNA methylation as a system of plant genomic immunity [J]. Trends Plant Sci, 2014, 19(5): 320 − 326. |
[48] |
CZECH B, HANNON G J. One loop to rule them all: the ping-pong cycle and piRNA-guided silencing [J]. Trends Biochem Sci, 2016, 41(4): 324 − 337. |
[49] |
XU Le, YUAN Kun, YUAN Meng, et al. Regulation of rice tillering by RNA-Directed DNA methylation at miniature inverted-repeat transposable elements [J]. Mol Plant, 2020, 13(6): 851 − 863. |
[50] |
MIROUZE M, REINDERS J, BUCHER E, et al. Selective epigenetic control of retrotransposition in Arabidopsis [J]. Nature, 2009, 461(7262): 427 − 430. |
[51] |
CHENG Chaoyang, TARUTANI Y, MIYAO A, et al. Loss of function mutations in the rice chromomethylase Os CMT 3a cause a burst of transposition [J]. Plant J, 2015, 83(6): 1069 − 1081. |
[52] |
HU Lanjuan, LI Ning, ZHANG Zhibin, et al. CG hypomethylation leads to complex changes in DNA methylation and transpositional burst of diverse transposable elements in callus cultures of rice [J]. Plant J, 2020, 101: 188 − 203. |
[53] |
ROWE H M, JAKOBSSON J, MESNARD D, et al. KAP1 controls endogenous retroviruses in embryonic stem cells [J]. Nature, 2010, 463(7278): 237 − 240. |
[54] |
MATSUI T, LEUNG D, MIYASHITA H, et al. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET [J]. Nature, 2010, 464(7290): 927 − 931. |
[55] |
IMBEAULT M, HELLEBOID P Y, TRONO D. KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks [J]. Nature, 2017, 543(7646): 550 − 554. |
[56] |
BERRENS R V, ANDREWS S, SPENSBERGER D, et al. An endosiRNA-based repression mechanism counteracts transposon activation during global DNA demethylation in embryonic stem cells [J]. Cell Stem Cell, 2017, 21(5): 694 − 703. |
[57] |
NOUROZ F, NOREEN S, HESLOP-HARRISON J S. Identification and evolutionary dynamics of CACTA DNA transposons in brassica [J]. Pak J Bot, 2017, 49(2): 789 − 798. |
[58] |
WANG Qingbiao, WANG Yanping, SUN Honghe, et al. Transposon-induced methylation of the RsMYB1 promoter disturbs anthocyanin accumulation in red-fleshed radish [J]. J Exp Bot, 2020, 71(9): 2537 − 2550. |
[59] |
KONG Yu, ROSE C M, CASS A A, et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity [J]. Nat Commun, 2019, 10: 5228. doi: 10.1038/s41467-019-13035-2. |
[60] |
LA Honggui, DING Bo, MISHRA G P, et al. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice [J]. Proc Natl Acad Sci, 2011, 108(37): 15498 − 15503. |
[61] |
KASHINO-FUJII M, YOKOSHO K, YAMAJI N, et al. Retrotransposon insertion and DNA methylation regulate aluminum tolerance in European barley accessions [J]. Plant Physiol, 2018, 178(2): 716 − 727. |
[62] |
CHOI J Y, PURUGGANAN M D. Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice [J]. Mol Biol Evol, 2018, 35(2): 365 − 382. |
[63] |
WALSH C P, CHAILLET J R, BESTOR T H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation [J]. Nat Genet, 1998, 20(2): 116 − 117. |
[64] |
ZHOU Y, CAMBARERI E, KINSEY J. DNA methylation inhibits expression and transposition of the neurospora tad retrotransposon [J]. Mol Genet Genomics, 2001, 265(4): 748 − 754. |
[65] |
CHERNYAVSKAYA Y, MUDBHARY R, ZHANG Chi, et al. Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling [J]. Development, 2017, 144(16): 2925 − 2939. |
[66] |
HOSAKA A, SAITO R, TAKASHIMA K, et al. Evolution of sequence-specific anti-silencing systems in Arabidopsis [J]. Nat Commun, 2017, 8: 2161. doi: 10.1038/s41467-017-02150-7. |
[67] |
FU Yu, KAWABE A, ETCHEVERRY M, et al. Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor [J]. EMBO J, 2013, 32(17): 2407 − 2417. |
[68] |
CUI Hongchang, FEDOROFF N V. Inducible DNA demethylation mediated by the maize suppressor-mutator transposon-encoded TnpA protein [J]. Plant Cell, 2002, 14(11): 2883 − 2899. |
[69] |
DUAN Chengguo, WANG Xingang, XIE Shaojun, et al. A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation [J]. Cell Res, 2017, 27(2): 226 − 240. |
[70] |
QIAN Weiqiang, MIKI D, ZHANG Heng, et al. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis [J]. Science, 2012, 336(6087): 1445 − 1448. |
[71] |
CHEN Xiaochao, SCHÖNBERGER B, MENZ J, et al. Plasticity of DNA methylation and gene expression under zinc deficiency in Arabidopsis roots [J]. Plant Cell Physiol, 2018, 59(9): 1790 − 1802. |
[72] |
MAGER S, LUDEWIG U. Massive loss of DNA methylation in nitrogen-, but not in phosphorus-deficient Zea mays roots is poorly correlated with gene expression differences [J]. Front Plant Sci, 2018, 9: 497. doi: 10.3389/fpls.2018.00497. |
[73] |
FERREIRA L J, AZEVEDO V, MAROCO J, et al. Salt tolerant and sensitive rice varieties display differential methylome flexibility under salt stress [J]. PLoS One, 2015, 10(5): e0124060. doi: 10.1371/journal.pone.0124060. |
[74] |
RODRÍGUEZ-NEGRETE E, LOZANO-DURÁN R, PIEDRA-AGUILERA A, et al. Geminivirus Rep protein interferes with the plant DNA methylation machinery and suppresses transcriptional gene silencing [J]. New Phytol, 2013, 199(2): 464 − 475. |
[75] |
LIANG Xiong, HOU Xue, LI Jianying, et al. High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean [J]. BMC Plant Biol, 2019, 19(1): 79. doi: 10.1186/s12870-019-1670-9. |
[76] |
YU A, LEPÈRE G, JAY F, et al. Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense [J]. Proc Natl Acad Sci, 2013, 110(6): 2389 − 2394. |
[77] |
ZHANG Meng, ZHANG Xuexian, GUO Liping, et al. Single-base resolution methylomes of cotton CMS system reveal epigenomic changes in response to high-temperature stress during anther development [J]. J Exp Bot, 2019, 71(3): 951 − 969. |
[78] |
HE S, VICKERS M, ZHANG J, et al. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation [J]. eLife, 2019, 8: e42530. doi: 10.7554/eLife.42530.002. |
[79] |
NISHIMURA H, HIMI E, EUN C H, et al. Transgenerational activation of an autonomous DNA transposon, Dart1-24, by 5-azaC treatment in rice [J]. Theor Appl Genet, 2019, 132(12): 3347 − 3355. |
[80] |
SECCO D, WANG Chuang, SHOU Huixia, et al. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements [J]. eLife, 2015, 4: e09343. doi: 10.7554/eLife.09343.001. |
[81] |
KOFLER R. Dynamics of transposable element invasions with piRNA clusters [J]. Mol Biol Evol, 2019, 36(7): 1457 − 1472. |
[82] |
GRAY Y H M. It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements [J]. Trends Genet, 2000, 16(10): 461 − 468. |