UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl)
Novel insights into gene silencing mechanisms in Zea mays and Arabidopsis
thaliana
Hövel, I.
Publication date
2016
Document Version
Final published version
Link to publication
Citation for published version (APA):
Hövel, I. (2016). Novel insights into gene silencing mechanisms in Zea mays and Arabidopsis
thaliana.
General rights
It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s)
and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open
content license (like Creative Commons).
Disclaimer/Complaints regulations
If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please
let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material
inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter
to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You
will be contacted as soon as possible.
References
Alleman, M., Sidorenko, L., McGinnis, K., Seshadri, V., Dorweiler, J.E., White, J., Sikkink, K., and Chandler, V.L. (2006). An RNA-dependent RNA polymerase is required for paramutation in
maize. Nature 442: 295–8.
Amano, T., Sagai, T., Tanabe, H., Mizushina, Y., Nakazawa, H., and Shiroishi, T. (2009).
Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription. Dev. Cell 16: 47–57.
Angel, A., Song, J., Dean, C., and Howard, M. (2011). A Polycomb-based switch underlying
quantitative epigenetic memory. Nature 476: 105–108.
Aramayo, R. and Metzenberg, R.L. (1996). Meiotic Transvection in Fungi. Cell 86: 103–113. Aravin, A.A., Naumova, N.M., Tulin, A. V, Vagin, V. V, Rozovsky, Y.M., and Gvozdev, V.A.
(2001). Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11: 1017–1027.
Arteaga-Vazquez, M., Sidorenko, L., Rabanal, F.A., Shrivistava, R., Nobuta, K., Green, P.J., Meyers, B.C., and Chandler, V.L. (2010). RNA-mediated trans -communication can establish
paramutation at the b1 locus in maize. PNAS 107: 12986–12991.
Arteaga-Vazquez, M.A. and Chandler, V.L. (2010). Paramutation in maize: RNA mediated
trans-generational gene silencing. Curr. Opin. Genet. Dev. 20: 156–63.
Audergon, P., Catania, S., Kagansky, A., and Tong, P. (2015). Restricted epigenetic inheritance of
H3K9 methylation. Science. 348: 132–135.
Bacher, C.P., Guggiari, M., Brors, B., Augui, S., Clerc, P., Avner, P., Eils, R., and Heard, E.
(2006). Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat. Cell Biol. 8: 293–299.
Bannister, A.J. and Kouzarides, T. (2011). Regulation of chromatin by histone modifications. Cell
Res. 21: 381–395.
Bantignies, F., Roure, V., Comet, I., Leblanc, B., Schuettengruber, B., Bonnet, J., Tixier, V., Mas, A., and Cavalli, G. (2011). Polycomb-dependent regulatory contacts between distant hox loci
in drosophila. Cell 144: 214–226.
Barah, P., Jayavelu, N.D., Rasmussen, S., Nielsen, H.B., Mundy, J., and Bones, A.M. (2013).
Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes. BMC Genomics 14: 722.
Barbour, J.-E.R., Liao, I.T., Stonaker, J.L., Lim, J.P., Lee, C.C., Parkinson, S.E., Kermicle, J., Simon, S. a., Meyers, B.C., Williams-Carrier, R., Barkan, a., and Hollick, J.B. (2012). required
to maintain repression2 Is a Novel Protein That Facilitates Locus-Specific Paramutation in Maize. Plant Cell 24: 1761–1775.
Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. (2007). High-Resolution Profiling of Histone Methylations in the Human Genome.
Cell 129: 823–837.
Bateson, W. and Pellew, C. (1915). On the genetics of “rogues” among culinary peas (Pisum
sativum). J. Genet. 5: 15–36.
Baù, D., Sanyal, A., Lajoie, B.R., Capriotti, E., Byron, M., Lawrence, J.B., Dekker, J., and Marti-Renom, M. a (2011). The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat. Struct. Mol. Biol. 18: 107–114.
Belele, C.L., Sidorenko, L., Stam, M., Bader, R., Arteaga-Vazquez, M., and Chandler, V.L.
(2013). Specific tandem repeats are sufficient for paramutation-induced trans-generational silencing. PLoS Genet. 9: e1003773.
Bernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M., and Jacobsen, S.E. (2008).
Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 3.
Berr, A. and Schubert, I. (2007). Interphase chromosome arrangement in Arabidopsis thaliana is
similar in differentiated and meristematic tissues and shows a transient mirror symmetry after nuclear division. Genetics 176: 853–863.
Berry, S., Hartley, M., Olsson, T.S.G., Dean, C., and Howard, M. (2015). Local chromatin
environment of a Polycomb target gene instructs its own epigenetic inheritance. Elife 4: e07205.
Blokland, R. Van, Lohuis, M., and Meyer, P. (1997). Condensation of chromatin in transcriptional
regions of an inactivated plant transgene : evidence for an active role of transcription in gene silencing. Mol. Gen. Genet.: 1–13.
Bond, D.M. and Baulcombe, D.C. (2015). Epigenetic transitions leading to heritable,
RNA-mediated de novo silencing in Arabidopsis thaliana. PNAS. 2014: 201413053.
Brink, R.A. (1956). A genetic change associated with the R locus in maize which is directed and
potentially reversible. Genetics 41: 872–889.
Bucher, E., Reinders, J., and Mirouze, M. (2012). Epigenetic control of transposon transcription
and mobility in Arabidopsis. Curr. Opin. Plant Biol. 15: 503–510.
Cai, S., Lee, C.C., and Kohwi-Shigematsu, T. (2006). SATB1 packages densely looped,
transcriptionally active chromatin for coordinated expression of cytokine genes. Nat. Genet. 38: 1278–88.
Campos, E.I. and Reinberg, D. (2009). Histones: annotating chromatin. Annu. Rev. Genet. 43: 559–
99.
Cao, X. and Jacobsen, S.E. (2002). Role of the Arabidopsis DRM Methyltransferases in De Novo
DNA Methylation and Gene Silencing. Curr. Biol. 12: 1138–1144.
Capuano, F., Mülleder, M., Kok, R., Blom, H.J., and Ralser, M. (2014). Cytosine DNA
methylation is found in Drosophila melanogaster but absent in saccharomyces cerevisiae, schizosaccharomyces pombe, and other yeast species. Anal. Chem. 86: 3697–3702.
Caron, H. (2013). The Human Transcriptome Map: Clustering of Highly Expressed Genes in
Castel, S.E. and Martienssen, R. (2013). RNA interference in the nucleus: roles for small RNAs in
transcription, epigenetics and beyond. Nat. Rev. Genet. 14: 100–12.
Cedar, H. and Bergman, Y. (2012). Programming of DNA methylation patterns. Annu Rev Biochem 81: 97–117.
Chan, S., Zilberman, D., and Xie, Z. (2004). RNA silencing genes control de novo DNA
methylation. Science 303: 2004.
Chan, S.W.-L., Zhang, X., Bernatavichute, Y. V., and Jacobsen, S.E. (2006). Two-Step
Recruitment of RNA-Directed DNA Methylation to Tandem Repeats. PLoS Biol. 4: e363.
Chandler, V.L. (2007). Paramutation: from maize to mice. Cell 128: 641–5.
Chandler, V.L., Eggleston, W.B., and Dorweiler, J.E. (2000). Paramutation in maize. Plant Mol.
Biol. 43: 121–145.
Chandler, V.L. and Stam, M. (2004). Chromatin conversations: mechanisms and implications of
paramutation. Nat. Rev. Genet. 5: 532–44.
Chen, N., Xu, Y., Wang, X., Du, C., Du, J., Yuan, M., Xu, Z., and Chong, K. (2011). OsRAN2,
essential for mitosis, enhances cold tolerance in rice by promoting export of intranuclear tubulin and maintaining cell division under cold stress. Plant, Cell Environ. 34: 52–64.
Chopra, S., Cocciolone, S.M., Bushman, S., Sangar, V., Mcmullen, M.D., and Peterson, T.
(2003). The Maize Unstable factor orange1 Is a Dominant Epigenetic Modifier ofTissue Specifically Silent Allele of pericarp color1. Genetics 163: 1135–1146.
