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Regulation of transposable elements in maize
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Regulation of transposable elements in maize Damon Lisch Maize is a typical plant with respect to the proportion of its genome that is composed of transposable elements (TEs), but it is unusual in the number of well-characterized active TEs that it hosts. This has made it possible to examine in some detail the factors responsible for regulating the activity of these elements, particularly the means by which they are recognized and epigenetically silenced. That analysis has revealed that TE silencing is a complex process that involves careful distinctions of different developmental times and tissue types. The available evidence from maize and other species suggests that these distinctions are made in order to generate information in somatic tissues that can be used to induce or reinforce silencing in germinal tissues. Address Department of Plant and Microbial Biology, University of California, Berkeley, CA, 111 Koshland Hall, Berkeley, CA 94720, United States Corresponding author: Lisch, Damon ([email protected])
Current Opinion in Plant Biology 2012, 15:511–516 This review comes from a themed issue on Cell signaling and gene regulation Edited by Jerzy Paszkowski and Robert A. Martienssen For a complete overview see the Issue and the Editorial Available online 22nd July 2012 1369-5266/$ – see front matter, # 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.pbi.2012.07.001
Introduction Much of what we understand about regulation of transposable elements (TEs) in plants comes from analysis of TEs that have been successfully silenced [1]. This analysis has proved to be a rich source of information, and the stable maintenance of TE silencing is far more dynamic than had been anticipated [2,3]. However, in order to fully understand TEs regulation it is essential to examine the behavior of active elements. Maize is host to an unusual number of these elements, whose behavior and regulation has been characterized for decades. Analysis of active TEs in maize has revealed how damaging that activity can be. Among other things, it can result in chromosomal rearrangements [4], insertional mutagenesis [5] and mis-regulation of gene expression [6]. Although Barbara McClintock originally framed this activity as a mechanism whose function is to reorganize the genome, the vast majority of changes induced by TE activity are clearly not beneficial, and plants, like all www.sciencedirect.com
eukaryotes, appear to devote considerable resources to their control. Host regulation in the form of epigenetic silencing is the major theme in transposon control, and TEs are, by far, the major target of epigenetic regulation in plants. For instance, at least 85% of the maize genome is composed of epigenetically silenced TEs [7,8]. Given that maize has a low-average sized plant genome [9], we are left with the remarkable and somewhat paradoxical conclusion that the single most successful stretch of plant DNA is a TE that has been silenced. This brief review will highlight some recent advances in our understanding of TE regulation in maize, with a particular focus on epigenetic silencing of otherwise active elements.
Recognition and silencing of TEs in maize We have known for several decades that TEs can transition from active to silenced states (what McClintock called ‘changes of phase’), and that this process is associated with DNA methylation [10,11]. However it was only recently that a mechanism for this process was elucidated using the Mutator system of TEs. This system is a family of Class II ‘cut and paste’ elements in maize that includes the autonomous MuDR element as well as several classes of non-autonomous elements [12]. MuDR elements can be heritably silenced by Muk, a naturally occurring rearranged version of MuDR that expresses a hairpin transcript that triggers transcriptional gene silencing (TGS) of MuDR elements via trans-acting siRNAs [13] (Figure 1). Both the initiation and maintenance of silencing of this TE are associated with H3K27 and H3K9 dimethylation as well as cytosine methylation in all three sequence contexts [14]. Efficient and stabile silencing of MuDR by Muk requires RMR1 (a chromatin remodeling factor homologous to RAD51) and two maize homologs of the histone chaperone NAP1 [15,16]. By contrast, this process does not require MOP1, which is encoded by the maize homolog of RNA-dependent RNA polymerase2 (RDR2), an important player in RNA-directed DNA methylation [17,18]. MOP1 is, however, required for stable maintenance of MuDR silencing [19]. Interestingly there is an abundant class of MuDR-homologous 24–26 nt small RNAs expressed in floral tissues that are dependent on MOP1 function. These small RNAs, which are derived from deeply silenced and fragmented MuDR elements, are not competent to silence active MuDR elements. This suggests that initiation and maintenance of silencing of TEs require distinct pathways in maize and that the presence of small RNAs is not always sufficient to trigger Current Opinion in Plant Biology 2012, 15:511–516
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Figure 1
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reproductively competent adult growth. One appealing hypothesis is that transition leaves represent an important check-point, during which transcripts that would normally be rapidly processed into small RNAs owing to LBL1/ RDR6 activity are permitted to accumulate, resulting in an increase in the pool of targets for silencing via this pathway. Subsequent restoration of Lbl1 expression in these tissues would then be expected to produce more efficient silencing. In support of this idea, both Lbl1 expression and MuDR TGS are restored in transition leaves as they mature. Of course this hypothesis would only make sense if the information produced by the transient downregulation of Lbl1 could be transmitted to the rest of the plant. Recent experiments demonstrating systemic movement from leaves to roots of catalytically active siRNAs derived from TEs suggests that this may in fact be the case [27,28].
AAAAA TIRA
TIRA Muk Current Opinion in Plant Biology
Muk-induced silencing of MuDR. Transcription from an ectopic promoter proceeds through a rearranged variant of MuDR, which includes portions of the 50 end of the element that have been duplicated and inverted. The resulting transcript forms a hairpin, which is processed into small RNAs that target MuDR elements for transcriptional gene silencing.
