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Craig Pikaard

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Craig S Pikaard
Methylating the DNA of the most repressed: special access required.
Jeremy R Haag; Michelle Marasco; Carrie D Nicora; Angela D Norbeck; Ljiljana Pasa-Tolic; Thomas Ream; Craig S Pikaard
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.
Andrzej T Wierzbicki; M Jordan Rowley; Haixu Tang; Ross Cocklin; Joseph R Ecker; Brian D Gregory; Ryan Lister; Anoop Mayampurath; Craig S Pikaard
Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome.

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All Publications

2013: Craig S Pikaard
Methylating the DNA of the most repressed: special access required.
Molecular cell 2013;49(6):1021-2.
2012: Jeremy R Haag; Michelle Marasco; Carrie D Nicora; Angela D Norbeck; Ljiljana Pasa-Tolic; Thomas Ream; Craig S Pikaard
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 2012;48(5):811-8.
2012: Andrzej T Wierzbicki; M Jordan Rowley; Haixu Tang; Ross Cocklin; Joseph R Ecker; Brian D Gregory; Ryan Lister; Anoop Mayampurath; Craig S Pikaard
Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome.
Genes & development 2012;26(16):1825-36.
2012: Frédéric Pontvianne; Hume Stroud; Todd Blevins; Chinmayi Chandrasekhara; Wei Feng; Steven E Jacobsen; Scott D Michaels; Craig S Pikaard
Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis.
Genes & development 2012;26(9):945-57.
2012: Ek Han Tan; Thomas Ream; Todd Blevins; Craig S Pikaard
Functional consequences of subunit diversity in RNA polymerases II and V.
Cell reports 2012;1(3):208-14.
2011: Jeremy R Haag; Craig S Pikaard
Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing.
Nature reviews. Molecular cell biology 2011;12(8):483-92.
2011: Rebecca Mosher; Craig S Pikaard; Juhyun Shin; Ek Han Tan; Robert L Fischer; David C Baulcombe
An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs.
PloS one 2011;6(10):e25756.
2010: 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; Julio Sáez-Vásquez
Nucleolin is required for DNA methylation state and the expression of rRNA gene variants in Arabidopsis thaliana.
PLoS genetics 2010;6(11):e1001225.
2010: Keith Earley; Frédéric Pontvianne; Andrzej T Wierzbicki; Todd Blevins; Sarah Tucker; Pedro Costa-Nunes; Olga Pontes; Craig S Pikaard
Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation.
Genes & development 2010;24(11):1119-32.
2010: Sarah Tucker; Alexa Vitins; Craig S Pikaard
Nucleolar dominance and ribosomal RNA gene silencing.
Current opinion in cell biology 2010;22(3):351-6.
2010: Zhihuan Gao; Hai-Liang Liu; Lucia Daxinger; Olga Pontes; Xinjian He; Weiqiang Qian; Huixin Lin; Mingtang Xie; Zdravko J Lorkovic; Shoudong Zhang; Daisuke Miki; Xiangqiang Zhan; Dominique Pontier; Thierry Lagrange; Hailing Jin; Antonius J M Matzke; Marjori Matzke; Craig S Pikaard; Jian-Kang Zhu
An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation.
Nature 2010;465(7294):106-9.
2010: Pedro Costa-Nunes; Olga Pontes; Sasha Preuss; Craig S Pikaard
Extra views on RNA-dependent DNA methylation and MBD6-dependent heterochromatin formation in nucleolar dominance.
Nucleus (Austin, Tex.) 2010;1(3):254-9.
2010: Ana Carvalho; Margarida Delgado; Augusta Barão; Márcia Frescatada; Edna Ribeiro; Craig S Pikaard; Wanda Viegas; Nuno Neves
Chromosome and DNA methylation dynamics during meiosis in the autotetraploid Arabidopsis arenosa.
Sexual plant reproduction 2010;23(1):29-37.
2010: S L Tucker; J Reece; Thomas Ream; Craig S Pikaard
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 Harbor symposia on quantitative biology 2010;75():285-97.
2009: Craig S Pikaard; Sarah Tucker
RNA-silencing enzymes Pol IV and Pol V in maize: more than one flavor?
PLoS genetics 2009;5(11):e1000736.