Ciabrelli, F. and Cavalli, G. (2015). Chromatin-driven behavior of topologically associating
domains. J. Mol. Biol. 427: 608–625.
Clark, R.M., Wagler, T.N., Quijada, P., and Doebley, J. (2006). A distant upstream enhancer at the
maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat. Genet. 38: 594–7.
Cléard, F., Moshkin, Y., Karch, F., and Maeda, R.K. (2006). Probing long-distance regulatory
interactions in the Drosophila melanogaster bithorax complex using Dam identification. Nat. Genet. 38: 931–5.
Coe, E.J. (1959). A regular and continuing conversion - type phenomenon at b locus in maize.
Maydica 24: 49–58.
Coe, E.J. (1966). The properties, origin and mechanism of conversion - type inheritance at the b
locus in maize. Genetics 53: 1035–1063.
Cokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C.D., Pradhan, S., Nelson, S.F., Pellegrini, M., and Jacobsen, S.E. (2008). Shotgun bisulphite sequencing of the
Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215–129.
Colot, V., Maloisel, L., and Rossignol, J. (1996). Interchromosomal Transfer of Epigenetic States in
Ascobolus : Transfer of DNA Methylation Is Mechanistically Related to Homologous Recombination. Cell 86: 855–864.
Cremer, T. and Cremer, C. (2001). Chromosome Territories, Nuclear Architecture and Gene
Crevillén, P., Sonmez, C., Wu, Z., and Dean, C. (2013). A gene loop containing the floral repressor
FLC is disrupted in the early phase of vernalization. EMBO J. 32: 140–8.
Crevillén, P., Yang, H., Cui, X., Greeff, C., Trick, M., Qiu, Q., Cao, X., and Dean, C. (2014).
Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state. Nature 515: 587–90.
Czechowski, T., Stitt, M., Altmann, T., and Udvardi, M.K. (2005). Genome-wide identification
and testing of superior reference genes for transcript normalization. Plant Physiol. 139: 5–17.
Das, O.P. and Messing, J. (1994). Variegated Phenotype and Developmental Methylation Changes
of a Maize Allele Originating From Epimutation. Genetics 136: 1121–1141.
Dekker, J. (2006). The three “C” s of chromosome conformation capture: controls, controls, controls.
Nat. Methods 3: 17–21.
Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002). Capturing Chromosome
Conformation. Science 295: 1306–1311.
Dellaporta, S.L., Wood, J., and Hicks, J.B. (1983). A plant DNA minipreparation: Version II. Plant
Mol. Biol. Report. 1: 19–21.
Deng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P.D., Dean, A., and Blobel, G. (2012).
Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149: 1233–1244.
Derkacheva, M., Steinbach, Y., Wildhaber, T., Mozgová, I., Mahrez, W., Nanni, P., Bischof, S., Gruissem, W., and Hennig, L. (2013). Arabidopsis MSI1 connects LHP1 to PRC2 complexes.
EMBO J. 5: 1–13.
Diéguez, M.J., Vaucheret, H., Paszkowski, J., and Mittelsten Scheid, O. (1998). Cytosine
methylation at CG and CNG sites is not a prerequisite for the initiation of transcriptional gene silencing in plants , but it is required for its maintenance. Mol. Gen. Genet. 259: 207–215.
Dietzel, S., Niemann, H., Brückner, B., Maurange, C., and Paro, R. (1999). The nuclear
distribution of polycomb during Drosophila melanogaster development shown with a GFP fusion protein. Chromosoma 108: 83–94.
Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S., and Ren, B. (2012).
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485: 376–380.
Dorweiler, J.E., Carey, C.C., Kubo, K.M., Hollick, J.B., Kermicle, J.L., and Chandler, V.L.
(2000). mediator of paramutation1 Is Required for Establishment and Maintenance of Paramutation at Multiple Maize Loci. Plant Cell 12: 2101–2118.
Dostie, J., Richmond, T. a., Arnaout, R. a., Selzer, R.R., Lee, W.L., Honan, T. a., Rubio, E.D., Krumm, A., Lamb, J., Nusbaum, C., Green, R.D., and Dekker, J. (2006). Chromosome
Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res. 16: 1299–1309.
Du, J. et al. (2012). Dual binding of chromomethylase domains to H3K9me2-containing
Du, J., Johnson, L.M., Groth, M., Feng, S., Hale, C.J., Li, S., Vashisht, A., Gallego-Bartolome, J., Wohlschlegel, J., Patel, D.J., and Jacobsen, S.E. (2014). Mechanism of DNA
methylation-directed histone methylation by KRYPTONITE. Mol. Cell 55: 495–504.
Duncan, I.W. (2002). Transvection effects in Drosophila. Annu. Rev. Genet. 36: 521–56.
Duvillie, B., Bucchini, D., Tang, T., and Jami, J. (1998). Imprinting at the Mouse Ins2 Locus : Evidence for cis - and trans - Allelic Interactions. Genomics 57: 52–57.
Edelman, L.B. and Fraser, P. (2012). Transcription factories: Genetic programming in three
dimensions. Curr. Opin. Genet. Dev. 22: 110–114.
Egelhofer, T. a et al. (2011). An assessment of histone-modification antibody quality. Nat. Struct.
Mol. Biol. 18: 91–93.
Eichten, S.R., Ellis, N. a., Makarevitch, I., Yeh, C.T., Gent, J.I., Guo, L., McGinnis, K.M., Zhang, X., Schnable, P.S., Vaughn, M.W., Dawe, R.K., and Springer, N.M. (2012). Spreading
of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons. PLoS Genet. 8.
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., and Otto, G. (2009). Real-time DNA sequencing
from single polymerase molecules. Science 133–138.
English, J.J. and Jones, J.D.G. (1998). Epigenetic Instability and Trans-Silencing Interactions
Associated With an SPT :: Ac T-DNA Locus in Tobacco. Genetics 148: 457–469.
Enke, R., Dong, Z., and Bender, J. (2011). Small RNAs prevent transcription-coupled loss of
histone H3 lysine 9 methylation in Arabidopsis thaliana. PLoS Genet. 7: e1002350.
Erhard, K.F. and Hollick, J.B. (2011). Paramutation: a process for acquiring trans-generational
regulatory states. Curr. Opin. Plant Biol. 14: 210–6.
Erhard, K.F., Parkinson, S.E., Gross, S.M., Barbour, J.-E.R., Lim, J.P., and Hollick, J.B.
(2013). Maize RNA polymerase IV defines trans-generational epigenetic variation. Plant Cell 25: 808–19.
Erhard, K.F., Stonaker, J.L., Parkinson, S.E., and Al., E. (2009). RNA Polymerase IV Functions
in Paramutation in Zea mays. Science 323: 1201–1205.
Eskeland, R., Leeb, M., Grimes, G.R., Kress, C., Boyle, S., Sproul, D., Gilbert, N., Fan, Y., Skoultchi, A.I., Wutz, A., and Bickmore, W. (2010). Ring1B Compacts Chromatin Structure and
Represses Gene Expression Independent of Histone Ubiquitination. Mol. Cell 38: 452–464.
Feng, S., Cokus, S., Schubert, V., Zhai, J., Pellegrini, M., and Jacobsen, S. (2014). Genome-wide
Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis. Mol. Cell 55: 694–707.
Feng, W. and Michaels, S.D. (2015). Accessing the Inaccessible: The Organization, Transcription,
Replication, and Repair of Heterochromatin in Plants. Annu. Rev. Genet. 49: 439–459.
Ferrari, K.J., Scelfo, A., Jammula, S., Cuomo, A., Barozzi, I., Stützer, A., Fischle, W., Bonaldi, T., and Pasini, D. (2014). Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active
Transcription and Enhancer Fidelity. Mol. Cell 53: 49–62.
Filippakopoulos, P. and Knapp, S. (2014). Targeting bromodomains: epigenetic readers of lysine
Fischer, U., Kuhlmann, M., Pecinka, A., Schmidt, R., and Mette, M.F. (2008). Local DNA
features affect RNA-directed transcriptional gene silencing and DNA methylation. Plant J. 53: 1– 10.