TE silencing. Other factors that are known to influence the stability of silencing of MuDR elements are low energy ions and UV-B radiation [20,21].
A role for somatic cells in heritable silencing? One surprising result stemming from analysis of Mukinduced silencing of MuDR is the involvement in somatic tissues of factors normally implicated in gene regulation. In Arabidopsis, SUPPRESSOR OF GENE SILENCING3 (SGS3), is required for RNA-DEPENDENT RNA POLYMERASE6 (RDR6) catalyzed production of dsRNAs required for the production of trans-acting siRNAs (tasiRNAs) [22], downregulation of cis-natural antisense gene pairs [23] and Viral-induced Gene Silencing (VIGs) [24,25]. The maize homolog of SGS3, Lbl1, is required for somatic methylation of MuDR triggered by Muk as well as downregulation of ZmARF3a, a target of the tasiRNA pathway [14,26]. Remarkably, all evidence of TGS of MuDR by Muk is absent in young leaves that represent a transition between juvenile and adult growth. This loss of TGS is associated with a reduction in Lbl1 expression in these leaves, and a mutant that alters the timing of this transition also alters both Lbl1 expression and MuDR silencing. The functional importance of this shift in Lbl1 expression is not known, but it is intriguing that it occurs just as the maize plant is transitioning from juvenile to Current Opinion in Plant Biology 2012, 15:511–516
In many ways, these observations mirror those made in pollen and endosperm [2,29,30,31]. In each case, it appears that silencing pathways are relaxed in cells and tissues adjacent to but not part of the germ line in order to ‘unmask’ potentially dangerous TEs by permitting them to express transcript that can be processed into small RNAs that can be transmitted to the germinal lineage. The efficacy of this process probably depends on the availability of TE variants that, if expressed, would trigger silencing in trans. Given the vast numbers of many TEs in the maize genome (including thousands of retroelements present in nested arrays) it is likely that there are many of these ‘zombie’ TEs in maize, poised to rise and kill the living elements if permitted to express transcript that are competent to trigger silencing in trans. With that in mind, it is interesting to note that maize is host to large numbers of 22 nt siRNAs, many of which match inverted repeats and most of which are not dependent on RDR2 [8,32,33]. These observations raise some interesting questions concerning strategies that plants employ to detect and silence active TEs. The rearrangement that gave rise to Muk was a germinally transmitted event, but rearrangements of MuDR (and many other TEs) can also occur in somatic tissue as well [34]. If small RNAs generated as a consequence of those somatic events could be transported to the shoot apical meristem (SAM), then plants could use those somatic events to generate a pool of silencing information in a manner quite similar to that employed for systemic silencing of viruses [35]. One might expect that this process would be cumulative during development as more and more somatic events contribute small doses of silencing information (Figure 2). This is in line with observations that spontaneous silencing of high copy number Mutator lines is progressive during development [36] but is not generally associated with the generation of heritably transmitted silencing loci [34]. Given that somatic tissues are more prone to experience the kinds of biotic and abiotic stresses that are known to activate www.sciencedirect.com
Regulation of transposable elements in maize Lisch 513
Figure 2
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Hypothetical model for independent somatic events leading to germinal silencing. Within individual cells or cell lineages in somatic tissue, transposition and rearrangements can result in the production of trans-acting siRNAs. These may include TE insertions into 50 or 30 UTRs such that TE sequences are expressed in sense and antisense orientation (A), expression of a TE in antisense orientation to a host gene (B), insertion of a TE into a nested array (C), two adjacent TEs in opposite orientation (D) or a rearrangement like that observed at Muk, resulting in a hairpin transcript (E). In each case, it is hypothesized that small quantities of trans-acting siRNAs are produced that are then transported to the shoot apical meristem where they contribute to heritable silencing. Note that this process may not be limited to TEs, since regulation of a number of host genes, such as sense-antisense gene pairs, also involves small RNA processing (F).
TE expression [37,38], leaves may be an ideal source of information concerning potentially damaging TEs. Indeed, it may even be in the interests of plants to relax some aspects of silencing machinery in leaves relative to the SAM in order to gain additional information [39]. Finally, given the involvement of SGS3 in stress-induced downregulation of sense-antisense gene pairs [23], this idea also raises the interesting possibility that similar www.sciencedirect.com
mechanisms may induce heritable modification of host genes as well.
Regulating retrotransposons Much of this discussion has focused on Class II TEs, but the vast majority of TEs in maize are Class I retroelements, primarily LTR retrotransposons [7]. Molecular dating and comparison between inbred lines has revealed Current Opinion in Plant Biology 2012, 15:511–516
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that these elements are capable of rapid expansion [40–43]. However, unlike the highly mutagenic Class I elements, these retroelements are rarely associated with new mutations. This observation, along with the fact that they are extensively methylated, suggests that they are essentially inert [8]. It is surprising, therefore, that these
elements are expressed at high levels in the SAM. Indeed, almost 10% of all transcripts in the SAM in maize are from retrotransposons [39]. Given the absence of evidence for frequent transposition of these elements, it seems likely that these transcripts are being employed by the host to reinforce silencing [16]. Given that most LTR
Figure 3
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Portrayal of the establishment of silencing of an otherwise active TE. (A) TE replication leads to a rearrangement similar to Muk. Transcript from the rearranged version of the TE is processed into trans-acting siRNAs, which trigger transcriptional gene silencing of similar functional versions of the TE, as well as the rearranged TE itself (B). (C) Subsequent relaxation of silencing in germline-adjacent tissues results in reinforcement of silencing via transacting siRNAs generated from reactivated rearranged elements. Current Opinion in Plant Biology 2012, 15:511–516
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Regulation of transposable elements in maize Lisch 515
retrotransposons are found in nested arrays, it may be that global expression of these high copy elements inevitably leads to large quantities of trans-acting siRNAs that may block translation and reinforce silencing. This is supported by the otherwise surprising observation that a mutation in Mop1 in maize results in derepression of low copy class II TEs but enhanced repression of higher copy heterochromatic retroelements [33]. It may be that the high copy number retroelements are also those with the most zombies members, so global enhancement of transcriptional activity may inevitably poison the well for potentially active variants via 22 nt trans-acting siRNAs. Given this, one might expect relative enhancement of 22 nt siRNAs from these elements in the SAM and in pollen, as is observed in floral tissues [32].