2009: Federico Tessadori; Martijn van Zanten; Penka Pavlova; Rachel Clifton; Frédéric Pontvianne; L Basten Snoek; Frank F Millenaar; Roeland Kees Schulkes; Roel Van Driel; Laurentius A C J Voesenek; Charles Spillane; Craig S Pikaard; Paul Fransz; Anton J M Peeters
Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana.
PLoS genetics 2009;5(9):e1000638.
2009: Olga Pontes; Pedro Costa-Nunes; Paul Vithayathil; Craig S Pikaard
RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway.
Molecular plant 2009;2(4):700-10.
2009: Xin-Jian He; Yi-Feng Hsu; Shihua Zhu; Andrzej T Wierzbicki; Olga Pontes; Craig S Pikaard; Hai-Liang Liu; Co-Shine Wang; Hailing Jin; Jian-Kang Zhu
An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein.
Cell 2009;137(3):498-508.
2009: Andrzej T Wierzbicki; Thomas Ream; Jeremy R Haag; Craig S Pikaard
RNA polymerase V transcription guides ARGONAUTE4 to chromatin.
Nature genetics 2009;41(5):630-4.
2009: Xin-Jian He; Yi-Feng Hsu; Olga Pontes; Jianhua Zhu; Jian Lu; Ray A Bressan; Craig S Pikaard; Co-Shine Wang; Jian-Kang Zhu
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 RNA-directed DNA methylation.
Genes & development 2009;23(3):318-30.
2009: Thomas Ream; Jeremy R Haag; Andrzej T Wierzbicki; Carrie D Nicora; Angela D Norbeck; Jian-Kang Zhu; Gretchen Hagen; Thomas J Guilfoyle; Ljiljana Pasa-Tolić; Craig S Pikaard
Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II.
Molecular cell 2009;33(2):192-203.
2009: Todd Blevins; Olga Pontes; Craig S Pikaard; Frederick Meins
Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis.
PloS one 2009;4(6):e5932.
2009: Jeremy R Haag; Olga Pontes; Craig S Pikaard
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.
2008: Sasha Preuss; Pedro Costa-Nunes; Sarah Tucker; Olga Pontes; Richard Lawrence; Rebecca Mosher; Kristin D Kasschau; James C Carrington; David C Baulcombe; Wanda Viegas; Craig S Pikaard
Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins.
Molecular cell 2008;32(5):673-84.
2008: Andrzej T Wierzbicki; Jeremy R Haag; Craig S Pikaard
Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes.
Cell 2008;135(4):635-48.
2008: Xianwu Zheng; Olga Pontes; Jianhua Zhu; Daisuke Miki; Fei Zhang; Wen-Xue Li; Kei Iida; Avnish Kapoor; Craig S Pikaard; Jian-Kang Zhu
ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis.
Nature 2008;455(7217):1259-62.
2008: Yasuyuki Onodera; Kosuke Nakagawa; Jeremy R Haag; Diane Pikaard; Tetsuo Mikami; Thomas Ream; Yusuke Ito; Craig S Pikaard
Sex-biased lethality or transmission of defective transcription machinery in Arabidopsis.
Genetics 2008;180(1):207-18.
2008: Craig S Pikaard; Jeremy R Haag; Thomas Ream; Andrzej T Wierzbicki
Roles of RNA polymerase IV in gene silencing.
Trends in plant science 2008;13(7):390-7.
2008: Olga Pontes; Craig S Pikaard
siRNA and miRNA processing: new functions for Cajal bodies.
Current opinion in genetics & development 2008;18(2):197-203.
2007: Jeremy R Haag; Craig S Pikaard
RNA polymerase I: a multifunctional molecular machine.
Cell 2007;131(7):1224-5.
2007: 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; Craig S Pikaard
Developing a new interdisciplinary lab course for undergraduate and graduate students: Plant cells and proteins.
Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology 2007;35(6):410-5.
2007: Keith W Earley; Molly S Shook; Brent Brower-Toland; Leslie Hicks; Craig S Pikaard
In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation.
The Plant journal : for cell and molecular biology 2007;52(4):615-26.
