Indiana University, Bloomington, IN  




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Jasleen Singh, Mishra V, Wang F, Huang HY, Pikaard CS. (2019). Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway. Mol Cell. 2019 Aug 8;75(3):576-589.e5. doi: 10.1016/j.molcel.2019.07.008. PDF

Jered Wendte, Jeremy Haag, Olga Pontes, Jasleen Singh, Sara Metcalf, Craig S. Pikaard (2019). The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation. Nucleic Acids Res. 2019 Jul 22. pii: gkz615. doi: 10.1093/nar/gkz615. [Epub ahead of print]. PDF

Ferrafiat L, Pflieger D, Singh J, Thieme M, Böhrer M, Himber C, Gerbaud A, Bucher E, Pikaard CS, Blevins T. (2019). The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis. Nucleic Acids Res. 2019 Aug 2. pii: gkz618. doi: 10.1093/nar/gkz618. [Epub ahead of print].

Todd Blevins, Ram Podicheti and Craig S. Pikaard (2019). 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.

Jing Wang, Todd Blevins, Ram Podicheti, Jeremy R. Haag, Ek Han Tan, Feng Wang and Craig S. Pikaard (2017). Mutation of Arabidopsis SMC4 identifies condensin as a co-repressor of pericentromeric transposons and conditionally-expressed genes. Genes and Development 31:1601-1614. PDF

Jered M. Wendte, Jeremy R. Haag, Jasleen Singh, Anastasia McKinlay, Olga M. Pontes and Craig S. Pikaard (2017) Functional dissection of the Pol V largest subunit CTD in RNA-directed DNA methylation. Cell Reports 19:2796-2808. PDF

Michelle Marasco and Craig S. Pikaard (2017). Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination. Nucleic Acids Research doi: 10.1093/nar/gkx794. PDF

Todd Blevins, Jing Wang, Frédéric Pontvianne and Craig S. Pikaard (2017). Hybrid incompatibility caused by an epiallele. Proc. Natl. Acad. Sci. 114:3702-3707. PDF

Anastasia McKinlay, Ram Podicheti, Ross Cocklin, Craig S Pikaard, Douglas B Rusch (2017).RNA polymerases IV and V influence the 3′ boundaries of Polymerase II transcription units in Arabidopsis. bioRxiv preprint, first posted online Feb. 15, 2017; doi:

Jered Wendte and Craig S. Pikaard (2017). The RNAs of RNA-directed DNA methylation. Biochem. Biophys. Acta. 1860:140-148; doi: 10.1016/j.bbagrm.2016.08.004. Epub 2016 Aug 10. PDF

Jered M. Wendte and Pikaard, Craig S. (2016).  Targeting Argonaute to chromatin. Genes & Development 30:2649-2650. PDF

Gireesha Mohannath, Frederic Pontvianne and Craig S. Pikaard (2016). Selective nucleolus organizer inactivation in Arabidopsis is a chromosomal position-effect phenomenon. Proc. Natl. Acad. Sci. 113: 13426-13431. PDF

Chinmayi Chandrasekhara, Gireesha Mohannath, Todd Blevins, Frederic Pontvianne and Craig S. Pikaard (2016). Chromosome-specific NOR inactivation explains selective rRNA gene silencing and dosage control in Arabidopsis. Genes & Development 30:177–190. PDF

Gireesha Mohannath and Craig S. Pikaard (2016). Analysis of rRNA gene methylation in Arabidopsis thaliana by CHEF-Conventional 2D gel electrophoresis. In: The Nucleolus- Methods and Protocols; a volume of the Methods in Molecular Biology series. Edited by Attila Nemeth. Humana Press, a part of Springer Science - Business Media, LLC.