Florentin, A., Damri, M., and Grafi, G. (2013). Stress induces plant somatic cells to acquire some
features of stem cells accompanied by selective chromatin reorganization. Dev. Dyn. 242: 1121– 1133.
Foerster, A.M., Dinh, H.Q., Sedman, L., Wohlrab, B., and Mittelsten Scheid, O. (2011). Genetic
rearrangements can modify chromatin features at epialleles. PLoS Genet. 7: e1002331.
Francis, K.E. and Spiker, S. (2005). Identification of Arabidopsis thaliana transformants without
selection reveals a high occurrence of silenced T-DNA integrations. Plant J. 41: 464–477.
Fransz, P. and De Jong, H. (2011). From nucleosome to chromosome: A dynamic organization of
genetic information. Plant J. 66: 4–17.
Fransz, P., De Jong, J.H., Lysak, M., Castiglione, M.R., and Schubert, I. (2002). Interphase
chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. PNAS. 99: 14584–9.
Fullwood, M.J., Han, Y., Chia-Lin, W., Xiaoan, R., and YYijun, R. (2012). Chromatin Interaction
Analysis Using Paired-End Tag Sequencing (ChIA-PET). Curr. Protoc. Mol. Biol. 185–210.
Gabriel, J.M. and Hollick, J.B. (2015). Paramutation in maize and related behaviors in metazoans.
Semin. Cell Dev. Biol. 44: 11–21.
Galbraith, D., Harkins, K., Maddox, J., Ayres, N., Sharma, D., and Firoozabady, E. (1983).
Rapid Flow Cytometric Analysis of the Cell Cycle in Intact Plant Tissues. Science 220: 1049–51.
Galbraith, D.W., Harkins, K.R., and Knapp, S. (1991). Systemic Endopolyploidy in Arabidopsis
thaliana. Plant Physiol. 96: 985–989.
Gao, Y. and Zhao, Y. (2013). Epigenetic suppression of T-DNA insertion mutants in Arabidopsis.
Mol. Plant 6: 539–45.
Gaydos, L.J., Wang, W., and Strome, S. (2014). H3K27me and PRC2 transmit a memory of
repression across generations and during development. Science 345: 1515–1519.
Gent, J.I., Ellis, N.A., Guo, L., Harkess, A.E., Yao, Y., Zhang, X., and Dawe, R.K. (2013). CHH
islands : de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res. 23: 628–637.
Gent, J.I., Madzima, T.F., Bader, R., Kent, M.R., Zhang, X., Stam, M., McGinnis, K.M., and Dawe, R.K. (2014). Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci
Undergoing RNA-Directed DNA Methylation. Plant Cell 26: 4903–4917.
Giacopelli, B.J. and Hollick, J.B. (2015). Trans-Homolog Interactions Facilitating Paramutation in
Maize. Plant Physiol. 168: 1226–1236.
Giresi, P.G., Kim, J., Mcdaniell, R.M., Giresi, P.G., Kim, J., Mcdaniell, R.M., Iyer, V.R., and Lieb, J.D. (2007). FAIRE ( Formaldehyde-Assisted Isolation of Regulatory Elements ) isolates
Goettel, W. and Messing, J. (2010). Divergence of gene regulation through chromosomal
rearrangements. BMC Genomics 11: 678.
Goettel, W. and Messing, J. (2013a). Epiallele biogenesis in maize. Gene 516: 8–23.
Goettel, W. and Messing, J. (2013b). Paramutagenicity of a p1 epiallele in maize. Theor. Appl.
Genet. 126: 159–77.
Grandjean, V., Gounon, P., Wagner, N., Martin, L., Wagner, K.D., Bernex, F., Cuzin, F., and Rassoulzadegan, M. (2009). The miR-124-Sox9 paramutation: RNA-mediated epigenetic control
of embryonic and adult growth. Development 136: 3647–3655.
Grandjean, V., Yaman, R., Cuzin, F., and Rassoulzadegan, M. (2007). Inheritance of an
epigenetic mark: the CpG DNA methyltransferase 1 is required for de novo establishment of a complex pattern of non-CpG methylation. PLoS One 2: e1136.
Grewal, S.I.S. and Jia, S. (2007). Heterochromatin revisited. Nat. Rev. Genet. 8: 35–46.
Grob, S., Schmid, M., and Grossniklaus, U. (2014). Hi-C Analysis in Arabidopsis Identifies the
KNOT, a Structure with Similarities to the flamenco Locus of Drosophila. Mol. Cell 55: 678–693.
Grob, S., Schmid, M.W., Luedtke, N.W., Wicker, T., and Grossniklaus, U. (2013).
Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biol. 14: R129.
Grosveld, F., van Assendelft, G., Greaves, D., and Kollias, G. (1987). Position-independent,
high-level expression of the human beta-globin gene in transgenic mice. Cell 51: 975–85.
Groszmann, M., Greaves, I.K., Fujimoto, R., Peacock, W.J., and Dennis, E.S. (2013). The role of
epigenetics in hybrid vigour. Trends Genet. 29: 684–690.
Gruntman, E., Qi, Y., Slotkin, R.K., Roeder, T., Martienssen, R., and Sachidanandam, R.
(2008). Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics 9: 371.
Guo, W., Fiziev, P., Yan, W., Cokus, S., Sun, X., Zhang, M.Q., Chen, P.-Y., and Pellegrini, M.
(2013). BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics 14: 774.
Gutiérrez-Marcos, J.F., Costa, L.M., Prà, M.D., Scholten, S., Kranz, E., Perez, P., and Dickinson, H.G. (2006). Epigenetic asymmetry of imprinted genes in plant gametes. Nat. Genet. 38: 876–878.
Haag, J.R., Brower-Toland, B., Krieger, E.K., Sidorenko, L., Nicora, C.D., Norbeck, A.D., Irsigler, A., LaRue, H., Brzeski, J., McGinnis, K., Ivashuta, S., Pasa-Tolic, L., Chandler, V.L., and Pikaard, C.S. (2014). Functional diversification of maize RNA polymerase IV and V subtypes
via alternative catalytic subunits. Cell Rep. 9: 378–90.
Hagège, H., Klous, P., Braem, C., Splinter, E., Dekker, J., Cathala, G., de Laat, W., and Forné, T. (2007). Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat.
Protoc. 2: 1722–33.
Hagemann, R. (1958). Somatische Konversion bei Lycopersicon Esculentum Mill. Z. Vererbungsl. 89: 587–613.
Hagemann, R. (1993). Studies towards a genetic and molecular analysis of paramutation at the
sulfurea locus of Lycopersicon esculentum Mill. In Molecular biology of tomato, J.I. Yoder, ed (Davis, Lancaster, Basel: Technomic Publishing Co), pp. 75–82.
Hale, C.J., Erhard, K.F., Lisch, D., and Hollick, J.B. (2009). Production and processing of siRNA
precursor transcripts from the highly repetitive maize genome. PLoS Genet. 5.
Hale, C.J., Stonaker, J.L., Gross, S.M., and Hollick, J.B. (2007). A novel Snf2 protein maintains
trans-generational regulatory states established by paramutation in maize. PLoS Biol. 5: 2156–2165.
Haring, M., Bader, R., Louwers, M., Schwabe, A., van Driel, R., and Stam, M. (2010). The role
of DNA methylation, nucleosome occupancy and histone modifications in paramutation. Plant J.
63: 366–78.
Haring, M., Offermann, S., Danker, T., Horst, I., Peterhansel, C., and Stam, M. (2007).
Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods 3: 11.
Hatada, I., Nabetani, A., Arai, Y., Ohishi, S., Suzuki, M., Miyabara, S., Nishimune, Y., and Mukai, T. (1997). Aberrant Methylation of an Imprinted Gene U2af1-rs1 Caused by Its Own
Transgene *. J. Biol. Chem. 272: 9120–9122.
Heintzman, N.D. Stuart, R.K., Hon, G., Fu, Y., Ching, C.W., Hawkins, R.D., Barrera, L.O., Van Calcar, S., Qu, C., Ching, K.A., Wang, W., Weng, Z., Green, R.D., Crawford, G.E., and Ren, B. (2007). Distinct and predictive chromatin signatures of transcriptional promoters and enhancers
in the human genome. Nat. Genet. 39: 311–8.