2007: Lisa M Smith; Olga Pontes; Iain Searle; Nataliya Yelina; Faridoon K Yousafzai; Alan J Herr; Craig S Pikaard; David C Baulcombe
An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis.
The Plant cell 2007;19(5):1507-21.
2007: Sasha Preuss; Craig S Pikaard
rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch.
Biochimica et biophysica acta 2007;1769(5-6):383-92.
2007: Hye Ryun Woo; Olga Pontes; Craig S Pikaard; Eric J Richards
VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization.
Genes & development 2007;21(3):267-77.
2007: Ana Caperta; Nuno Neves; Wanda Viegas; Craig S Pikaard; Sasha Preuss
Relationships between transcription, silver staining, and chromatin organization of nucleolar organizers in Secale cereale.
Protoplasma 2007;232(1-2):55-9.
2007: Olga Pontes; Richard Lawrence; Manuela Silva; Sasha Preuss; Pedro Costa-Nunes; Keith Earley; Nuno Neves; Wanda Viegas; Craig S Pikaard
Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance.
PloS one 2007;2(11):e1157.
2007: Michelle S Lewis; Diane J Pikaard; Mikhail Nasrallah; Jed H Doelling; Craig S Pikaard
Locus-specific ribosomal RNA gene silencing in nucleolar dominance.
PloS one 2007;2(8):e815.
2007: Craig S Pikaard; Olga Pontes
Heterochromatin: condense or excise.
Nature cell biology 2007;9(1):19-20.
2006: Carey Fei Li; Olga Pontes; Mahmoud El-Shami; Ian R Henderson; Yana V Bernatavichute; Simon W-L Chan; Thierry Lagrange; Craig S Pikaard; Steven E Jacobsen
An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.
Cell 2006;126(1):93-106.
2006: Olga Pontes; Carey Fei Li; Jeremy R Haag; Thomas Ream; Alexa Vitins; Steven E Jacobsen; Pedro Costa Nunes; Craig S Pikaard
The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.
Cell 2006;126(1):79-92.
2006: Keith Earley; Richard Lawrence; Olga Pontes; Rachel Reuther; Angel J Enciso; Manuela Silva; Nuno Neves; Michael Gross; Wanda Viegas; Craig S Pikaard
Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance.
Genes & development 2006;20(10):1283-93.
2006: Keith W Earley; Jeremy R Haag; Olga Pontes; Kristen Opper; Tom Juehne; Keming Song; Craig S Pikaard
Gateway-compatible vectors for plant functional genomics and proteomics.
The Plant journal : for cell and molecular biology 2006;45(4):616-29.
2006: Craig S Pikaard
Cell biology of the Arabidopsis nuclear siRNA pathway for RNA-directed chromatin modification.
Cold Spring Harbor symposia on quantitative biology 2006;71():473-80.
2005: Yasuyuki Onodera; Jeremy R Haag; Thomas Ream; Olga Pontes; Pedro Costa Nunes; Craig S Pikaard
Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.
Cell 2005;120(5):613-22.
2005: Shuang Chang; Craig S Pikaard
Transcript profiling in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation.
The Journal of biological chemistry 2005;280(1):796-804.
2005: Craig S Pikaard; Sasha Preuss; Keith Earley; Richard Lawrence; Michelle S Lewis; Z Jeffrey Chen
Detecting differential expression of parental or progenitor alleles in genetic hybrids and allopolyploids.
Methods in enzymology 2005;395():554-69.
2005: Karen McGinnis; Vicki L Chandler; Karen Cone; Heidi F Kaeppler; Shawn M Kaeppler; Arthur Kerschen; Craig S Pikaard; Eric Richards; Lyudmila Sidorenko; Todd Smith; Nathan M Springer; Tuya Wulan
Transgene-induced RNA interference as a tool for plant functional genomics.
Methods in enzymology 2005;392():1-24.
2004: Olga Pontes; Nuno Neves; Manuela Silva; Michelle S Lewis; Andreas Madlung; Luca Comai; Wanda Viegas; Craig S Pikaard
Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(52):18240-5.
2004: Richard Lawrence; Craig S Pikaard
Chromatin turn ons and turn offs of ribosomal RNA genes.
Cell cycle (Georgetown, Tex.) 2004;3(7):880-3.