Frédéric Pontvianne, Marie-Christine Carpentier, Nathalie Durut, Veronika Pavlištová, Karin Jaske, Sarka Schorova,_Hugues Parrinello, Marine Rohmer, Craig S. Pikaard, Miloslava Fojtova, Jiri Fajkus and Julio Saez-Vasquez (2016). Identification of nucleolus-associated chromatin domains in A. thaliana reveals a role for the nucleolus in 3D organization of the A. thaliana genome. Cell Reports. PDF

Todd Blevins, Ram Podicheti, Vibhor Mishra, Jing Wang, Doug Rusch, Haixu Tang and Craig S. Pikaard (2015). Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. eLife 2015, Oct 2;4. pii: e09591. doi: 10.7554/eLife.09591. PDF

Ream, Thomas S., Jeremy R. Haag, Frederic Pontvianne, Carrie D. Nicora, Angela D. Norbeck, Ljiljana PašaTolić and Craig S. Pikaard. (2015).  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 Research 43: 4163-4178. PDF

Craig S. Pikaard and Ortrun Mittelsten-Scheid (2014).  Epigenetic Regulation in Plants. In: Epigenetics; edited by David Allis, Thomas Jenuwein and Danny Reinberg. Cold Spring Harb Perspect Biol. 2014 Dec 1;6(12). pii: a019315. doi: 10.1101/cshperspect.a019315. Review. PDF

Haag, Jeremy R., Brent Brower-Toland, Elysia K. Krieger, Lyudmila Sidorenko, Carrie D. Nicora, Angela D. Norbeck, Andre Irsigler, Huachun LaRue, Jan Brzeski, Karen McGinnis, Sergey Ivashuta, Ljiljana Pasa-Tolic, Vicki L. Chandler, and Craig S. Pikaard (2014). Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits. Cell Reports 9: 378-390. PDF

Todd Blevins, Frédéric Pontvianne, Ross Cocklin, Ram Podicheti, Chinmayi Chandrasekhara, Satwica Yerneni, Chris Braun, Brandon Lee, Doug Rusch, Keithanne Mockaitis, Haixu Tang and Craig S. Pikaard (2014). A two-step process for epigenetic inheritance in Arabidopsis. Molecular Cell 54:30-42. PDF

Pikaard, Craig S. Nucleolar Dominance. In: eLS 2014, John Wiley & Sons Ltd: Chichester [DOI: 10.1002/9780470015902.a0005976.pub2]

Thomas Ream, Jeremy Haag and Craig S. Pikaard (2014). Plant multisubunit RNA polymerases IV and V. In: Nucleic Acid Polymerases, edited by Katsuhiko Murakami and Michael Trakselis. Springer-Verlag, Berlin Heidelberg. PDF

Frederic Pontvianne, Todd Blevins, Chinmayi Chandrasekhara, Iva Mozgova, Christiane Hassel, Olga M.F. Pontes, Sarah Tucker, Petr Mokros, Veronika Muchova, Jiri Fajkus, and Craig S. Pikaard (2013). Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states. Genes and Development 27:1545–1550. PDF

Olga Pontes, Alexa Vitins, Thomas Ream, E. Hong, C.S. Pikaard and Pedro Cosata-Nunes. (2013). Intersection of Small RNA Pathways in Arabidopsis thaliana Sub-Nuclear Domains. PLoS One; 2013 Jun 12;8(6):e65652. doi: 10.1371/journal.pone.0065652.

Pikaard, Craig S., Jeremy R. Haag, Olga M.F. Pontes, Todd Blevins and Ross Cocklin (2013). A transcription fork model for Pol IV and Pol V-dependent RNA-directed DNA methylation. Cold Spring Harb Symp Quant Biol.,  Volume LXXVII, doi:10.1101/sqb.2013.77.014803. PDF

Pikaard, Craig S. (2013). Voices: what’s most surprising in nuclear biology. Cell 152: 1207-1208.  PDF

Pikaard, Craig S. (2013). Methylating the DNA of the most repressed: special access required. Molecular Cell 49:1021-1022. PDF

Jeremy R. Haag, Thomas S. Ream, Michelle Marasco, Carrie D. Nicora, Angela D. Norbeck, Ljiljana Pasa-Tolic and Craig S. Pikaard (2012). 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. Molecular Cell 48, 811–818, PDF

[Pikaard, primary author], The EPIC Planning Committee (2012). Reading the Second Code:Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment. Plant Cell 24: 2257-2261. PDF

Wierzbicki, A.T., Ross Cocklin, Anoop Mayampurath, Ryan Lister, M. Jordan Rowley, Brian D. Gregory, Joseph R. Ecker, Haixu Tang and Craig S. Pikaard (2012). Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs and cytosine methylation in the Arabidopsis epigenome. Genes & Development 26: 1825-1836. PDF