Heinz, S., Romanoski, C.E., Benner, C., and Glass, C.K. (2015). The selection and function of cell
type-specific enhancers. Nat Rev Mol Cell Biol 16: 144–154.
Helliwell, C., Robertson, M., Finnegan, E.J., Buzas, D.M., and Dennis, E.S. (2011).
Vernalization-repression of Arabidopsis FLC requires promoter sequences but not antisense transcripts. PLoS One 6.
Heo, J.B. and Sung, S. (2011). Vernalization-Mediated Epigenetic Silencing by a Long Intronic
Noncoding RNA. Science 331: 76–79.
Herman, H., Lu, M., Anggraini, M., Sikora, A., Chang, Y., Yoon, B.J., and Soloway, P.D.
(2003). Trans allele methylation and paramutation-like effects in mice. Nat. Genet. 34: 199–202.
Hiratani, I., Ryba, T., Itoh, M., Yokochi, T., Schwaiger, M., Chang, C.W., Lyou, Y., Townes, T.M., Schübeler, D., and Gilbert, D.M. (2008). Global reorganization of replication domains
during embryonic stem cell differentiation. PLoS Biol. 6: 2220–2236.
Hollick, J. and Patterson, G. (2000). Paramutation alters regulatory control of the maize pl locus.
Genetics 154: 1827–1838.
Hollick, J.B. (2012). Paramutation: a trans-homolog interaction affecting heritable gene regulation.
Curr. Opin. Plant Biol. 15: 536–43.
Hollick, J.B. and Chandler, V.L. (1998). Epigenetic Allelic States of a Maize Transcriptional
Regulatory Locus Exhibit Overdominant Gene Action. Genetics 150: 891–897.
Hollick, J.B., Kermicle, J.L., and Parkinson, S.E. (2005). Rmr6 maintains meiotic inheritance of
Hollick, J.B., Patterson, G.I., Coe, E.H., Cone, J.K.C., and Chandler, V.L. (1995). Allelic
Interactions Heritably Alter the Activity of a Metastable Maize pl Allele. Genetics 141: 709–719.
Holoch, D. and Moazed, D. (2015). RNA-mediated epigenetic regulation of gene expression. Nat.
Rev. Genet. 16: 71–84.
Horike, S., Cai, S., Miyano, M., Cheng, J.-F., and Kohwi-Shigematsu, T. (2005). Loss of
silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat. Genet. 37: 31–40.
Houwelingen, A. Van, Souer, E., Mol, J., and Koes, R. (1999). Epigenetic Interactions among
Three dTph1 Transposons in Two Homologous Chromosomes Activate a New Excision – Repair Mechanism in Petunia. Plant Cell 11: 1319–1336.
Hövel, I., Louwers, M., Marieke, L., and Stam, M. (2012). 3C Technologies in plants. Methods 58:
204–211.
Hövel, I., Pearson, N.A., and Stam, M. (2015). Cis-acting determinants of paramutation. Semin.
Cell Dev. Biol. 44: 22–32.
Huang, Y., Kendall, T., Forsythe, E.S., Dorantes-Acosta, A., Li, S., Caballero-Pérez, J., Chen, X., Arteaga-Vázquez, M., Beilstein, M. a., and Mosher, R. (2015). Ancient origin and recent
innovations of RNA polymerase IV and V. Mol. Biol. Evol. 32: 1788–1799.
Huettel, B., Kanno, T., Daxinger, L., Aufsatz, W., Matzke, A.J.M., and Matzke, M. (2006).
Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J. 25: 2828–2836.
Huettel, B., Kanno, T., Daxinger, L., Bucher, E., van der Winden, J., Matzke, a. J.M., and Matzke, M. (2007). RNA-directed DNA methylation mediated by DRD1 and Pol IVb: A versatile
pathway for transcriptional gene silencing in plants. Biochim. Biophys. Acta - Gene Struct. Expr.
1769: 358–374.
Inzé, D. and De Veylder, L. (2006). Cell cycle regulation in plant development. Annu. Rev. Genet. 40: 77–105.
Jackson, J.P., Lindroth, A.M., Cao, X., and Jacobsen, S.E. (2002). Control of CpNpG DNA
methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556–60.
Jaenisch, R. and Bird, A. (2003). Epigenetic regulation of gene expression: how the genome
integrates intrinsic and environmental signals. Nat. Genet. 33: 245–54.
Jia, Y., Lisch, D.R., Ohtsu, K., Scanlon, M.J., Nettleton, D., and Schnable, P.S. (2009). 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. 5.
Jiang, C. and Pugh, B.F. (2009). Nucleosome positioning and gene regulation: advances through
genomics. Nat. Rev. Genet. 10: 161–172.
Johnson, L.M., Du, J., Hale, C.J., Bischof, S., Feng, S., Chodavarapu, R.K., Zhong, X., Marson, G., Pellegrini, M., Segal, D.J., Patel, D.J., and Jacobsen, S.E. (2014). SRA- and
SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature 507: 124–8.
Jones, L., Ratcliff, F., and Baulcombe, D.C. (2001). RNA-directed transcriptional gene silencing in
plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr. Biol. 11: 747–757.
Kanazawa, A., O’Dell, M., and Hellen, R.P. (2007). The Binding of Nuclear Factors to the as-1
Element in the CaMV 35S Promoter is Affected by Cytosine Methylation in Vitro. Plant Biol 9: 435–441.
Kapoor, M., Baba, A., Kubo, K., Shibuya, K., Matsui, K., Tanaka, Y., and Takatsuji, H. (2005).
Transgene-triggered, epigenetically regulated ectopic expression of a flower homeotic gene pMADS3 in Petunia. Plant J. 43: 649–61.
Karmodiya, K., Krebs, A.R., Oulad-Abdelghani, M., Kimura, H., and Tora, L. (2012). H3K9
and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics 13: 424.
Kassis, J.A. (2012). Transvection in 2012: site-specific transgenes reveal a plethora of
trans-regulatory effects. Genetics 191: 1037–9.
Kermicle, J.L. (1996). Epigenetic Silencing and Activation of a Maize r Gene. Epigenetic Mech.
Gene Regul.: 267–287.
Kermicle, J.L., Eggleston, W.B., and Alleman, M. (1995). Organization of Paramutagenicity in
R-stippled Maize. Genetics 141: 361–372.
Khaitová, L.C., Fojtová, M., Křížová, K., Lunerová, J., Fulneček, J., Depicker, A., and Kovařík, A. (2011). Paramutation of tobacco transgenes by small RNA-mediated transcriptional gene
silencing. Epigenetics 6: 650–660.
Kiani, J., Grandjean, V., Liebers, R., Tuorto, F., Ghanbarian, H., Lyko, F., Cuzin, F., and Rassoulzadegan, M. (2013). RNA-mediated epigenetic heredity requires the cytosine
methyltransferase Dnmt2. PLoS Genet. 9: e1003498.
Kim, S.I., Veena, and Gelvin, S.B. (2007). Genome-wide analysis of Agrobacterium T-DNA
integration sites in the Arabidopsis genome generated under non-selective conditions. Plant J. 51: 779–791.
Kurukuti, S., Tiwari, V.K., Tavoosidana, G., Pugacheva, E., Murrell, A., Zhao, Z., Lobanenkov, V., Reik, W., and Ohlsson, R. (2006). CTCF binding at the H19 imprinting control region
mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. PNAS. 103: 10684–9.
Lanzuolo, C., Roure, V., Dekker, J., Bantignies, F., and Orlando, V. (2007). Polycomb response
elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat. Cell Biol. 9: 1167–1174.
Laudencia-Chingcuanco, D. and Fowler, D.B. (2012). Genotype-dependent burst of transposable
element expression in crowns of hexaploid wheat (Triticum aestivum L.) during cold acclimation. Comp. Funct. Genomics 2012.