makes it clear that TEs are capable of rapid expansion in copy number. This would suggest that TEs (successful parasites that they are) employ equally sophisticated strategies to evade inactivation, but that subject has been largely unexplored [47]. Analysis of currently active maize TEs that have managed to avoid silencing will undoubtedly help elucidate this process.
Acknowledgements I apologize to all of my colleagues whose contributions I could not cite or discuss owing to the size limitations set on this manuscript. The preparation of this manuscript was supported by a grant from the National Science Foundation (DBI-0820828).
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as:
Self control Finally, it is worth considering the degree to which TEs may regulate their own activity. Unlike viruses, TEs cannot, as a rule, escape their hosts, so selection can favor such regulation. This certainly appears to be the case for Ac elements in maize, whose copy number and levels of activity are moderate relative to some other TE systems such as Mutator. Ac elements exhibit dosage effects, such that increasing quantities of the transposase results in decreasing levels of activity [44]. There are also data suggesting that Spm may also be self-limiting. Experiments with transgenic Spm elements suggests that binding of the transposase to the subterminal repeats of the element can inhibit transcription, suggesting a negative feedback loop that may limit overall levels of activity [45]. Interestingly, there is also evidence from both maize and snapdragon that binding of the transposase may also prevent or reverse TIR methylation, suggesting that transposase can, in some cases, protect themselves from silencing [10,46].
Conclusions There is a clear theme that is emerging from analysis of regulation of plant TEs and maize TEs in particular. These selfish genetic elements must amplify their copy number to insure their long-term survival. To do so they depend on transcript from autonomous elements, which, as a consequence of that amplification, are prone to produce aberrant transcript for a variety of reasons, from position effects to rearrangements (Figure 3). A subset of these transcripts can trigger silencing of active elements in trans. Elements that produce those transcripts can then be recruited by the host to silence the family to which they belong. Evidence from endosperm, pollen and transition leaves suggest that plants engage in sophisticated strategies to gather as much information as possible about their TE complements while minimizing the danger of damage to the germline. They do this by permitting expression of elements in tissues and cells adjacent to but excluded from the germinal lineage. The net effect of this carefully choreographed process is stable silencing of vast numbers of potentially harmful TEs. However, comparative analysis of plant genomes www.sciencedirect.com
of special interest of outstanding interest 1.
Lisch D: Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 2009, 60:43-66.
Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, Feijo JA, Martienssen RA: Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 2009, 136:461-472. Provided evidence that epigenetic silencing of TEs is relaxed in the vegitative cells of pollen and for concomitant processing and movement of a novel small RNAs from that cell into the germinative nuclei.
2.
3.
Martienssen R: Molecular biology. Small RNA makes its move. Science 2010, 328:834-835.
4.
Yu C, Zhang J, Peterson T: Genome rearrangements in maize induced by alternative transposition of reversed ac/ds termini. Genetics 2011, 188:59-67.
5.
Liu S, Yeh CT, Ji T, Ying K, Wu H, Tang HM, Fu Y, Nettleton D, Schnable PS: Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet 2009, 5:e1000733.
6.
Candela H, Hake S: The art and design of genetic screens: maize. Nat Rev Genet 2008, 9:192-203.
7.
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al.: The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326:1112-1115. A landmark paper describing sequencing of the maize genome. Demonstrated that an average sized plant genome is composed largely of TEs.
8.
Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW: Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 2009, 21:1053-1069. The first genome-wide analysis of epigentic modifications in maize that identified important epigenetic differences between different tissues. Also demonstated that large genomes like that of maize have considerably more complex small RNA populations than do small genomes. 9.
Lisch D, Bennetzen JL: Transposable element origins of epigenetic gene regulation. Curr Opin Plant Biol 2011, 14:156-161.