Frédéric Pontvianne, Chinmayi Chandrasekhara, Wei Feng, Todd Blevins, Hume Stroud, Steve E. Jacobsen, Scott D. Michaels and Craig S. Pikaard (2012).  Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes & Development 26: 945-957. PDF

Ek Han Tan, Todd Blevins, Thomas Ream and Craig S. Pikaard (2012). Functional consequences of subunit diversity in RNA polymerases II and V. Cell Reports 1:208-214. PDF

Jeremy Haag and Craig S. Pikaard (2011) RNA Polymerases IV and V: orchestrators of RNA mediated transcriptional silencing in plants. Nature Reviews Mol. Cell Biol. 12: 483-492. PDF

Mosher RA, Tan EH, Shin J, Fischer RL, Pikaard CS, Baulcombe DC. (2011). An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs. PLoS One. 2011;6(10):e25756. PDF

Paul Hoffer, Sergey Ivashuta, Olga Pontes, Alexa Vitins, Craig Pikaard, Andrew Mroczka and Toni Voelker (2011). Posttranscriptional Gene Silencing in Nuclei. Proc. Natl. Acad. Sci. USA 108:409-414.PDF

Tucker, Sarah L., Joshua Reece, Thomas S. Ream, and Craig S. Pikaard (2010). Evolutionary history of  plant multisubunit RNA Polymerases IV and V: subunit origins via genome-wide and segmental gene duplications, retrotransposition and lineage-specific sub-functionalization. Cold Spring Harb Symp Quant Biol. 75:285-97. PDF

Frédéric Pontvianne, Mohamed Abou-Ellail, Julien Douet, Pascale Comella, Isabel Matia, Chinmayi Chandrasekhara, Anne DeBures, Todd Blevins, Richard Cooke, Francisco J. Medina, Sylvette Tourmente, Craig S. Pikaard and Julio Sáez-Vásquez (2010). Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana. PLoS Genetics 6(11): e1001225. doi:10.1371/journal.pgen.1001225. PDF

Sarah Tucker, Alexa Vitins and Craig S. Pikaard (2010). Nucleolar dominance and ribosomal RNA gene silencing. Curr. Opin. Cell Biol. 22:351–356. PDF

Zhihuan Gao, Hai-Liang Liu, Marjori Matzke, Antonius Matzke, Olga Pontes, Xinjian He, Weiqiang Qian, Mingtang Xie, Dominique Pontier, Thierry Lagrange, Steven E. Jacobsen, Hailing Jin, Craig S. Pikaard, and Jian-Kang Zhu (2010). A novel methyl DNA binding protein interacts with AGO4 and RNA polymerase II and functions in RNA-directed DNA methylation in Arabidopsis. Nature 465: 106-109. PDF

Keith W. Earley, Frédéric Pontvianne, Andrzej T. Wierzbicki, Todd Blevins, Sarah Tucker, Pedro Costa-Nunes, Olga Pontes and Craig S. Pikaard (2010). Complex roles of Arabidopsis HISTONE DEACETYLASE 6 in developmental silencing of rRNA gene variants: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation. Genes & Development 24: 1119-1132. PDF

Pontvianne, Frédéric, Todd Blevins and Craig S. Pikaard (2010). Arabidopsis Histone Lysine Methyltransferases. Advances in Botanical Res. 53:1-22. PDF

Pedro Costa-Nunes, Olga Pontes, Sasha B. Preuss and Craig S. Pikaard (2010). RNA-dependent DNA methylation and MBD6-dependent heterochromatin formation in nucleolar dominance. Nucleus 1:3, 1-6; May/June 2010. PDF

Blevins T, Pontes O, Pikaard CS, Meins F Jr.(2009). Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis. PLoS One. 2009 Jun 16;4(6):e5932 PDF

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.(2009). Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet. 2009 Sep;5(9):e1000638. Epub 2009 Sep 4.