Law, J., Du, J., Hale, C.J., Feng, S., Krajewski, K., Palanca, A.M.S., Strahl, B.D., Patel, D.J., and Jacobsen, S.E. (2013). Polymerase IV occupancy at RNA-directed DNA methylation sites
requires SHH1. Nature 498: 385–389.
Law, J. a., Vashisht, A. a., Wohlschlegel, J. a., and Jacobsen, S.E. (2011). SHH1, a Homeodomain
protein required for DNA Methylation, as well as RDR2, RDM4, and Chromatin remodeling factors, associate with RNA Polymerase IV. PLoS Genet. 7.
Law, J. and Jacobsen, S.E. (2010). Establishing, maintaining and modifying DNA methylation
patterns in plants and animals. Nat. Rev. Genet. 11: 204–220.
Lei, M., Zhang, H., Julian, R., Tang, K., Xie, S., and Zhu, J.-K. (2015). Regulatory link between
DNA methylation and active demethylation in Arabidopsis. PNAS. 112: 3553–7.
Leighton, P., Saam, J., Ingram, R., Stewart, C., and Tilghman, S. (1995). An enhancer deletion
affects both H19 and Igf2 expression. Genes Dev. PA, JR Saam, RS Ingram, CL Stewart, SM. Tilghman. 1995. “An Enhanc. Deletion Affect. Both H19 Igf2 Expression.” Genes Dev. 9: 2079–9.
Lettice, L. a., Heaney, S.J.H., Purdie, L. a., Li, L., de Beer, P., Oostra, B. a., Goode, D., Elgar, G., Hill, R.E., and de Graaff, E. (2003). A long-range Shh enhancer regulates expression in the
developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12: 1725– 1735.
Li, C., Chen, C., Gao, L., Yang, S., Nguyen, V., Shi, X., Siminovitch, K., Kohalmi, S.E., Huang, S., Wu, K., Chen, X., and Cui, Y. (2015a). The Arabidopsis SWI2/SNF2 Chromatin Remodeler
BRAHMA Regulates Polycomb Function during Vegetative Development and Directly Activates the Flowering Repressor Gene SVP. PLoS Genet. 11: 1–25.
Li, H. and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler
transform. Bioinformatics 25: 1754–1760.
Li, Q. et al. (2014a). Genetic perturbation of the maize methylome. Plant Cell 26: 4602–16.
Li, Q. et al. (2015b). RNA-directed DNA methylation enforces boundaries between heterochromatin
and euchromatin in the maize genome. PNAS. 112:14728-33
Li, Q., Eichten, R, S., Hermanson, P.J., and Springer, N.M. (2014b). Inheritance patterns and
stability of DNA methylation variation in maize near-isogenic lines. Genetics 196: 667–76.
Li, S., Vandivier, L.E., Tu, B., Gao, L., Won, S.Y., Li, S., Zheng, B., Gregory, B.D., and Chen, X. (2015c). Detection of pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis
reveals features and regulation of sirna biogenesis. Genome Res. 25: 235–245.
Lieberman-Aiden, E. et al. (2009). Comprehensive mapping of long-range interactions reveals
folding principles of the human genome. Science 326: 289–93.
Lisch, D. (2012). How important are transposons for plant evolution? Nat Rev Genet 14: 49–61. Lister, R., O’Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, H., and
Ecker, J.R. (2008). Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Cell 133: 523–536.
Liu, H. et al. (2008). Transvection mediated by the translocated cyclin D1 locus in mantle cell
lymphoma. J. Exp. Med. 205: 1843–58.
Liu, Z.-W., Shao, C.-R., Zhang, C.-J., Zhou, J.-X., Zhang, S.-W., Li, L., Chen, S., Huang, H.-W., Cai, T., and He, X.-J. (2014). The SET domain proteins SUVH2 and SUVH9 are required for Pol
V occupancy at RNA-directed DNA methylation loci. PLoS Genet. 10: e1003948.
Locatelli, S., Piatti, P., Motto, M., and Rossi, V. (2009). Chromatin and DNA modifications in the
Opaque2-mediated regulation of gene transcription during maize endosperm development. Plant Cell 21: 1410–27.
Louwers, M., Bader, R., Haring, M., van Driel, R., de Laat, W., and Stam, M. (2009a). Tissue-
and expression level-specific chromatin looping at maize b1 epialleles. Plant Cell 21: 832–42.
Louwers, M., Splinter, E., van Driel, R., de Laat, W., and Stam, M. (2009b). Studying physical
chromatin interactions in plants using Chromosome Conformation Capture (3C). Nat. Protoc. 4: 1216–29.
De Lucia, F., Crevillen, P., Jones, A.M.E., Greb, T., and Dean, C. (2008). A PHD-polycomb
repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. PNAS. 105: 16831–16836.
Luff, B., Pawlowski, L., and Bender, J. (1999). An Inverted Repeat Triggers Cytosine Methylation
of Identical Sequences in Arabidopsis. Mol. Cell 3: 505–511.
Lund, G., Das, O.P., and Messing, J. (1995). Tissue-specific DNase I-sensitive sites of the maize P
gene and their changes upon epimutation. Plant J. 7: 797–807.
Makarevitch, I., Waters, A.J., West, P.T., Stitzer, M., Hirsch, C.N., Ross-Ibarra, J., and Springer, N.M. (2015). Transposable Elements Contribute to Activation of Maize Genes in
Response to Abiotic Stress. PLoS Genet. 11.
Martienssen, R. (2003). Maintenance of heterochromatin by RNA interference of tandem repeats.
Nat. Genet. 35: 213–4.
Martin, C., Mayeda, C., Davis, C., Ericsson, C., Knafels, J., Mathog, D., Celniker, S., Lewis, E., and Palazzolo, M. (1995). Complete sequence of the bithorax complex of Drosophila. PNAS. 92:
8398–402.
Mathieu, O., Probst, A. V, and Paszkowski, J. (2005). Distinct regulation of histone H3
methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J. 24: 2783–91.
Mathieu, O., Reinders, J., Čaikovski, M., Smathajitt, C., and Paszkowski, J. (2007).
Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation. Cell
130: 851–862.
Matzke, A.J.M. (1989). Reversible methylation and inactivation of marker in sequentially
transformed tobacco plants genes. EMBO J. 8: 643–649.
Matzke, M., Mette, M., and Jakowitsch, J. (2001). A test for transvection in plants: DNA pairing
may lead to trans-activation or silencing of complex heteroalleles in tobacco. Genetics 158: 451– 461.
Matzke, M. and Mosher, R. (2014). RNA-directed DNA methylation: an epigenetic pathway of
increasing complexity. Nat. Rev. Genet. 15: 394–408.
Matzke, M.A. and Matzke, A.J.M. (1991). Differential inactivation and methylation of a transgene
in plants by two suppressor loci containing homologous sequences. Plant Mol. Biol. 16: 821–830.
McGinnis, K.M., Springer, C., Lin, Y., Carey, C.C., and Chandler, V. (2006). Transcriptionally
silenced transgenes in maize are activated by three mutations defective in paramutation. Genetics
173: 1637–1647.
Meyer, P. and Heidmann, I. (1994). Epigenetic variants of a transgenic petunia line show
hypermethylation in transgene DNA: an indication for specific recognition of foreign DNA in transgenic plants. Mol. Gen. Genet. 243: 390–9.
Meyer, P., Heidmann, I., and Niedenhof, I. (1993). Differences in DNA-methylation are associated
with a paramutation phenomenon in transgenic petunia. Plant J. 4: 89–100.
Mishiba, K.I., Nishihara, M., Nakatsuka, T., Abe, Y., Hirano, H., Yokoi, T., Kikuchi, A., and Yamamura, S. (2005). Consistent transcriptional silencing of 35S-driven transgenes in gentian.
Plant J. 44: 541–556.
Mitchell, J. a. and Fraser, P. (2008). Transcription factories are nuclear subcompartments that
remain in the absence of transcription. Genes Dev. 22: 20–25.
Mittelsten Scheid, O., Afsar, K., and Paszkowski, J. (2003). Formation of stable epialleles and
their paramutation-like interaction in tetraploid Arabidopsis thaliana. Nat. Genet. 34: 450–454.
