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  1. Blevins T, Podicheti R, Pikaard CS. Analysis of siRNA Precursors Generated by RNA Polymerase IV and RNA-Dependent RNA Polymerase 2 in Arabidopsis. Methods Mol Biol. 2019;1933:33-48. doi: 10.1007/978-1-4939-9045-0_2. PubMed PMID: 30945177.
  2. Marasco M, Li W, Lynch M, Pikaard CS. Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination. Nucleic Acids Res. 2017 Nov 2;45(19):11315-11326. doi: 10.1093/nar/gkx794. PubMed PMID: 28977461; PubMed Central PMCID: PMC5737373.
  3. Wang J, Blevins T, Podicheti R, Haag JR, Tan EH, Wang F, Pikaard CS. Mutation of Arabidopsis SMC4 identifies condensin as a corepressor of pericentromeric transposons and conditionally expressed genes. Genes Dev. 2017 Aug 1;31(15):1601-1614. doi: 10.1101/gad.301499.117. Epub 2017 Sep 7. PubMed PMID: 28882854; PubMed Central PMCID: PMC5630024.
  4. Wendte JM, Haag JR, Singh J, McKinlay A, Pontes OM, Pikaard CS. Functional Dissection of the Pol V Largest Subunit CTD in RNA-Directed DNA Methylation. Cell Rep. 2017 Jun 27;19(13):2796-2808. doi: 10.1016/j.celrep.2017.05.091. PubMed PMID: 28658626; PubMed Central PMCID: PMC5541899.
  5. Blevins T, Wang J, Pflieger D, Pontvianne F, Pikaard CS. Hybrid incompatibility caused by an epiallele. Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3702-3707. doi: 10.1073/pnas.1700368114. Epub 2017 Mar 7. PubMed PMID: 28270603; PubMed Central PMCID: PMC5389275.
  6. Wendte JM, Pikaard CS. The RNAs of RNA-directed DNA methylation. Biochim Biophys Acta Gene Regul Mech. 2017 Jan;1860(1):140-148. doi: 10.1016/j.bbagrm.2016.08.004. Epub 2016 Aug 10. Review. PubMed PMID: 27521981; PubMed Central PMCID: PMC5203809.
  7. Wendte JM, Pikaard CS. Targeting Argonaute to chromatin. Genes Dev. 2016 Dec 15;30(24):2649-2650. doi: 10.1101/gad.294900.116. PubMed PMID: 28087710; PubMed Central PMCID: PMC5238723.
  8. Mohannath G, Pontvianne F, Pikaard CS. Selective nucleolus organizer inactivation in Arabidopsis is a chromosome position-effect phenomenon. Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):13426-13431. doi: 10.1073/pnas.1608140113. Epub 2016 Nov 7. PubMed PMID: 27821753; PubMed Central PMCID: PMC5127337.
  9. Pontvianne F, Carpentier MC, Durut N, Pavlištová V, Jaške K, Schořová Š, Parrinello H, Rohmer M, Pikaard CS, Fojtová M, Fajkus J, Sáez-Vásquez J. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome. Cell Rep. 2016 Aug 9;16(6):1574-1587. doi: 10.1016/j.celrep.2016.07.016. Epub 2016 Jul 28. PubMed PMID: 27477271; PubMed Central PMCID: PMC5279810.
  10. Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P. 50 years of Arabidopsis research: highlights and future directions. New Phytol. 2016 Feb;209(3):921-44. doi: 10.1111/nph.13687. Epub 2015 Oct 14. Review. PubMed PMID: 26465351.
  11. Chandrasekhara C, Mohannath G, Blevins T, Pontvianne F, Pikaard CS. Chromosome-specific NOR inactivation explains selective rRNA gene silencing and dosage control in Arabidopsis. Genes Dev. 2016 Jan 15;30(2):177-90. doi: 10.1101/gad.273755.115. Epub 2016 Jan 7. PubMed PMID: 26744421; PubMed Central PMCID: PMC4719308.