10. Fedoroff N, Schlappi M, Raina R: Epigenetic regulation of the maize Spm transposon. Bioessays 1995, 17:291-297. 11. Chandler VL, Walbot V: DNA modification of a maize transposable element correlates with loss of activity. Proc Natl Acad Sci USA 1986, 83:1767-1771. 12. Lisch D: Mutator transposons. Trends Plant Sci 2002, 7:498-504. 13. Slotkin RK, Freeling M, Lisch D: Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet 2005, 37:641-644. Current Opinion in Plant Biology 2012, 15:511–516
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Provided the first characterization of a locus that can trigger heritable epigenetic silencing of a transposable element. 14. Li H, Freeling M, Lisch D: Epigenetic reprogramming during vegetative phase change in maize. Proc Natl Acad Sci USA 2010, 107:22184-22189. Provided evidence that vegitative-to-adult phase transition in maize is a distinct phase of growth during which trans-acting RNA-directed DNA methylation is transiently relaxed. 15. Woodhouse MR, Freeling M, Lisch D: Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors. PLoS Biol 2006, 4:e339. Demonstrated a clear connection between paramutation and transposon silencing in maize. 16. Hale CJ, Erhard KF Jr, Lisch D, Hollick JB: Production and processing of siRNA precursor transcripts from the highly repetitive maize genome. PLoS Genet 2009, 5:e1000598. 17. Zhang H, Zhu JK: RNA-directed DNA methylation. Curr Opin Plant Biol 2011, 14:142-147. 18. Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, Sikkink K, Chandler VL: An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 2006, 442:295-298. Described cloning of the first mutation that is required for paramutation in maize and demonstrated a direct role for the production of small RNAs in this process. 19. Woodhouse MR, Freeling M, Lisch D: The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize. Genetics 2006, 172:579-592. 20. Qian Y, Cheng X, Liu Y, Jiang H, Zhu S, Cheng B: Reactivation of a silenced minimal Mutator transposable element system following low-energy nitrogen ion implantation in maize. Plant Cell Rep 2010, 29:1365-1376. 21. Questa JI, Walbot V, Casati P: Mutator transposon activation after UV-B involves chromatin remodeling. Epigenetics 2010, 5:352-363. 22. Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS: SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 2004, 18:2368-2379.
With reference [31], provided evidence for global hypomethylation of TEs in plant endosperms. Together, these analyses suggest that the primary function of this process may be for TE silencing in the embryo. 31. Gehring M, Bubb KL, Henikoff S: Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009, 324:1447-1451. 32. Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong DH, Yen Y et al.: Distinct size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA 2008, 105:14958-14963. Demonstrated that the mop1 mutation is required for production of distinct size classes of small RNAs in maize. 33. Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, Schnable PS: Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. PLoS Genet 2009, 5:e1000737. 34. Lisch D, Chomet P, Freeling M: Genetic characterization of the Mutator system in maize: behavior and regulation of Mu transposons in a minimal line. Genetics 1995, 139:1777-1796. 35. Melnyk CW, Molnar A, Baulcombe DC: Intercellular and systemic movement of RNA silencing signals. EMBO J 2011, 30:3553-3563. 36. Martienssen R, Baron A: Coordinate suppression of mutations caused by Robertson’s mutator transposons in maize. Genetics 1994, 136:1157-1170. 37. Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR: Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 2009, 461:1130-1134. Provided evidence for a direct influence of recently activated MITE transposons on adjacent genes in rice and demonstrated a role in abiotic stress in this process. 38. Maumus F, Allen AE, Mhiri C, Hu H, Jabbari K, Vardi A, Grandbastien MA, Bowler C: Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics 2009, 10:624. 39. Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MC, Beck J, Buckner B et al.: Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant J 2007, 52:391-404.
23. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK: Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2005, 123:1279-1291.
40. Bennetzen JL: Patterns in grass genome evolution. Curr Opin Plant Biol 2007, 10:176-181.
24. Glick E, Zrachya A, Levy Y, Mett A, Gidoni D, Belausov E, Citovsky V, Gafni Y: Interaction with host SGS3 is required for suppression of RNA silencing by tomato yellow leaf curl virus V2 protein. Proc Natl Acad Sci USA 2008, 105:157-161.
41. Bousios A, Kourmpetis YA, Pavlidis P, Minga E, Tsaftaris A, Darzentas N: The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. Plant J 2012, 69:475-488.
25. Muangsan N, Beclin C, Vaucheret H, Robertson D: Geminivirus VIGS of endogenous genes requires SGS2/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants. Plant J 2004, 38:1004-1014.
42. Wang Q, Dooner HK: Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 2006, 103:17644-17649.
26. Nogueira FT, Madi S, Chitwood DH, Juarez MT, Timmermans MC: Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev 2007, 21:750-755. 27. Chitwood DH, Timmermans MC: Small RNAs are on the move. Nature 2010, 467:415-419. 28. Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC: Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 2010, 328:872-875. Provided convincing evidence for the mobility of trans-acting siRNAs in plants. 29. Mosher RA, Melnyk CW: siRNAs and DNA methylation: seedy epigenetics. Trends Plant Sci 2010, 15:204-210. 30. Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D: Genome-wide demethylation of Arabidopsis endosperm. Science 2009, 324:1451-1454.
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43. Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, Sanmiguel PJ, Bennetzen JL: Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet 2009, 5:e1000732. 44. Scofield SR, English JJ, Jones JD: High level expression of the Activator transposase gene inhibits the excision of Dissociation in tobacco cotyledons. Cell 1993, 75:507-517. 45. Schlappi M, Raina R, Fedoroff N: Epigenetic regulation of the maize Spm transposable element: novel activation of a methylated promoter by TnpA. Cell 1994, 77:427-437. 46. Hashida SN, Uchiyama T, Martin C, Kishima Y, Sano Y, Mikami T: The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase. Plant Cell 2006, 18:104-118. 47. Lisch D, Slotkin RK: Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts. Int Rev Cell Mol Biol 2011, 292:119-152.