Mlotshwa, S., Pruss, G.J., Gao, Z., Mgutshini, N.L., Li, J., Chen, X., Bowman, L.H., and Vance, V. (2010). Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S
promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing. Plant J. 64: 699–704.
Moindrot, B., Audit, B., Klous, P., Baker, A., Thermes, C., De Laat, W., Bouvet, P., Mongelard, F., and Arneodo, A. (2012). 3D chromatin conformation correlates with replication timing and is
conserved in resting cells. Nucleic Acids Res. 40: 9470–9481.
Molnar, A., Melnyk, C.W., Bassett, A., Hardcastle, T.J., Dunn, R., and Baulcombe, D.C. (2010).
Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 328: 872–5.
Montavon, T. and Soshnikova, N. (2014). Hox gene regulation and timing in embryogenesis. Semin.
Cell Dev. Biol. 34: 76–84.
Mozgova, I. and Hennig, L. (2015). The Polycomb Group Protein Regulatory Network. Annu. Rev.
Plant Biol 66: 269–96.
Murrell, A., Heeson, S., and Reik, W. (2004). Interaction between differentially methylated regions
partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet. 36: 889–893.
Nagano, T., Lubling, Y., Stevens, T.J., Schoenfelder, S., Yaffe, E., Dean, W., Laue, E.D., Tanay, A., and Fraser, P. (2013). Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.
Nature 502: 59–64.
Naito, K., Zhang, F., Tsukiyama, T., Saito, H., Hancock, C.N., Richardson, A.O., Okumoto, Y., Tanisaka, T., and Wessler, S.R. (2009). Unexpected consequences of a sudden and massive
transposon amplification on rice gene expression. Nature 461: 1130–1134.
Nobuta, K. et al. (2008). Distinct size distribution of endogenous siRNAs in maize : Evidence from deep sequencing in the mop1-1 mutant. PNAS 105: 14958–14963.
Nora, E.P. et al. (2012). Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Nature 485: 381–385.
O’Sullivan, J., Sontam, D., Grierson, R., and Jones, B. (2009). Characterization of chromosomal
integration sites for heterologous gene expression in Saccharomyces cerevisiae. Yeast 26: 545–551.
Ohtsu, K. et al. (2007). Global gene expression analysis of the shoot apical meristem of maize (Zea
Pacific Biosciences of California, I. (2014). Pacific Biosciences : SMRT Sequencing Advantage. http://www.pacificbiosciences.com/products/smrt-technology/smrt-sequencing-advantage/
(accessed April 08, 2015)
Palstra, R.-J., Simonis, M., Klous, P., Brasset, E., Eijkelkamp, B., and de Laat, W. (2008).
Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS One 3: e1661.
Palstra, R.-J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F., and de Laat, W. (2003). The
β-globin nuclear compartment in development and erythroid differentiation. Nat. Genet. 35: 190– 194.
Panavas, T., Weir, J., and Walker, E.L. (1999). The Structure and Paramutagenicity of the
R-marbled Haplotype of Zea mays. Genetics 153: 979–991.
Park, Y.-D., Papp, I., Moscone, E.A., Iglesias, V.A., Vaucheret, H., Matzke, A.J.M., and Matzke, M.A. (1996). Gene silencing mediated by promotor homology occurs at the level of
transcription and results in meiotically heritable alterations in methylation and gene activity. Plant J. 9: 183–194.
Patterson, G., Thorpe, C., and Chandler, V. (1993). Paramutation, an allelic interaction, is
associated with a stable and heritable reduction of transcription of the maize b regulatory gene. Genetics 135: 881–894.
Patterson, G.I., Kubo, K.M., Shroyer, T., and Chandler, V.L. (1995). Sequences Required for
Paramutation of the Maize. Genetics 140: 1389–1406.
Patterson, K., Molloy, L., Qu, W., and Clark, S. (2011). DNA methylation: bisulphite modification
and analysis. J. Vis. Exp. 1–9.
Paul, A.-L. and Ferl, R.J. (1998). Higher order chromatin structures in maize and Arabidopsis. Plant
Cell 10: 1349–1359.
Penterman, J., Uzawa, R., and Fischer, R.L. (2007). Genetic interactions between DNA
demethylation and methylation in Arabidopsis. Plant Physiol. 145: 1549–1557.
Pilu, R., Panzeri, D., Cassani, E., Cerino Badone, F., Landoni, M., and Nielsen, E. (2009). A
paramutation phenomenon is involved in the genetics of maize low phytic acid1-241 trait. Heredity (Edinb). 102: 236–45.
Pires, N.D. and Grossniklaus, U. (2014). Different yet similar: evolution of imprinting in flowering
plants and mammals. F1000Prime Rep. 6: 12–15.
Pirrotta, V. and Li, H.B. (2012). A view of nuclear Polycomb bodies. Curr. Opin. Genet. Dev. 22:
101–109.
Plank, J.L. and Dean, A. (2014). Enhancer function: Mechanistic and genome-wide insights come
together. Mol. Cell 55: 5–14.
Pombo, A. and Branco, M.R. (2007). Functional organisation of the genome during interphase.
Curr. Opin. Genet. Dev. 17: 451–455.
Qin, H., Dong, Y., and von Arnim, A.G. (2003). Epigenetic interactions between Arabidopsis
Quinlan, A.R. (2014). BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr.
Protoc. Bioinforma. 47.
Rajeevkumar, S., Anunanthini, P., and Sathishkumar, R. (2015). Epigenetic silencing in
transgenic plants. Front. Plant Sci. 6: 693.
Rassoulzadegan, M., Grandjean, V., Gounon, P., Vincent, S., Gillot, I., and Cuzin, F. (2006).
RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441: 469– 474.
Rassoulzadegan, M., Magliano, M., and Cuzin, F. (2002). Transvection effects involving DNA
methylation during meiosis in the mouse. EMBO J. 21: 440–450.
Ream, T.S., Haag, J.R., Wierzbicki, A.T., Nicora, C.D., Norbeck, A.D., Zhu, J.K., Hagen, G., Guilfoyle, T.J., Pasa-Tolic, L., and Pikaard, C.S. (2009). Subunit Compositions of the
RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II. Mol. Cell 33: 192–203.
Regulski, M. et al. (2013). The maize methylome influences mRNA splice sites and reveals
widespread paramutation-like switches guided by small RNA. Genome Res. 23: 1651–62.
Renner, O. (1959). Somatic conversion in the heredity of the cruciata character in Oenothera.
Heredity (Edinb). 13: 283–288.
Ritchie, S., Hanway, J., and Benson, G. (1992). How a Corn Plant Develops. Sp. Rpt. #48. Iowa
State University of Science and Technology. Cooperative Extension Service.
Roberts, A. and Pachter, L. (2013). Streaming fragment assignment for real-time analysis of
sequencing experiments. Nat. Methods 10: 71–3.
Ronshaugen, M. and Levine, M. (2004). Visualization of trans-homolog enhancer-promoter
interactions at the Abd-B hox locus in the Drosophila embryo. Dev. Cell 7: 925–932.
Rosa, S., De Lucia, F., Mylne, J.S., Zhu, D., Ohmido, N., Pendle, A., Kato, N., Shaw, P., and Dean, C. (2013). Physical clustering of FLC alleles during polycomb-mediated epigenetic silencing
in vernalization. Genes Dev. 27: 1845–1850.
Roudier, F. et al. (2011). Integrative epigenomic mapping defines four main chromatin states in
Arabidopsis. EMBO J. 30: 1928–38.
Sandhu, K.S., Shi, C., Sjölinder, M., Zhao, Z., Göndör, A., Liu, L., Tiwari, V.K., Guibert, S., Emilsson, L., Imreh, M.P., and Ohlsson, R. (2009). Nonallelic transvection of multiple imprinted
loci is organized by the H19 imprinting control region during germline development. Genes Dev.
23: 2598–2603.
Sapetschnig, A., Sarkies, P., Lehrbach, N.J., and Miska, E. (2015). Tertiary siRNAs Mediate
Paramutation in C. elegans. PLoS Genet. 11: e1005078.