Xin-Jian He, Yi-Feng Hsu, Shihua Zhu, Andrzej Wierzbicki, Olga Pontes, Craig Pikaard, Co-Shine Wang, Hailing Jin, Jian-Kang Zhu (2009). An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 137:498-508 PDF

Andrzej Wierzbicki, Thomas Ream, Jeremy Haag and Craig S. PIkaard (2009). RNA Polymerase V transcription guides ARGONAUTE4 to chromatin. Nature Genetics 41: 630-634.PDF

Olga Pontes, Pedro Costa-Nunes, Paul Vithayathil, and Craig S. Pikaard (2009). RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independent of the 24 nt siRNA-directed DNA methylation pathway. Molecular Plant 2:700-710. Epub 2009 Mar 24.PDF

Xin-Jian He, Yi-Feng Hsu, Olga Pontes, Jianhua Zhu, Jian Lu, Ray A. Bressan, Craig Pikaard, Co-Shine Wang, Jian-Kang Zhu (2009). NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for siRNA production, RNA-directed DNA methylation, and transcriptional gene silencing. Genes & Development 23:318–330. PDF

Pikaard, Craig S. and Sarah Tucker (2009). RNA silencing enzymes Pol IV and Pol V in maize: more than one flavor? PLoS Genetics 5(11): e1000736. doi:10.1371/journal.pgen.1000736

Haag, Jeremy R. , Olga Pontes and Craig S. Pikaard (2009). 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 4(1): e4110. doi:10.1371/journal.pone.0004110. PDF

Thomas S. Ream, Jeremy R. Haag, Andrzej Wierzbicki, Carrie D. Nicora, Angela Norbeck, Jian-Kang Zhu, Gretchen Hagen, Thomas J. Guilfoyle, Ljiljana Paša-Tolić and Craig S. Pikaard (2009). Subunit compositions of the RNA silencing enzymes, Pol IV and Pol V reveal their origins as specialized forms of RNA Polymerase II. Molecular Cell 33:192-203. Epub 2008 Dec 24. PDF

Ana Carvalho, Margarida Delgado, Augusta Barao, Marcia Frescatada, Edna Ribeiro, Craig S. Pikaard, Wanda Viegas, Nuno Neves (2009) Chromosome and DNA methylation dynamics during meiosis in the autotetraploid Arabidopsis arenosa. Sex Plant Reprod. DOI 10.1007/s00497-009-0115-2

Preuss, Sasha, Pedro Costa-Nunes, Sarah Tucker, Olga Pontes, Richard J. Lawrence, Rebecca Mosher, Kristin D. Kasschau, James C. Carrington, David C. Baulcombe, Wanda Viegas and Craig S. Pikaard (2008). Multi-megabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine binding proteins. Molecular Cell 32:673-684. PDF

Wierzbicki, Andrzej, Jeremy Haag and Craig S. Pikaard (2008). Noncoding transcription by RNA Polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135:635-648. PDF

Zheng, Xianwu, Olga Pontes, Jianhua Zhu, Avnish Kapoor, Craig S. Pikaard  and Jian-Kang Zhu (2008).  ROS3, a small RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 455:1259-62.

Onodera, Y., Kosuke Nakagawa, Jeremy R. Haag, Diane Pikaard, Tetsuo Mikami, Thomas Ream, Yusuke Ito and Craig S. Pikaard (2008). Sex-biased lethality or transmission of defective transcription machinery in Arabidopsis. Genetics 180: 207-218. PDF (early online version).

Pontes, Olga and Craig S. Pikaard (2008). siRNA and miRNA processing: new roles for Cajal bodies. Curr. Opin. Gen. Dev. 18:197-203. PDF

Pikaard, Craig S., Jeremy R. Haag, Thomas Ream and Andrzej Wierzbicki (2008). Roles of RNA polymerase IV in gene silencing. Trends Plant Sci. 13:390-397.PDF

Haag, Jeremy and Craig S. Pikaard (2007). RNA Polymerase I: a multifunctional molecular machine. Cell 131: 1224-1225 PDF

Caperta, Anna D., Nuno Neves, Wanda Viegas, Craig S. Pikaard and Sasha B. Preuss (2007). Relationships between transcription, silver staining, and chromatin organization of nucleolar organizers in Secale cereale. Protoplasma 232: 55-59.