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Regulation of transposable elements in maize Damon Lisch Maize is a typical plant with respect to the proportion of its genome that is composed of transposable elements (TEs), but it is unusual in the number of well-characterized active TEs that it hosts. This has made it possible to examine in some detail the factors responsible for regulating the activity of these elements, particularly the means by which they are recognized and epigenetically silenced. That analysis has revealed that TE silencing is a complex process that involves careful distinctions of different developmental times and tissue types. The available evidence from maize and other species suggests that these distinctions are made in order to generate information in somatic tissues that can be used to induce or reinforce silencing in germinal tissues. Address Department of Plant and Microbial Biology, University of California, Berkeley, CA, 111 Koshland Hall, Berkeley, CA 94720, United States Corresponding author: Lisch, Damon ([email protected])
Current Opinion in Plant Biology 2012, 15:511–516 This review comes from a themed issue on Cell signaling and gene regulation Edited by Jerzy Paszkowski and Robert A. Martienssen For a complete overview see the Issue and the Editorial Available online 22nd July 2012 1369-5266/$ – see front matter, # 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.pbi.2012.07.001
Introduction Much of what we understand about regulation of transposable elements (TEs) in plants comes from analysis of TEs that have been successfully silenced [1]. This analysis has proved to be a rich source of information, and the stable maintenance of TE silencing is far more dynamic than had been anticipated [2,3]. However, in order to fully understand TEs regulation it is essential to examine the behavior of active elements. Maize is host to an unusual number of these elements, whose behavior and regulation has been characterized for decades. Analysis of active TEs in maize has revealed how damaging that activity can be. Among other things, it can result in chromosomal rearrangements [4], insertional mutagenesis [5] and mis-regulation of gene expression [6]. Although Barbara McClintock originally framed this activity as a mechanism whose function is to reorganize the genome, the vast majority of changes induced by TE activity are clearly not beneficial, and plants, like all www.sciencedirect.com
eukaryotes, appear to devote considerable resources to their control. Host regulation in the form of epigenetic silencing is the major theme in transposon control, and TEs are, by far, the major target of epigenetic regulation in plants. For instance, at least 85% of the maize genome is composed of epigenetically silenced TEs [7,8]. Given that maize has a low-average sized plant genome [9], we are left with the remarkable and somewhat paradoxical conclusion that the single most successful stretch of plant DNA is a TE that has been silenced. This brief review will highlight some recent advances in our understanding of TE regulation in maize, with a particular focus on epigenetic silencing of otherwise active elements.
Recognition and silencing of TEs in maize We have known for several decades that TEs can transition from active to silenced states (what McClintock called ‘changes of phase’), and that this process is associated with DNA methylation [10,11]. However it was only recently that a mechanism for this process was elucidated using the Mutator system of TEs. This system is a family of Class II ‘cut and paste’ elements in maize that includes the autonomous MuDR element as well as several classes of non-autonomous elements [12]. MuDR elements can be heritably silenced by Muk, a naturally occurring rearranged version of MuDR that expresses a hairpin transcript that triggers transcriptional gene silencing (TGS) of MuDR elements via trans-acting siRNAs [13] (Figure 1). Both the initiation and maintenance of silencing of this TE are associated with H3K27 and H3K9 dimethylation as well as cytosine methylation in all three sequence contexts [14]. Efficient and stabile silencing of MuDR by Muk requires RMR1 (a chromatin remodeling factor homologous to RAD51) and two maize homologs of the histone chaperone NAP1 [15,16]. By contrast, this process does not require MOP1, which is encoded by the maize homolog of RNA-dependent RNA polymerase2 (RDR2), an important player in RNA-directed DNA methylation [17,18]. MOP1 is, however, required for stable maintenance of MuDR silencing [19]. Interestingly there is an abundant class of MuDR-homologous 24–26 nt small RNAs expressed in floral tissues that are dependent on MOP1 function. These small RNAs, which are derived from deeply silenced and fragmented MuDR elements, are not competent to silence active MuDR elements. This suggests that initiation and maintenance of silencing of TEs require distinct pathways in maize and that the presence of small RNAs is not always sufficient to trigger Current Opinion in Plant Biology 2012, 15:511–516
512 Cell signaling and gene regulation
Figure 1
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reproductively competent adult growth. One appealing hypothesis is that transition leaves represent an important check-point, during which transcripts that would normally be rapidly processed into small RNAs owing to LBL1/ RDR6 activity are permitted to accumulate, resulting in an increase in the pool of targets for silencing via this pathway. Subsequent restoration of Lbl1 expression in these tissues would then be expected to produce more efficient silencing. In support of this idea, both Lbl1 expression and MuDR TGS are restored in transition leaves as they mature. Of course this hypothesis would only make sense if the information produced by the transient downregulation of Lbl1 could be transmitted to the rest of the plant. Recent experiments demonstrating systemic movement from leaves to roots of catalytically active siRNAs derived from TEs suggests that this may in fact be the case [27,28].
AAAAA TIRA
TIRA Muk Current Opinion in Plant Biology
Muk-induced silencing of MuDR. Transcription from an ectopic promoter proceeds through a rearranged variant of MuDR, which includes portions of the 50 end of the element that have been duplicated and inverted. The resulting transcript forms a hairpin, which is processed into small RNAs that target MuDR elements for transcriptional gene silencing.
TE silencing. Other factors that are known to influence the stability of silencing of MuDR elements are low energy ions and UV-B radiation [20,21].
