Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length of TEs, yet this information may provide crucial insights into the dynamics between hosts and TEs. By focusing on 6456 carefully annotated, full-length Sirevirus LTR retrotransposons in maize, we show that their silencing associates with underlying characteristics of the TE sequence and also uncover three features of the host-TE interaction. First, siRNA mapping varies among families and among elements, but particularly along the length of elements. Within the cis-regulatory portion of the LTRs, a complex palindrome-rich region acts as a hotspot of both siRNA matching and sequence evolution. These patterns are consistent across leaf, tassel, and immature ear libraries, but particularly emphasized for floral tissues and 21- to 22-nt siRNAs. Second, this region has the ability to form hairpins, making it a potential template for the production of miRNA-like, hairpin-derived small RNAs. Third, Sireviruses are targeted by siRNAs as a decreasing function of their age, but the oldest elements remain highly targeted, partially by siRNAs that cross-map to the youngest elements. We show that the targeting of older Sireviruses reflects their conserved palindromes. Altogether, we hypothesize that the palindromes aid the silencing of active elements and influence transposition potential, siRNA targeting levels, and ultimately the fate of an element within the genome.

Central European Institute of Technology Masaryk University 62500 Brno Czech Republic

Department of Agronomy University of Cordoba 14014 Cordoba Spain; Department of Ecology and Evolutionary Biology UC Irvine Irvine California 92697 USA;

Department of Ecology and Evolutionary Biology UC Irvine Irvine California 92697 USA;

School of Life Sciences University of Sussex Brighton BN1 9RH United Kingdom; Institute of Applied Biosciences Centre for Research and Technology Hellas 57001 Thessaloniki Greece;

SOKENDAI Hayama Kanagawa 240 0193 Japan;

Zobrazit více v PubMed

Araujo PG, Casacuberta JM, Costa APP, Hashimoto RY, Grandbastien MA, Van Sluys MA. 2001. Retrolyc1 subfamilies defined by different U3 LTR regulatory regions in the Lycopersicon genus. Mol Genet Genomics 266: 35–41. PubMed

Axtell MJ. 2013a. Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64: 137–159. PubMed

Axtell MJ. 2013b. ShortStack: comprehensive annotation and quantification of small RNA genes. RNA 19: 740–751. PubMed PMC

Barber WT, Zhang W, Win H, Varala KK, Dorweiler JE, Hudson ME, Moose SP. 2012. Repeat associated small RNAs vary among parents and following hybridization in maize. Proc Natl Acad Sci 109: 10444–10449. PubMed PMC

Bologna NG, Voinnet O. 2014. The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol 65: 473–503. PubMed

Bousios A, Darzentas N. 2013. Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world. Mob DNA 4: 9. PubMed PMC

Bousios A, Darzentas N, Tsaftaris A, Pearce SR. 2010. Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? BMC Genomics 11: 89. PubMed PMC

Bousios A, Kourmpetis YA, Pavlidis P, Minga E, Tsaftaris A, Darzentas N. 2012a. The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. Plant J 69: 475–488. PubMed

Bousios A, Minga E, Kalitsou N, Pantermali M, Tsaballa A, Darzentas N. 2012b. MASiVEdb: the Sirevirus Plant Retrotransposon Database. BMC Genomics 13: 158. PubMed PMC

Cantu D, Vanzetti LS, Sumner A, Dubcovsky M, Matvienko M, Distelfeld A, Michelmore RW, Dubcovsky J. 2010. Small RNAs, DNA methylation and transposable elements in wheat. BMC Genomics 11: 408. PubMed PMC

Chen PY, Cokus SJ, Pellegrini M. 2010. BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics 11: 203. PubMed PMC

Creasey KM, Zhai J, Borges F, Van Ex F, Regulski M, Meyers BC, Martienssen RA. 2014. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature 508: 411–415. PubMed PMC

Darzentas N, Bousios A, Apostolidou V, Tsaftaris AS. 2010. MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences. Bioinformatics 26: 2452–2454. PubMed

Diez CM, Meca E, Tenaillon MI, Gaut BS. 2014. Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome. PLoS Genet 10: e1004298. PubMed PMC

Du J, Tian Z, Bowen NJ, Schmutz J, Shoemaker RC, Ma J. 2010. Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR swapping in soybean. Plant Cell 22: 48–61. PubMed PMC

Feng SH, Cokus SJ, Zhang XY, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, et al. 2010. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci 107: 8689–8694. PubMed PMC

Fultz D, Choudury SG, Slotkin RK. 2015. Silencing of active transposable elements in plants. Curr Opin Plant Biol 27: 67–76. PubMed

Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, Dawe RK. 2013. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res 23: 628–637. PubMed PMC

Grandbastien MA. 2015. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. Biochim Biophys Acta 1849: 403–416. PubMed

Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Res 36: W70–W74. PubMed PMC

He G, Chen B, Wang X, Li X, Li J, He H, Yang M, Lu L, Qi Y, Wang X, et al. 2013. Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol 14: R57. PubMed PMC

Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE. 2006. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 38: 721–725. PubMed

Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS. 2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci 108: 2322–2327. PubMed PMC

Ito H, Gaubert H, Bucher E, Mirouze M, Vaillant I, Paszkowski J. 2011. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472: 115–159. PubMed

Johnson LM, Du JM, Hale CJ, Bischof S, Feng SH, Chodavarapu RK, Zhong XH, Marson G, Pellegrini M, Segal DJ, et al. 2014. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature 507: 124–128. PubMed PMC

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772–780. PubMed PMC

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639–1645. PubMed PMC

Law JA, Du JM, Hale CJ, Feng SH, Krajewski K, Palanca AMS, Strahl BD, Patel DJ, Jacobsen SE. 2013. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 498: 385–389. PubMed PMC

Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26: 589–595. PubMed PMC

Li H, Freeling M, Lisch D. 2010. Epigenetic reprogramming during vegetative phase change in maize. Proc Natl Acad Sci 107: 22184–22189. PubMed PMC

Lisch D. 2009. Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 66: 43–66. PubMed

Lisch D, Slotkin RK. 2011. Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts. In International review of cell and molecular biology (ed. Jeon KW), Vol. 292, pp. 119–152. Elsevier Academic Press, San Diego, CA. PubMed

Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523–536. PubMed PMC

Ma JX, Bennetzen JL. 2004. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci 101: 12404–12410. PubMed PMC

Ma JX, Devos KM, Bennetzen JL. 2004. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14: 860–869. PubMed PMC

Marí-Ordóñez A, Marchais A, Etcheverry M, Martin A, Colot V, Voinnet O. 2013. Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet 45: 1029–1039. PubMed

Matzke MA, Mosher RA. 2014. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15: 394–408. PubMed

McCue AD, Panda K, Nuthikattu S, Choudury SG, Thomas EN, Slotkin RK. 2015. ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation. EMBO J 34: 20–35. PubMed PMC

Mergia A, Prattlowe E, Shaw KE, Renshaw-Gegg LW, Luciw PA. 1992. cis-acting regulatory regions in the long terminal repeat of simian foamy virus type-1. J Virol 66: 251–257. PubMed PMC

Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T. 2001. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212–214. PubMed

Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong DH, Yen Y, et al. 2008. Distinct size distribution of endogenous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci 105: 14958–14963. PubMed PMC

Panda K, Slotkin RK. 2013. Proposed mechanism for the initiation of transposable element silencing by the RDR6-directed DNA methylation pathway. Plant Signal Behav 8: pii: e25206. PubMed PMC

R Core Team. 2015. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria: http://www.R-project.org/.

Ragupathy R, You FM, Cloutier S. 2013. Arguments for standardizing transposable element annotation in plant genomes. Trends Plant Sci 18: 367–376. PubMed

Regulski M, Lu Z, Kendall J, Donoghue MT, Reinders J, Llaca V, Deschamps S, Smith A, Levy D, McCombie WR, et al. 2013. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res 23: 1651–1662. PubMed PMC

Sharma A, Schneider KL, Presting GG. 2008. Sustained retrotransposition is mediated by nucleotide deletions and interelement recombinations. Proc Natl Acad Sci 105: 15470–15474. PubMed PMC

Slotkin RK, Freeling M, Lisch D. 2005. Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat Genet 37: 641–644. PubMed

Slotkin RK, Vaughn M, Borges F, Tanurdžic´ M, Becker JD, Feijó JA, Martienssen RA. 2009. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461–472. PubMed PMC

Takuno S, Gaut BS. 2013. Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acad Sci 110: 1797–1802. PubMed PMC

Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, Cruaud C, Poulain J, Berdasco M, Fraga MF, et al. 2009. A role for RNAi in the selective correction of DNA methylation defects. Science 323: 1600–1604. PubMed

Vernhettes S, Grandbastien MA, Casacuberta JM. 1998. The evolutionary analysis of the Tnt1 retrotransposon in Nicotiana species reveals the high variability of its regulatory sequences. Mol Biol Evol 15: 827–836. PubMed

Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW. 2009. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21: 1053–1069. PubMed PMC

West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer NM. 2014. Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS One 9: e105267. PubMed PMC

Wicker T, Buchmann JP, Keller B. 2010. Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res 20: 1229–1237. PubMed PMC

Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153: 193–205. PubMed PMC

Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D. 2009. A genome-wide characterization of microRNA genes in maize. PLoS Genet 5: e1000716. PubMed PMC

Epigenetic targeting of transposon relics: beating the dead horses of the genome?

Considerations and complications of mapping small RNA high-throughput data to transposable elements