Schafer, D. (2013). Mechanisms Underlying Epigenetic Gene Silencing in Maize. Thesis, University
of Warwick.
Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., and Lohmann, J.U. (2005). A gene expression map of Arabidopsis thaliana
Schoenfelder, S. et al. (2010). Preferential associations between co-regulated genes reveal a
transcriptional interactome in erythroid cells. Nat. Genet. 42: 53–61.
Schotta, G., Ebert, A., Dorn, R., and Reuter, G. (2003). Position-effect variegation and the genetic
dissection of chromatin regulation in Drosophila. Semin. Cell Dev. Biol. 14: 67–75.
Schubert, V., Berr, A., and Meister, A. (2012). Interphase chromatin organisation in Arabidopsis
nuclei: Constraints versus randomness. Chromosoma 121: 369–387.
Schwartz, Y.B. and Pirrotta, V. (2013). A new world of Polycombs: unexpected partnerships and
emerging functions. Nat. Rev. Genet. 14: 853–64.
Sekhon, R.S., Lin, H., Childs, K.L., Hansey, C.N., Buell, C.R., de Leon, N., and Kaeppler, S.M.
(2011). Genome-wide atlas of transcription during maize development. Plant J. 66: 553–63.
Sekhon, R.S., Wang, P.-H., Sidorenko, L., Chandler, V.L., and Chopra, S. (2012). Maize
Unstable factor for orange1 is required for maintaining silencing associated with paramutation at the pericarp color1 and booster1 loci. PLoS Genet. 8: e1002980.
Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., and Cavalli, G. (2012). Three-dimensional folding and functional organization
principles of the Drosophila genome. Cell 148: 458–472.
Shlyueva, D., Stampfel, G., and Stark, A. (2014). Transcriptional enhancers: from properties to
genome-wide predictions. Nat. Rev. Genet. 15: 272–86.
Sidorenko, L. and Chandler, V. (2008). RNA-dependent RNA polymerase is required for
enhancer-mediated transcriptional silencing associated with paramutation at the maize p1 gene. Genetics 180: 1983–93.
Sidorenko, L., Dorweiler, J.E., Cigan, a M., Arteaga-Vazquez, M., Vyas, M., Kermicle, J., Jurcin, D., Brzeski, J., Cai, Y., and Chandler, V.L. (2009). A dominant mutation in mediator of
paramutation2, one of three second-largest subunits of a plant-specific RNA polymerase, disrupts multiple siRNA silencing processes. PLoS Genet. 5: e1000725.
Sidorenko, L. V, Li, X., Cocciolone, S.M., Chopra, S., Tagliani, L., Bowen, B., Daniels, M., and Peterson, T. (2000). Complex structure of a maize Myb gene promoter : functional analysis in transgenic plants. Plant J. 22: 471–482.
Sidorenko, L. V and Peterson, T. (2001). Transgene-Induced Silencing Identifies Sequences
Involved in the Establishment of Paramutation of the Maize p1 Gene. Plant Cell 13: 319–335.
SIGnAL (2013). Salk Institute Genomic Analysis Laboratory Arabidopsis sequence indexed TDNA
insertion. 321. http://signal.salk.edu/tdna_FAQs.html (accessed April 08, 2015).
Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., and de Laat, W. (2006). Nuclear organization of active and inactive chromatin domains uncovered
by chromosome conformation capture-on-chip (4C). Nat. Genet. 38: 1348–54.
Singh, J., Freeling, M., and Lisch, D. (2008). A position effect on the heritability of epigenetic
silencing. PLoS Genet. 4.
Siomi, M.C., Sato, K., Pezic, D., and Aravin, A. (2011). PIWI-interacting small RNAs: the
Sirri, V., Urcuqui-Inchima, S., Roussel, P., and Hernandez-Verdun, D. (2008). Nucleolus: The
fascinating nuclear body. Histochem. Cell Biol. 129: 13–31.
Sloan, A.E., Sidorenko, L., and McGinnis, K.M. (2014). Diverse gene silencing mechanisms with
distinct requirements for RNA polymerase subunits in Zea mays. Genetics 198: 1031–1042.
Slotkin, R.K. and Martienssen, R. (2007). Transposable elements and the epigenetic regulation of
the genome. Nat. Rev. Genet. 8: 272–85.
Šmigová, J., Juda, P., Bártová, E., and Raška, I. (2013). Dynamics of Polycomb chromatin
domains under conditions of increased molecular crowding. Biol. Cell 105: 519–534.
Soppe, W.J.J., Jacobsen, S.E., Alonso-Blanco, C., Jackson, J.P., Kakutani, T., and Koornneef, M. (2000). The Late Flowering Phenotype of fwa Mutants Is Caused by Gain-of-Function
Epigenetic Alleles of a Homeodomain Gene. Mol. Cell 6: 791–802.
De Souza, F.S.J., Franchini, L.F., and Rubinstein, M. (2013). Exaptation of transposable elements
into novel Cis-regulatory elements: Is the evidence always strong? Mol. Biol. Evol. 30: 1239–1251.
Spellman, P.T. and Rubin, G.M. (2002). Evidence for large domains of similarly expressed genes in
the Drosophila genome. J. Biol. 1: 5.
Splinter, E., Grosveld, F., and De Laat, W. (2004). 3C Technology: Analyzing the Spatial
Organization of Genomic Loci In Vivo. Methods Enzymol. 375: 493–507.
Splinter, E. and de Laat, W. (2011). The complex transcription regulatory landscape of our genome:
control in three dimensions. EMBO J. 30: 4345–4355.
Stadhouders, R. et al. (2011). Dynamic long-range chromatin interactions control Myb
proto-oncogene transcription during erythroid development. EMBO J. 31: 986–999.
Stam, M. (2009). Paramutation: a heritable change in gene expression by allelic interactions in trans.
Mol. Plant 2: 578–88.
Stam, M., Belele, C., Dorweiler, J.E., and Chandler, V.L. (2002a). Differential chromatin structure
within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 16: 1906–1918.
Stam, M., Belele, C., Ramakrishna, W., Dorweiler, J.E., Bennetzen, J.L., and Chandler, V.L.
(2002b). The Regulatory Regions Required for B Paramutation and Expression Are Located Far Upstream of the Maize b1 Transcribed Sequences. Genetics 930: 917–930.
Stonaker, J.L., Lim, J.P., Erhard, K.F., and Hollick, J.B. (2009). Diversity of Pol IV function is
defined by mutations at the maize rmr7 locus. PLoS Genet. 5: e1000706.
De Storme, N., Copenhaver, G.P., and Geelen, D. (2012). Production of diploid male gametes in
Arabidopsis by cold-induced destabilization of post-meiotic radial microtubule arrays. Plant Physiol. 160: 1808–1826.
Stroud, H., Do, T., Du, J., Zhong, X., Feng, S., Johnson, L., Patel, D.J., and Jacobsen, S.E.
(2014). Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat. Struct. Mol. Biol. 21: 64–72.
Stroud, H., Greenberg, M.V.C., Feng, S., Bernatavichute, Y. V., and Jacobsen, S.E. (2013).
Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152: 352–364.
Struhl, K. and Segal, E. (2013). Determinants of nucleosome positioning. Nat. Struct. Mol. Biol. 20:
267–73.
Suter, C.M. and Martin, D.I.K. (2010). Paramutation: the tip of an epigenetic iceberg? Trends
Genet. 26: 9–14.
Sutherland, H. and Bickmore, W. (2009). Transcription factories: gene expression in unions? Nat.
Rev. Genet. 10: 457–466.
Swarbreck, D., Wilks, C., Lamesch, P., Berardini, T.Z., Garcia-Hernandez, M., Foerster, H., Li, D., Meyer, T., Muller, R., Ploetz, L., Radenbaugh, A., Singh, S., Swing, V., Tissier, C., Zhang, P., Huala, E. (2008). The Arabidopsis Information Resource (TAIR): Gene structure and function
annotation. Nucleic Acids Res. 36: 1009–1014.
Swiezewski, S., Liu, F., Magusin, A., and Dean, C. (2009). Cold-induced silencing by long
antisense transcripts of an Arabidopsis Polycomb target. Nature 462: 799–802.