A role for somatic cells in heritable silencing? One surprising result stemming from analysis of Mukinduced silencing of MuDR is the involvement in somatic tissues of factors normally implicated in gene regulation. In Arabidopsis, SUPPRESSOR OF GENE SILENCING3 (SGS3), is required for RNA-DEPENDENT RNA POLYMERASE6 (RDR6) catalyzed production of dsRNAs required for the production of trans-acting siRNAs (tasiRNAs) [22], downregulation of cis-natural antisense gene pairs [23] and Viral-induced Gene Silencing (VIGs) [24,25]. The maize homolog of SGS3, Lbl1, is required for somatic methylation of MuDR triggered by Muk as well as downregulation of ZmARF3a, a target of the tasiRNA pathway [14,26]. Remarkably, all evidence of TGS of MuDR by Muk is absent in young leaves that represent a transition between juvenile and adult growth. This loss of TGS is associated with a reduction in Lbl1 expression in these leaves, and a mutant that alters the timing of this transition also alters both Lbl1 expression and MuDR silencing. The functional importance of this shift in Lbl1 expression is not known, but it is intriguing that it occurs just as the maize plant is transitioning from juvenile to Current Opinion in Plant Biology 2012, 15:511–516
In many ways, these observations mirror those made in pollen and endosperm [2,29,30,31]. In each case, it appears that silencing pathways are relaxed in cells and tissues adjacent to but not part of the germ line in order to ‘unmask’ potentially dangerous TEs by permitting them to express transcript that can be processed into small RNAs that can be transmitted to the germinal lineage. The efficacy of this process probably depends on the availability of TE variants that, if expressed, would trigger silencing in trans. Given the vast numbers of many TEs in the maize genome (including thousands of retroelements present in nested arrays) it is likely that there are many of these ‘zombie’ TEs in maize, poised to rise and kill the living elements if permitted to express transcript that are competent to trigger silencing in trans. With that in mind, it is interesting to note that maize is host to large numbers of 22 nt siRNAs, many of which match inverted repeats and most of which are not dependent on RDR2 [8,32,33]. These observations raise some interesting questions concerning strategies that plants employ to detect and silence active TEs. The rearrangement that gave rise to Muk was a germinally transmitted event, but rearrangements of MuDR (and many other TEs) can also occur in somatic tissue as well [34]. If small RNAs generated as a consequence of those somatic events could be transported to the shoot apical meristem (SAM), then plants could use those somatic events to generate a pool of silencing information in a manner quite similar to that employed for systemic silencing of viruses [35]. One might expect that this process would be cumulative during development as more and more somatic events contribute small doses of silencing information (Figure 2). This is in line with observations that spontaneous silencing of high copy number Mutator lines is progressive during development [36] but is not generally associated with the generation of heritably transmitted silencing loci [34]. Given that somatic tissues are more prone to experience the kinds of biotic and abiotic stresses that are known to activate www.sciencedirect.com
Regulation of transposable elements in maize Lisch 513
Figure 2
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Hypothetical model for independent somatic events leading to germinal silencing. Within individual cells or cell lineages in somatic tissue, transposition and rearrangements can result in the production of trans-acting siRNAs. These may include TE insertions into 50 or 30 UTRs such that TE sequences are expressed in sense and antisense orientation (A), expression of a TE in antisense orientation to a host gene (B), insertion of a TE into a nested array (C), two adjacent TEs in opposite orientation (D) or a rearrangement like that observed at Muk, resulting in a hairpin transcript (E). In each case, it is hypothesized that small quantities of trans-acting siRNAs are produced that are then transported to the shoot apical meristem where they contribute to heritable silencing. Note that this process may not be limited to TEs, since regulation of a number of host genes, such as sense-antisense gene pairs, also involves small RNA processing (F).
TE expression [37,38], leaves may be an ideal source of information concerning potentially damaging TEs. Indeed, it may even be in the interests of plants to relax some aspects of silencing machinery in leaves relative to the SAM in order to gain additional information [39]. Finally, given the involvement of SGS3 in stress-induced downregulation of sense-antisense gene pairs [23], this idea also raises the interesting possibility that similar www.sciencedirect.com
mechanisms may induce heritable modification of host genes as well.
Regulating retrotransposons Much of this discussion has focused on Class II TEs, but the vast majority of TEs in maize are Class I retroelements, primarily LTR retrotransposons [7]. Molecular dating and comparison between inbred lines has revealed Current Opinion in Plant Biology 2012, 15:511–516
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that these elements are capable of rapid expansion [40–43]. However, unlike the highly mutagenic Class I elements, these retroelements are rarely associated with new mutations. This observation, along with the fact that they are extensively methylated, suggests that they are essentially inert [8]. It is surprising, therefore, that these
elements are expressed at high levels in the SAM. Indeed, almost 10% of all transcripts in the SAM in maize are from retrotransposons [39]. Given the absence of evidence for frequent transposition of these elements, it seems likely that these transcripts are being employed by the host to reinforce silencing [16]. Given that most LTR
Figure 3
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Portrayal of the establishment of silencing of an otherwise active TE. (A) TE replication leads to a rearrangement similar to Muk. Transcript from the rearranged version of the TE is processed into trans-acting siRNAs, which trigger transcriptional gene silencing of similar functional versions of the TE, as well as the rearranged TE itself (B). (C) Subsequent relaxation of silencing in germline-adjacent tissues results in reinforcement of silencing via transacting siRNAs generated from reactivated rearranged elements. Current Opinion in Plant Biology 2012, 15:511–516
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Regulation of transposable elements in maize Lisch 515
retrotransposons are found in nested arrays, it may be that global expression of these high copy elements inevitably leads to large quantities of trans-acting siRNAs that may block translation and reinforce silencing. This is supported by the otherwise surprising observation that a mutation in Mop1 in maize results in derepression of low copy class II TEs but enhanced repression of higher copy heterochromatic retroelements [33]. It may be that the high copy number retroelements are also those with the most zombies members, so global enhancement of transcriptional activity may inevitably poison the well for potentially active variants via 22 nt trans-acting siRNAs. Given this, one might expect relative enhancement of 22 nt siRNAs from these elements in the SAM and in pollen, as is observed in floral tissues [32].