  12. Mohannath G, Pikaard CS. Analysis of rRNA Gene Methylation in Arabidopsis thaliana by CHEF-Conventional 2D Gel Electrophoresis. Methods Mol Biol. 2016;1455:183-202. doi: 10.1007/978-1-4939-3792-9_14. PubMed PMID: 27576719; PubMed Central PMCID: PMC5310131.
  13. Blevins T, Podicheti R, Mishra V, Marasco M, Wang J, Rusch D, Tang H, Pikaard CS. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. Elife. 2015 Oct 2;4:e09591. doi: 10.7554/eLife.09591. PubMed PMID: 26430765; PubMed Central PMCID: PMC4716838.
  14. Ream TS, Haag JR, Pontvianne F, Nicora CD, Norbeck AD, Paša-Tolić L, Pikaard CS. Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit. Nucleic Acids Res. 2015 Apr 30;43(8):4163-78. doi: 10.1093/nar/gkv247. Epub 2015 Mar 26. PubMed PMID: 25813043; PubMed Central PMCID: PMC4417161.
  15. Pikaard CS, Mittelsten Scheid O. Epigenetic regulation in plants. Cold Spring Harb Perspect Biol. 2014 Dec 1;6(12):a019315. doi: 10.1101/cshperspect.a019315. Review. PubMed PMID: 25452385; PubMed Central PMCID: PMC4292151.
  16. Haag JR, Brower-Toland B, Krieger EK, Sidorenko L, Nicora CD, Norbeck AD, Irsigler A, LaRue H, Brzeski J, McGinnis K, Ivashuta S, Pasa-Tolic L, Chandler VL, Pikaard CS. Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits. Cell Rep. 2014 Oct 9;9(1):378-390. doi: 10.1016/j.celrep.2014.08.067. Epub 2014 Oct 2. PubMed PMID: 25284785; PubMed Central PMCID: PMC4196699.
  17. Blevins T, Pontvianne F, Cocklin R, Podicheti R, Chandrasekhara C, Yerneni S, Braun C, Lee B, Rusch D, Mockaitis K, Tang H, Pikaard CS. A two-step process for epigenetic inheritance in Arabidopsis. Mol Cell. 2014 Apr 10;54(1):30-42. doi: 10.1016/j.molcel.2014.02.019. Epub 2014 Mar 20. PubMed PMID: 24657166; PubMed Central PMCID: PMC3988221.
  18. Pontvianne F, Blevins T, Chandrasekhara C, Mozgová I, Hassel C, Pontes OM, Tucker S, Mokros P, Muchová V, Fajkus J, Pikaard CS. Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states. Genes Dev. 2013 Jul 15;27(14):1545-50. doi: 10.1101/gad.221648.113. PubMed PMID: 23873938; PubMed Central PMCID: PMC3731543.
  19. Pontes O, Vitins A, Ream TS, Hong E, Pikaard CS, Costa-Nunes P. Intersection of small RNA pathways in Arabidopsis thaliana sub-nuclear domains. PLoS One. 2013;8(6):e65652. doi: 10.1371/journal.pone.0065652. Print 2013. PubMed PMID: 23776518; PubMed Central PMCID: PMC3680462.
  20. Pikaard CS, Haag JR, Pontes OM, Blevins T, Cocklin R. A transcription fork model for Pol IV and Pol V-dependent RNA-directed DNA methylation. Cold Spring Harb Symp Quant Biol. 2012;77:205-12. doi: 10.1101/sqb.2013.77.014803. Epub 2013 Apr 8. PubMed PMID: 23567894.
  21. Pikaard CS. Methylating the DNA of the most repressed: special access required. Mol Cell. 2013 Mar 28;49(6):1021-2. doi: 10.1016/j.molcel.2013.03.013. PubMed PMID: 23541038; PubMed Central PMCID: PMC3641553.
  22. Dekker J, Wysocka J, Mattaj I, Lieberman Aiden E, Pikaard C. Nuclear biology: what's been most surprising?. Cell. 2013 Mar 14;152(6):1207-8. doi: 10.1016/j.cell.2013.02.041. PubMed PMID: 23616995; PubMed Central PMCID: PMC4149748.