Tan-Wong, S.M., Wijayatilake, H.D., and Proudfoot, N.J. (2009). Gene loops function to maintain
transcriptional memory through interaction with the nuclear pore complex. Genes Dev. 23: 2610– 2624.
Tessadori, F., van Zanten, M., Pavlova, P., Clifton, R., Pontvianne, F., Snoek, L.B., Millenaar, F.F., Schulkes, R.K., van Driel, R., Voesenek, L.A., Spillane, C., Pikaard, C.S., Fransz, P., Peeters, A.J. (2009). PHYTOCHROME B and HISTONE DEACETYLASE 6 control
light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet. 5: 14–17.
Tiwari, V.K., McGarvey, K.M., Licchesi, J.D.F., Ohm, J.E., Herman, J.G., Schübeler, D., and Baylin, S.B. (2008). PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping.
PLoS Biol. 6
Tolhuis, B., Blom, M., Kerkhoven, R.M., Pagie, L., Teunissen, H., Nieuwland, M., Simonis, M., de Laat, W., van Lohuizen, M., and van Steensel, B. (2011). Interactions among polycomb
domains are guided by chromosome architecture. PLoS Genet. 7.
Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F., and De Laat, W. (2002). Looping and
interaction between hypersensitive sites in the active ß-globin locus. Mol. Cell 10: 1453–1465.
Toufighi, K., Brady, S.M., Austin, R., Ly, E., and Provart, N.J. (2005). The botany array resource:
e-Northerns, expression angling, and promoter analyses. Plant J. 43: 153–163.
Turck, F., Roudier, F., Farrona, S., Martin-Magniette, M.L., Guillaume, E., Buisine, N., Gagnot, S., Martienssen, R. a., Coupland, G., and Colot, V. (2007). Arabidopsis TFL2/LHP1
specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet. 3: 0855–0866.
Umbarger, M. a. et al. (2011). The three-dimensional architecture of a bacterial genome and its
alteration by genetic perturbation. Mol. Cell 44: 252–264.
De Vanssay, A., Bougé, A.-L., Boivin, A., Hermant, C., Teysset, L., Delmarre, V., Ronsseray, S., and Antoniewski, C. (2013). Profiles of piRNA abundances at emerging or established piRNA loci
Walker, E. (1998). Paramutation of the r1 locus of maize is associated with increased cytosine
methylation. Genetics 148: 1973–1981.
Walker, E.L. and Panavas, T. (2001). Structural Features and Methylation Patterns Associated With
Paramutation at the r1 Locus of Zea mays. Genetics 159: 1201–1215.
Wang, C., Liu, C., Roqueiro, D., Grimm, D., Schwab, R., Becker, C., Lanz, C., and Weigel, D.
(2015). Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res.
25: 246–256.
Wang, Y., Tang, X., Cheng, Z., Mueller, L., Giovannoni, J., and Tanksley, S.D. (2006).
Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome. Genetics 172: 2529–40.
Van de Werken, H.J.G. Landan, G., Holwerda, S.J., Hoichman, M., Klous, P., Chachik, R., Splinter, E., Valdes-Quezada, C., Oz, Y., Bouwman, B.A., Verstegen, M.J., de Wit, E., Tanay, A., de Laat, W. (2012a). Robust 4C-seq data analysis to screen for regulatory DNA interactions.
Nat Methods 9: 969–972.
Van de Werken, H.J.G., De Vree, P.J.P., Splinter, E., Holwerda, S.J.B., Klous, P., De Wit, E., and De Laat, W. (2012b). 4C technology: Protocols and data analysis. Methods Enzymol.
513:89-112.
West, P. Van, Kamoun, S., Klooster, J.W. Van, and Govers, F. (1999). Internuclear Gene
Silencing in Phytophthora infestans. Mol. Cell 3: 339–348.
West, P.T., Li, Q., Ji, L., Eichten, S.R., Song, J., Vaughn, M.W., Schmitz, R.J., and Springer, N.M. (2014). Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS
One 9: 1–10.
Wierzbicki, A.T., Cocklin, R., Mayampurath, A., Lister, R., Rowley, M.J., Gregory, B.D., Ecker, J.R., Tang, H., and Pikaard, C.S. (2012). Spatial and functional relationships among Pol
V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev. 26: 1825–1836.
Wierzbicki, A.T., Haag, J.R., and Pikaard, C.S. (2008). Noncoding Transcription by RNA
Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes. Cell 135: 635–648.
Wisman, E., Ramanna, M.S., and Koornneef, M. (1993). Isolation of a new paramutagenic allele
of the sulfurea locus in the tomato cultivar Moneymaker following in vitro culture. Theor. Appl. Genet. 87: 289–294.
De Wit, E. and de Laat, W. (2012). A decade of 3C technologies: Insights into nuclear organization.
Genes Dev. 26: 11–24.
Woodhouse, M.R., Freeling, M., and Lisch, D. (2006). The mop1 (mediator of paramutation1)
mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize. Genetics 172: 579–592.
Worch, S., Hansmann, I., and Schlote, D. (2008). Paramutation-like effects at the mouse scapinin
(Phactr3) locus. J. Mol. Biol. 377: 605–8.
Xie, W. et al. (2013). Epigenomic analysis of multilineage differentiation of human embryonic stem
Xu, N., Tsai, C.-L., and Lee, J. (2006). Transient Homologous Chromosome Pairing Marks the
Onset of X Inactivation. Science 311: 1149–1152.
Xu, Y., Wang, Y., Stroud, H., Gu, X., Sun, B., Gan, E.-S., Ng, K.-H., Jacobsen, S.E., He, Y., and Ito, T. (2013). A Matrix Protein Silences Transposons and Repeats through Interaction with
Retinoblastoma-Associated Proteins. Curr. Biol. 23: 345–350.
Xue, W., Ruprecht, C., Street, N., Hematy, K., Chang, C., Frommer, W.B., Persson, S., and Niittylä, T. (2012). Paramutation-like interaction of T-DNA loci in Arabidopsis. PLoS One 7:
e51651.
Yang, H., Howard, M., and Dean, C. (2014). Antagonistic roles for H3K36me3 and H3K27me3 in
the cold-induced epigenetic switch at Arabidopsis FLC. Curr. Biol. 24: 1793–1797.
Zemach, A., Kim, M.Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., Harmer, S.L., and Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin. Cell 153: 193–205.
Zhang, H. et al. (2013). DTF1 is a core component of RNA-directed DNA methylation and may
assist in the recruitment of Pol IV. PNAS. 110: 8290–5.
Zhang, H. and Zhu, J.K. (2012). Active DNA demethylation in plants and animals. Cold Spring
Harb. Symp. Quant. Biol. 77: 161–173.
Zhang, X., Clarenz, O., Cokus, S., Bernatavichute, Y. V., Pellegrini, M., Goodrich, J., and Jacobsen, S.E. (2007). Whole-genome analysis of histone H3 lysine 27 trimethylation in
Arabidopsis. PLoS Biol. 5: 1026–1035.
Zhao, Z. Tavoosidana, G., Sjölinder, M., Göndör, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K.S., Singh, U., Pant, V., Tiwari, V., Kurukuti, S., Ohlsson, R. (2006).
Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38: 1341–1347.
Zheng, B., Wang, Z., Li, S., and Yu, B. (2009). Intergenic transcription by RNA polymerase II
coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev. 23: 2850–2860.
Zheng, Q., Rowley, M.J., Böhmdorfer, G., Sandhu, D., Gregory, B.D., and Wierzbicki, A.T.
(2012). RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes. Plant J. 179–189.
Zhong, X., Hale, C.J., Law, J., Johnson, L.M., Feng, S., Tu, A., and Jacobsen, S.E. (2012). DDR
complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat. Struct. Mol. Biol. 19: 870–5.
Zhou, V.W., Goren, A., and Bernstein, B.E. (2011). Charting histone modifications and the
functional organization of mammalian genomes. Nat. Rev. Genet. 12: 7–18.
Zhu, D., Rosa, S., and Dean, C. (2015). Nuclear organization changes and the epigenetic silencing