makes it clear that TEs are capable of rapid expansion in copy number. This would suggest that TEs (successful parasites that they are) employ equally sophisticated strategies to evade inactivation, but that subject has been largely unexplored [47]. Analysis of currently active maize TEs that have managed to avoid silencing will undoubtedly help elucidate this process.
Acknowledgements I apologize to all of my colleagues whose contributions I could not cite or discuss owing to the size limitations set on this manuscript. The preparation of this manuscript was supported by a grant from the National Science Foundation (DBI-0820828).
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as:
Self control Finally, it is worth considering the degree to which TEs may regulate their own activity. Unlike viruses, TEs cannot, as a rule, escape their hosts, so selection can favor such regulation. This certainly appears to be the case for Ac elements in maize, whose copy number and levels of activity are moderate relative to some other TE systems such as Mutator. Ac elements exhibit dosage effects, such that increasing quantities of the transposase results in decreasing levels of activity [44]. There are also data suggesting that Spm may also be self-limiting. Experiments with transgenic Spm elements suggests that binding of the transposase to the subterminal repeats of the element can inhibit transcription, suggesting a negative feedback loop that may limit overall levels of activity [45]. Interestingly, there is also evidence from both maize and snapdragon that binding of the transposase may also prevent or reverse TIR methylation, suggesting that transposase can, in some cases, protect themselves from silencing [10,46].
Conclusions There is a clear theme that is emerging from analysis of regulation of plant TEs and maize TEs in particular. These selfish genetic elements must amplify their copy number to insure their long-term survival. To do so they depend on transcript from autonomous elements, which, as a consequence of that amplification, are prone to produce aberrant transcript for a variety of reasons, from position effects to rearrangements (Figure 3). A subset of these transcripts can trigger silencing of active elements in trans. Elements that produce those transcripts can then be recruited by the host to silence the family to which they belong. Evidence from endosperm, pollen and transition leaves suggest that plants engage in sophisticated strategies to gather as much information as possible about their TE complements while minimizing the danger of damage to the germline. They do this by permitting expression of elements in tissues and cells adjacent to but excluded from the germinal lineage. The net effect of this carefully choreographed process is stable silencing of vast numbers of potentially harmful TEs. However, comparative analysis of plant genomes www.sciencedirect.com
of special interest of outstanding interest 1.
Lisch D: Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 2009, 60:43-66.
Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, Feijo JA, Martienssen RA: Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 2009, 136:461-472. Provided evidence that epigenetic silencing of TEs is relaxed in the vegitative cells of pollen and for concomitant processing and movement of a novel small RNAs from that cell into the germinative nuclei.
2.
3.
Martienssen R: Molecular biology. Small RNA makes its move. Science 2010, 328:834-835.
4.
Yu C, Zhang J, Peterson T: Genome rearrangements in maize induced by alternative transposition of reversed ac/ds termini. Genetics 2011, 188:59-67.
5.
Liu S, Yeh CT, Ji T, Ying K, Wu H, Tang HM, Fu Y, Nettleton D, Schnable PS: Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet 2009, 5:e1000733.
6.
Candela H, Hake S: The art and design of genetic screens: maize. Nat Rev Genet 2008, 9:192-203.
7.
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al.: The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326:1112-1115. A landmark paper describing sequencing of the maize genome. Demonstrated that an average sized plant genome is composed largely of TEs.
8.
Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW: Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 2009, 21:1053-1069. The first genome-wide analysis of epigentic modifications in maize that identified important epigenetic differences between different tissues. Also demonstated that large genomes like that of maize have considerably more complex small RNA populations than do small genomes. 9.
Lisch D, Bennetzen JL: Transposable element origins of epigenetic gene regulation. Curr Opin Plant Biol 2011, 14:156-161.