Joseph M. Jez, Daniel P. Schachtman, R. Howard Berg, Christopher G. Taylor, Sixue Chen, Leslie M. Hicks, Jan G. Jaworski, Thomas J. Smith, Erik Nielsen and Craig S. Pikaard

 (2007). Developing a New Interdisciplinary Lab Course for Undergraduate and Graduate Students: Plant Cells and Proteins. Biochemistry and Molecular Biology Education 35(6): 410-415. PDF

Pontes, Olga, Richard J. Lawrence, Manuela Silva, Sasha Preuss, Keith Earley, Nuno Neves, Wanda Viegas and Craig S. Pikaard (2007). Postembryonic Establishment of Megabase-Scale Gene Silencing in Nucleolar Dominance. PLoS ONE 2(11): e1157. PDF

Earley, Keith, Molly Shook, Brent Brower-Toland, Leslie Hicks and Craig S. Pikaard (2007). In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation. The Plant Journal. 52:615-626. PDF

Lewis, Michelle, Diane J. Pikaard, Mikhail Nasrallah, Jed H. Doelling and Craig S. Pikaard (2007). Locus-specific rRNA gene silencing in nucleolar dominance. PLoS ONE 2(8): e815. doi:10.1371/journal.pone.0000815 Pubmed; PDF

Smith, Lisa M, Olga Pontes, I. Searle, N. Yelina, FK Yousafzai, Alan J. Herr, Craig S. Pikaard, David C. Baulcombe (2007). An SNF2 Protein Associated with Nuclear RNA Silencing and the Spread of a Silencing Signal between Cells in Arabidopsis. Plant Cell 19: 1507-1521 Pubmed; PDF

Preuss Sasha and Craig S. Pikaard (2007). rRNA gene silencing and nucleolar dominance: Insights into a chromosome-scale epigenetic on/off switch.Biochim Biophys Acta. 1769: 383-392 Pubmed; PDF

Pikaard, Craig and Olga Pontes (2007). Heterochromatin: Condense or Excise. Nature Cell Biology 9:19-20 Pubmed; PDF

Woo, Hye Ryun, Olga Pontes, Craig S Pikaard and Eric J Richards (2007).VIM1, a non-MBD class methylcytosine-binding protein required for centromeric heterochromatinization. Genes & Development 21: 267-277. Pubmed; PDF

Pikaard, Craig S. (2006). Cell biology of the Arabidopsis nuclear siRNA pathway for RNA-directed chromatin modification. Cold Spring Harb Symp Quant Biol. 71: 473-80. Pubmed; PDF

Pontes, Olga, Carey Fei Li, Pedro Costa Nunes, Jeremy Haag, Thomas Ream, Alexa Vitins, Steven E. Jacobsen and Craig S. Pikaard (2006). The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126: 79-92. Pubmed PDF

Li, Carey F., Olga Pontes, Mahmoud El-Shami, Ian R. Henderson, Yana V. Bernatavichute, Simon W.-L. Chan, Thierry Lagrange, Craig S. Pikaard, and Steven E. Jacobsen (2006). An ARGONAUTE-containing nuclear processing center co-localized with Cajal bodies in Arabidopsis thaliana. Cell 126:93-106. Pubmed PDF

Earley, Keith, Richard J. Lawrence, Olga Pontes, Rachel Reuther, Angel J. Enciso, Manuela Silva, Nuno Neves, Michael Gross, Wanda Viegas, and Craig S. Pikaard (2006). Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes & Development 20:1283-1293. Pubmed PDF

Earley, Keith, Jeremy R. Haag, Olga Pontes, Kristen Opper, Tom Juehne, Keming Song, and Craig S. Pikaard (2006). Gateway-compatible vectors for plant functional genomics and proteomics. The Plant J. 45:616-629 Pubmed PDF

Onodera, Yasuyuki, Jeremy Haag, Thomas Ream, Pedro Costa Nunes, Olga Pontes and Craig S. Pikaard (2005). Plant Nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120:613-622 Pubmed PDF

Pikaard, Craig S, Sasha Preuss, Keith Earley, Richard J. Lawrence, Michelle S. Lewis and Z. Jeffrey Chen (2005). Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids. Methods Enzymol. 395:554-69. Pubmed; PDF

Neves, Nuno, Wanda Viegas and Craig S. Pikaard (2005). Nucleolar dominance and rRNA gene dosage control: a paradigm for transcriptional regulation via an epigenetic on/off switch. In: Plant Epigenetics, edited by Peter Meyer. Blackwell Publishing. Sheffield, UK.