  23. Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, Pasa-Tolic L, Pikaard CS. In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol Cell. 2012 Dec 14;48(5):811-8. doi: 10.1016/j.molcel.2012.09.027. Epub 2012 Nov 8. PubMed PMID: 23142082; PubMed Central PMCID: PMC3532817.
  24. Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev. 2012 Aug 15;26(16):1825-36. doi: 10.1101/gad.197772.112. Epub 2012 Aug 1. PubMed PMID: 22855789; PubMed Central PMCID: PMC3426761.
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  26. Pontvianne F, Blevins T, Chandrasekhara C, Feng W, Stroud H, Jacobsen SE, Michaels SD, Pikaard CS. Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes Dev. 2012 May 1;26(9):945-57. doi: 10.1101/gad.182865.111. PubMed PMID: 22549957; PubMed Central PMCID: PMC3347792.
  27. Tan EH, Blevins T, Ream TS, Pikaard CS. Functional consequences of subunit diversity in RNA polymerases II and V. Cell Rep. 2012 Mar 29;1(3):208-14. doi: 10.1016/j.celrep.2012.01.004. PubMed PMID: 22550619; PubMed Central PMCID: PMC3339255.
  28. Mosher RA, Tan EH, Shin J, Fischer RL, Pikaard CS, Baulcombe DC. An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs. PLoS One. 2011;6(10):e25756. doi: 10.1371/journal.pone.0025756. Epub 2011 Oct 7. PubMed PMID: 22003406; PubMed Central PMCID: PMC3189211.
  29. Haag JR, Pikaard CS. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol. 2011 Jul 22;12(8):483-92. doi: 10.1038/nrm3152. Review. PubMed PMID: 21779025.
  30. Tucker SL, Reece J, Ream TS, Pikaard CS. Evolutionary history of plant multisubunit RNA polymerases IV and V: subunit origins via genome-wide and segmental gene duplications, retrotransposition, and lineage-specific subfunctionalization. Cold Spring Harb Symp Quant Biol. 2010;75:285-97. doi: 10.1101/sqb.2010.75.037. Epub 2011 Mar 29. PubMed PMID: 21447813.
  31. Hoffer P, Ivashuta S, Pontes O, Vitins A, Pikaard C, Mroczka A, Wagner N, Voelker T. Posttranscriptional gene silencing in nuclei. Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):409-14. doi: 10.1073/pnas.1009805108. Epub 2010 Dec 20. PubMed PMID: 21173264; PubMed Central PMCID: PMC3017132.
  32. Pontvianne F, Abou-Ellail M, Douet J, Comella P, Matia I, Chandrasekhara C, Debures A, Blevins T, Cooke R, Medina FJ, Tourmente S, Pikaard CS, Sáez-Vásquez J. Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana. PLoS Genet. 2010 Nov 24;6(11):e1001225. doi: 10.1371/journal.pgen.1001225. PubMed PMID: 21124873; PubMed Central PMCID: PMC2991258.
  33. Tucker S, Vitins A, Pikaard CS. Nucleolar dominance and ribosomal RNA gene silencing. Curr Opin Cell Biol. 2010 Jun;22(3):351-6. doi: 10.1016/ Epub 2010 Apr 12. PubMed PMID: 20392622; PubMed Central PMCID: PMC2912983.
  34. Earley KW, Pontvianne F, Wierzbicki AT, Blevins T, Tucker S, Costa-Nunes P, Pontes O, Pikaard CS. Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation. Genes Dev. 2010 Jun 1;24(11):1119-32. doi: 10.1101/gad.1914110. PubMed PMID: 20516197; PubMed Central PMCID: PMC2878650.
  35. Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJ, Matzke M, Pikaard CS, Zhu JK. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. 2010 May 6;465(7294):106-9. doi: 10.1038/nature09025. Epub 2010 Apr 21. PubMed PMID: 20410883; PubMed Central PMCID: PMC2865564.