10. Fedoroff N, Schlappi M, Raina R: Epigenetic regulation of the maize Spm transposon. Bioessays 1995, 17:291-297. 11. Chandler VL, Walbot V: DNA modification of a maize transposable element correlates with loss of activity. Proc Natl Acad Sci USA 1986, 83:1767-1771. 12. Lisch D: Mutator transposons. Trends Plant Sci 2002, 7:498-504. 13. Slotkin RK, Freeling M, Lisch D: Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet 2005, 37:641-644. Current Opinion in Plant Biology 2012, 15:511–516
516 Cell signaling and gene regulation
Provided the first characterization of a locus that can trigger heritable epigenetic silencing of a transposable element. 14. Li H, Freeling M, Lisch D: Epigenetic reprogramming during vegetative phase change in maize. Proc Natl Acad Sci USA 2010, 107:22184-22189. Provided evidence that vegitative-to-adult phase transition in maize is a distinct phase of growth during which trans-acting RNA-directed DNA methylation is transiently relaxed. 15. Woodhouse MR, Freeling M, Lisch D: Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors. PLoS Biol 2006, 4:e339. Demonstrated a clear connection between paramutation and transposon silencing in maize. 16. Hale CJ, Erhard KF Jr, Lisch D, Hollick JB: Production and processing of siRNA precursor transcripts from the highly repetitive maize genome. PLoS Genet 2009, 5:e1000598. 17. Zhang H, Zhu JK: RNA-directed DNA methylation. Curr Opin Plant Biol 2011, 14:142-147. 18. Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, Sikkink K, Chandler VL: An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 2006, 442:295-298. Described cloning of the first mutation that is required for paramutation in maize and demonstrated a direct role for the production of small RNAs in this process. 19. Woodhouse MR, Freeling M, Lisch D: The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize. Genetics 2006, 172:579-592. 20. Qian Y, Cheng X, Liu Y, Jiang H, Zhu S, Cheng B: Reactivation of a silenced minimal Mutator transposable element system following low-energy nitrogen ion implantation in maize. Plant Cell Rep 2010, 29:1365-1376. 21. Questa JI, Walbot V, Casati P: Mutator transposon activation after UV-B involves chromatin remodeling. Epigenetics 2010, 5:352-363. 22. Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS: SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 2004, 18:2368-2379.
With reference [31], provided evidence for global hypomethylation of TEs in plant endosperms. Together, these analyses suggest that the primary function of this process may be for TE silencing in the embryo. 31. Gehring M, Bubb KL, Henikoff S: Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009, 324:1447-1451. 32. Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong DH, Yen Y et al.: Distinct size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA 2008, 105:14958-14963. Demonstrated that the mop1 mutation is required for production of distinct size classes of small RNAs in maize. 33. Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, Schnable PS: Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. PLoS Genet 2009, 5:e1000737. 34. Lisch D, Chomet P, Freeling M: Genetic characterization of the Mutator system in maize: behavior and regulation of Mu transposons in a minimal line. Genetics 1995, 139:1777-1796. 35. Melnyk CW, Molnar A, Baulcombe DC: Intercellular and systemic movement of RNA silencing signals. EMBO J 2011, 30:3553-3563. 36. Martienssen R, Baron A: Coordinate suppression of mutations caused by Robertson’s mutator transposons in maize. Genetics 1994, 136:1157-1170. 37. Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR: Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 2009, 461:1130-1134. Provided evidence for a direct influence of recently activated MITE transposons on adjacent genes in rice and demonstrated a role in abiotic stress in this process. 38. Maumus F, Allen AE, Mhiri C, Hu H, Jabbari K, Vardi A, Grandbastien MA, Bowler C: Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics 2009, 10:624. 39. Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MC, Beck J, Buckner B et al.: Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant J 2007, 52:391-404.
23. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK: Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2005, 123:1279-1291.
40. Bennetzen JL: Patterns in grass genome evolution. Curr Opin Plant Biol 2007, 10:176-181.
24. Glick E, Zrachya A, Levy Y, Mett A, Gidoni D, Belausov E, Citovsky V, Gafni Y: Interaction with host SGS3 is required for suppression of RNA silencing by tomato yellow leaf curl virus V2 protein. Proc Natl Acad Sci USA 2008, 105:157-161.
41. Bousios A, Kourmpetis YA, Pavlidis P, Minga E, Tsaftaris A, Darzentas N: The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. Plant J 2012, 69:475-488.
25. Muangsan N, Beclin C, Vaucheret H, Robertson D: Geminivirus VIGS of endogenous genes requires SGS2/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants. Plant J 2004, 38:1004-1014.
42. Wang Q, Dooner HK: Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 2006, 103:17644-17649.
26. Nogueira FT, Madi S, Chitwood DH, Juarez MT, Timmermans MC: Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev 2007, 21:750-755. 27. Chitwood DH, Timmermans MC: Small RNAs are on the move. Nature 2010, 467:415-419. 28. Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC: Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 2010, 328:872-875. Provided convincing evidence for the mobility of trans-acting siRNAs in plants. 29. Mosher RA, Melnyk CW: siRNAs and DNA methylation: seedy epigenetics. Trends Plant Sci 2010, 15:204-210. 30. Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D: Genome-wide demethylation of Arabidopsis endosperm. Science 2009, 324:1451-1454.
Current Opinion in Plant Biology 2012, 15:511–516
43. Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, Sanmiguel PJ, Bennetzen JL: Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet 2009, 5:e1000732. 44. Scofield SR, English JJ, Jones JD: High level expression of the Activator transposase gene inhibits the excision of Dissociation in tobacco cotyledons. Cell 1993, 75:507-517. 45. Schlappi M, Raina R, Fedoroff N: Epigenetic regulation of the maize Spm transposable element: novel activation of a methylated promoter by TnpA. Cell 1994, 77:427-437. 46. Hashida SN, Uchiyama T, Martin C, Kishima Y, Sano Y, Mikami T: The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase. Plant Cell 2006, 18:104-118. 47. Lisch D, Slotkin RK: Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts. Int Rev Cell Mol Biol 2011, 292:119-152.
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