Chang, Shuang and Craig S. Pikaard (2005). Transcript profiling in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation. J. Biol. Chem. 280:796-804. Pubmed PDF

McGinnis, Karen, Vicki Chandler, Karen Cone, Heidi Kaeppler, Shawn Kaeppler, Arthur Kerschen, Craig Pikaard, Eric Richards, Lyudmila Sidorenko, Todd Smith, Nathan Springer, Tuya Wulan (2005). Transgene-induced RNA Interference as a Tool for Plant Functional Genomics. Methods in Enzymology 392:1-24. Pubmed

Pontes, Olga, Nuno Neves, Manuela Silva, Michelle S. Lewis, Andreas Madlung, Luca Comai, Wanda Viegas and Craig S. Pikaard (2004). Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc. Natl. Acad. Sci. USA 101: 18240-18245. Pubmed PDF

Lawrence, Richard J., Keith Earley, Olga Pontes, Manuela Silva, Z. Jeffrey Chen, Nuno Neves, Wanda Viegas and Craig S. Pikaard (2004). A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Molecular Cell 13:599-609. Pubmed PDF

Probst, Aline V., Mathilde Fagard, Florence Proux, Philippe Mourrain, Stéphanie Boutet, Keith Earley, Richard J. Lawrence, Craig S. Pikaard, Jane Murfett, Ian Furner, Hervé Vaucheret and Ortrun Mittelsten Scheid (2004). Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 16:1021-1034. Pubmed PDF

Lewis, Michelle S., James M. Cheverud, and Craig S. Pikaard. (2004). Evidence for NORs as the units of regulation in nucleolar dominance in Arabidopsis thaliana inter-ecotype hybrids. Genetics 167:931-939. Pubmed PDF

Lawrence, Richard J. and Craig S. Pikaard (2004). Chromatin turn ons and turn offs of ribosomal RNA genes. Cell Cycle 3:e23-e26. Pubmed PDF

Preuss, Sasha and Craig S. Pikaard (2003). Targeted gene silencing in plants using RNA interference. In Engelke, D. (editor): RNA Interference (RNAi): Nuts & Bolts of siRNA Technology, pp23-36. DNA Press. PDF

Pontes, Olga, Richard J. Lawrence, Nuno Neves, Manuela Silva, Jae-Hyeok Lee, Z. Jeffrey Chen, Wanda Viegas, and Craig S. Pikaard (2003). Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis. Proc. Natl. Acad. Sci. USA 100:11418-11423 Pubmed PDF

Lawrence, Richard and Craig S. Pikaard (2003). Transgene-induced RNA interference: a strategy for overcoming gene redundancy in polyploids to generate loss-of-function mutations. The Plant J. 36: 114-121. Pubmed PDF

Pikaard C.S. (2003) Nucleolar Dominance. In: Cooper DN (ed.) Nature Encyclopedia of the Human Genome, vol. 4, pp. 399-402. London: Nature Publishing Group. PDF

Saez-Vasquez, Julio, Annie-Claude Albert, Keith Earley and Craig S. Pikaard. (2003). RNA polymerase I holoenzymes from broccoli (Brassica oleracea) and frog (Xenopus laevis): purification and transcriptional analyses. Methods in Enzymology 370: 121-138. Pubmed

Grummt, Ingrid and Craig S. Pikaard (2003). Epigenetic silencing of RNA polymerase I transcription. Nature Reviews Mol. Cell Biol. 4:641-649 Pubmed PDF

Pandey, Ritu, Andreas Muller, Carolyn A. Napoli, David Selinger, Craig Pikaard, Eric Richards, Judith Bender, David W. Mount, and Richard A. Jorgensen (2002). Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 30 5036-5055. Pubmed PDF

McStay, Brian, Marvin R. Paule, Michael C. Schultz, Ian Willis and Craig S. Pikaard. (2002) Oddpols united: new insights into transcription by RNA polymerases I and III. Gene Expression 10: 263-270. Pubmed

Pikaard, Craig S. and Richard J. Lawrence. (2002). Uniting the paths to gene silencing. Nature Genetics 32:340-341. Pubmed PDF

Caudy, Amy A. and Craig S. Pikaard (2002). Xenopus ribosomal RNA gene intergenic spacer elements conferring transcriptional enhancement and nucleolar dominance-like competition in oocytes. J. Biol. Chem. 277: 31577-31584. Pubmed PDF