  36. Costa-Nunes P, Pontes O, Preuss SB, Pikaard CS. Extra views on RNA-dependent DNA methylation and MBD6-dependent heterochromatin formation in nucleolar dominance. Nucleus. 2010 May-Jun;1(3):254-9. doi: 10.4161/nucl.1.3.11741. Epub 2010 Mar 2. PubMed PMID: 21327072; PubMed Central PMCID: PMC3027031.
  37. Carvalho A, Delgado M, Barão A, Frescatada M, Ribeiro E, Pikaard CS, Viegas W, Neves N. Chromosome and DNA methylation dynamics during meiosis in the autotetraploid Arabidopsis arenosa. Sex Plant Reprod. 2010 Mar;23(1):29-37. doi: 10.1007/s00497-009-0115-2. Epub 2009 Sep 16. PubMed PMID: 20165961.
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  39. Pontvianne F, Blevins T, Pikaard CS. Arabidopsis Histone Lysine Methyltransferases. Adv Bot Res. 2010 Jan 1;53:1-22. doi: 10.1016/S0065-2296(10)53001-5. PubMed PMID: 20703330; PubMed Central PMCID: PMC2918895.
  40. Pikaard CS, Tucker S. RNA-silencing enzymes Pol IV and Pol V in maize: more than one flavor?. PLoS Genet. 2009 Nov;5(11):e1000736. doi: 10.1371/journal.pgen.1000736. Epub 2009 Nov 20. PubMed PMID: 19956537; PubMed Central PMCID: PMC2780373.
  41. Tessadori F, van Zanten M, Pavlova P, Clifton R, Pontvianne F, Snoek LB, Millenaar FF, Schulkes RK, van Driel R, Voesenek LA, Spillane C, Pikaard CS, Fransz P, Peeters AJ. Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet. 2009 Sep;5(9):e1000638. doi: 10.1371/journal.pgen.1000638. Epub 2009 Sep 4. PubMed PMID: 19730687; PubMed Central PMCID: PMC2728481.
  42. Pontes O, Costa-Nunes P, Vithayathil P, Pikaard CS. RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway. Mol Plant. 2009 Jul;2(4):700-710. doi: 10.1093/mp/ssp006. Epub 2009 Mar 24. PubMed PMID: 19825650; PubMed Central PMCID: PMC2902898.
  43. Blevins T, Pontes O, Pikaard CS, Meins F Jr. Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis. PLoS One. 2009 Jun 16;4(6):e5932. doi: 10.1371/journal.pone.0005932. PubMed PMID: 19529764; PubMed Central PMCID: PMC2691480.
  44. Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet. 2009 May;41(5):630-4. doi: 10.1038/ng.365. Epub 2009 Apr 19. PubMed PMID: 19377477; PubMed Central PMCID: PMC2674513.
  45. He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin H, Zhu JK. An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell. 2009 May 1;137(3):498-508. doi: 10.1016/j.cell.2009.04.028. PubMed PMID: 19410546; PubMed Central PMCID: PMC2700824.
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  48. Haag JR, Pontes O, Pikaard CS. Metal A and metal B sites of nuclear RNA polymerases Pol IV and Pol V are required for siRNA-dependent DNA methylation and gene silencing. PLoS One. 2009;4(1):e4110. doi: 10.1371/journal.pone.0004110. Epub 2009 Jan 1. PubMed PMID: 19119310; PubMed Central PMCID: PMC2605557.
  49. Preuss SB, Costa-Nunes P, Tucker S, Pontes O, Lawrence RJ, Mosher R, Kasschau KD, Carrington JC, Baulcombe DC, Viegas W, Pikaard CS. Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell. 2008 Dec 5;32(5):673-84. doi: 10.1016/j.molcel.2008.11.009. PubMed PMID: 19061642; PubMed Central PMCID: PMC2741319.
  50. Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell. 2008 Nov 14;135(4):635-48. doi: 10.1016/j.cell.2008.09.035. PubMed PMID: 19013275; PubMed Central PMCID: PMC2602798.