Pikaard, Craig S. (2002). Transcription and tyranny in the nucleolus: the organization, activation, dominance and repression of ribosomal RNA genes. The Arabidopsis Book, eds. C.R. Somerville and E.M. Meyerowitz, American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0083 PDF

Lewis, Michelle S. and Craig S. Pikaard. Restricted chromosomal silencing in nucleolar dominance (2001). Proc. Natl. Acad. Sci. USA 98:14536-14540. Pubmed PDF

Pikaard, Craig S. (2001). Genomic change and gene silencing in polyploids. Trends in Genetics 17:675-677. Pubmed PDF

Saez-Vasquez, Julio, Markus Meissner and Craig S. Pikaard. RNA polymerase I holoenzyme-promoter DNA complexes include an associated CK2-like protein kinase (2001). Plant Molecular Biology 47: 449-460. Pubmed

Saez-Vasquez, Julio and Craig S. Pikaard (2000). RNA polymerase I holoenzyme-promoter interactions. Journal of Biological Chemistry 275: 37173-37180. Pubmed PDF

Pikaard, Craig S. (2000). Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in hybrids. Plant Molecular Biology 43: 163-177. Pubmed PDF

Pikaard, Craig S. (2000). The epigenetics of nucleolar dominance. Trends In Genetics 16:495-500. Pubmed PDF

[contributing author, Pikaard] The Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815. PDF

Albert, Annie-Claude, Michael Denton, Milko Kermekchiev, and Craig S. Pikaard (1999). Histone acetyltransferase and protein kinase activities co-purify with a Xenopus RNA polymerase I holoenzyme self-sufficient for promoter-dependent transcription. Molecular and Cellular Biology 19: 796-806. Pubmed

Frieman, Matthew, Z. Jeffrey Chen, Julio Saez-Vasquez, L. Annie Shen, and Craig S. Pikaard (1999). RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors: tests of transcription factor involvement in nucleolar dominance. Genetics 152:451-460. Pubmed

Pikaard, Craig S. (1999). Nucleolar dominance and silencing of transcription. Trends in Plant Science 4:478-483. Pubmed

Chen, Z. Jeffrey, Luca Comai and Craig S. Pikaard (1998). Gene dosage and stochastic effects determine the severity and direction of uniparental rRNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc. Natl. Acad. Sci. USA 95: 14891-14896. Pubmed PDF

Pikaard, Craig S. and Z. Jeffrey Chen (1998). Nucleolar dominance. In: Transcription of ribosomal RNA genes by eukaryotic RNA polymerase I, Marvin Paule, editor. R.G. Landes Co., Georgetown, TX. pp: 277-294.

Pikaard, Craig S. (1998). Chromosome topology: organizing genes by loops and bounds. Plant Cell 10: 1229-1232. Pubmed

Pikaard, Craig S. (1997). Making Ribosomes - Fourth International Symposium on Ribosome Synthesis and Nucleolar Function: A meeting brief. In HMS Beagle: A BioMedNet Publication ( Issue 16 (Sept. 19).

Gaudino, Reginald J. and Craig S. Pikaard (1997). Cytokinin induction of RNA polymerase I transcription in Arabidopsis thaliana. Journal of Biological Chemistry 272: 6799-6804. Pubmed

Chen, Z. Jeffrey and Craig S. Pikaard (1997). Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proc. Natl. Acad. Sci. USA 94: 3442-3447. Pubmed PDF

Chen, Z. J. and Craig S. Pikaard (1997). Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes & Development 11: 2124-2136. Pubmed PDF

Kermekchiev, Milko, Jerry Workman and Craig S. Pikaard (1997). Nucleosome Binding by the Polymerase I Transactivator Upstream Binding Factor Displaces Linker Histone H1. Molecular and Cellular Biology 17: 5833-5842. Pubmed

Saez-Vasquez, J. and Craig S. Pikaard (1997). Extensive purification of a putative RNA polymerase I holoenzyme from plants that accurately initiates rRNA gene transcription in vitro. Proc. Natl. Acad. Sci. USA 94: 11869-11874. Pubmed PDF

Copenhaver, Gregory P. and Craig S. Pikaard (1996). RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4. The Plant Journal 9: 259-272. Pubmed PDF

Copenhaver, Gregory P. and Craig S. Pikaard (1996). Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for homogenization during concerted evolution. The Plant Journal 9: 273-282. Pubmed PDF

Copenhaver, Gregory P. and Craig S. Pikaard (1996). Pulsed-field gel electrophoresis of Arabidopsis thaliana chromosomal DNA. Weeds World 3I:17-25.

Doelling, Jed H. and Craig S. Pikaard (1996). Species-specificity of rRNA gene transcription in plants manifested as a switch in polymerase specificity. Nucleic Acids Research 24: 4725-4732. Pubmed

Copenhaver, Gregory P., Jed H. Doelling, J. Scott Gens and Craig S. Pikaard (1995). Use of RFLPs larger than 100 kbp to map the position and internal organization of the nucleolus organizer region on chromosome 2 in Arabidopsis thaliana. The Plant Journal 7: 273-286.

Doelling, Jed H. and Craig S. Pikaard (1995). The minimal ribosomal RNA gene promoter of Arabidopsis thaliana includes a critical element at the transcription initiation site. The Plant Journal 8: 683-692. Pubmed

Reeder, R.H., Craig S. Pikaard and Brian McStay (1995). UBF, an architectural element for RNA polymerase I promoters. Nucleic Acids & Mol. Biol. 9: 251-263.

Pikaard, Craig S. (1994). Ribosomal gene promoter domains can function as artificial enhancers of RNA polymerase I transcription, supporting a promoter origin for natural enhancers in Xenopus. Proc. Natl. Acad. Sci. USA. 91: 464-468. Pubmed

Copenhaver, Gregory P., Christopher D. Putnam, Michael L. Denton and Craig S. Pikaard (1994). The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids. Nucleic Acids Research 22: 2651-2657. Pubmed

Putnam, Christopher D., Gregory P.Copenhaver, Michael L. Denton and Craig S. Pikaard (1994). The RNA polymerase I transactivator UBF requires its dimerization domain and HMG-box 1 to bend, wrap and positively supercoil enhancer DNA. Molecular and Cellular Biology 14: 6476-6488. Pubmed

Doelling, Jed H. and Craig S. Pikaard (1993). Transient expression in Arabidopsis thaliana protoplasts derived from rapidly established cell suspension cultures. Plant Cell Reports 12: 241-244.

Doelling, Jed H., Reginald Gaudino, and Craig S. Pikaard (1993). Functional analysis of Arabidopsis thaliana rRNA gene and spacer promoters by transient expression. Proc. Natl. Acad. Sci. USA 90: 7528-7532. Pubmed

Putnam, Christopher D. and Craig S. Pikaard (1992). Cooperative binding of the Xenopus RNA polymerase I transcription factor xUBF to repetitive ribosomal gene enhancers. Molecular and Cellular Biology 12: 4970-4980. Pubmed

Pikaard, Craig S., Louise K. Pape, Sheryl L. Henderson, Kenneth Ryan, Mark Paalman, Margaret A. Lopata, Ronald H. Reeder, and Barbara Sollner-Webb, 1990.Enhancers for RNA polymerase I in mouse ribosomal DNA. Molecular and Cellular Biology 10:4816-4825. Pubmed

McStay, B., Chin-Hwa Hu, Craig S. Pikaard and Ronald H. Reeder (1990). xUBF and Rib1 are both required for formation of a stable RNA polymerase I promoter complex in X. laevis. EMBO Journal 10: 2297-2303. Pubmed

Pikaard, Craig S., Brian McStay, Michael C. Schultz, Stephen P. Bell and Ronald H. Reeder, 1989. The Xenopus laevis ribosomal gene enhancers bind an essential Pol I transcription factor, XUBF. Genes and Development 3:1779-1788. Pubmed

Bell, Stephen P., Craig S. Pikaard, Ronald H. Reeder and Robert Tjian, 1989. Molecular mechanisms governing species-specific transcription of ribosomal RNA. Cell 59:489-497. Pubmed

Pikaard, Craig S. and Ronald H. Reeder, 1988. Sequence elements essential for function of the Xenopus laevis ribosomal DNA enhancers. Molecular and Cellular Biology 8:4282-4288. Pubmed

Jasleen Singh, Mishra V, Wang F, Huang HY, Pikaard CS. (2019). Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway. Mol Cell. 2019 Aug 8;75(3):576-589.e5. doi: 10.1016/j.molcel.2019.07.008.