2004: Michelle S Lewis; James M Cheverud; Craig S Pikaard
Evidence for nucleolus organizer regions as the units of regulation in nucleolar dominance in Arabidopsis thaliana interecotype hybrids.
Genetics 2004;167(2):931-9.
2004: Aline V Probst; Mathilde Fagard; Florence Proux; Philippe Mourrain; Stéphanie Boutet; Keith Earley; Richard Lawrence; Craig S Pikaard; Jane Murfett; Ian Furner; Hervé Vaucheret; Ortrun Mittelsten Scheid
Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats.
The Plant cell 2004;16(4):1021-34.
2004: Richard Lawrence; Keith Earley; Olga Pontes; Manuela Silva; Z Jeffrey Chen; Nuno Neves; Wanda Viegas; Craig S Pikaard
A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance.
Molecular cell 2004;13(4):599-609.
2003: Richard Lawrence; Craig S Pikaard
Transgene-induced RNA interference: a strategy for overcoming gene redundancy in polyploids to generate loss-of-function mutations.
The Plant journal : for cell and molecular biology 2003;36(1):114-21.
2003: Olga Pontes; Richard Lawrence; Nuno Neves; Manuela Silva; Jae-Hyeok Lee; Z Jeffrey Chen; Wanda Viegas; Craig S Pikaard
Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin topology and rRNA gene transcription in Arabidopsis.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11418-23.
2003: Ingrid Grummt; Craig S Pikaard
Epigenetic silencing of RNA polymerase I transcription.
Nature reviews. Molecular cell biology 2003;4(8):641-9.
2003: Julio Saez-Vasquez; Annie-Claude Albert; Keith Earley; Craig S Pikaard
Purification and transcriptional analysis of RNA polymerase I holoenzymes from broccoli (Brassica oleracea) and frog (Xenopus laevis).
Methods in enzymology 2003;370():121-38.
2002: Ritu Pandey; Andreas Müller; Carolyn A Napoli; David A Selinger; Craig S Pikaard; Eric J Richards; Judith Bender; David W Mount; Richard A Jorgensen
Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.
Nucleic acids research 2002;30(23):5036-55.
2002: Craig S Pikaard; Richard Lawrence
Uniting the paths to gene silencing.
Nature genetics 2002;32(3):340-1.
2002: Amy A Caudy; Craig S Pikaard
Xenopus ribosomal RNA gene intergenic spacer elements conferring transcriptional enhancement and nucleolar dominance-like competition in oocytes.
The Journal of biological chemistry 2002;277(35):31577-84.
2002: Craig S Pikaard
Transcription and tyranny in the nucleolus: the organization, activation, dominance and repression of ribosomal RNA genes.
The Arabidopsis book / American Society of Plant Biologists 2002;1():e0083.
2002: Brian McStay; Marvin Paule; Michael C Schultz; Ian M Willis; Craig S Pikaard
Oddpols united: new insights into transcription by RNA polymerases I and III.
Gene expression 2002;10(5-6):263-9.
2001: Michelle S Lewis; Craig S Pikaard
Restricted chromosomal silencing in nucleolar dominance.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(25):14536-40.
2001: Julio Saez-Vasquez; Markus Meissner; Craig S Pikaard
RNA polymerase I holoenzyme-promoter complexes include an associated CK2-like protein kinase.
Plant molecular biology 2001;47(3):449-59.
2000: Julio Saez-Vasquez; Craig S Pikaard
RNA polymerase I holoenzyme-promoter interactions.
The Journal of biological chemistry 2000;275(47):37173-80.
2000: Craig S Pikaard
Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids.
Plant molecular biology 2000;43(2-3):163-77.
1999: Matthew Frieman; ZJ Chen; Julio Saez-Vasquez; L A Shen; Craig S Pikaard
RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors: Tests of transcription factor involvement in nucleolar dominance.
Genetics 1999;152(1):451-60.
1999: A C Albert; M Denton; M Kermekchiev; Craig S Pikaard
Histone acetyltransferase and protein kinase activities copurify with a putative Xenopus RNA polymerase I holoenzyme self-sufficient for promoter-dependent transcription.
Molecular and cellular biology 1999;19(1):796-806.
1998: ZJ Chen; Luca Comai; Craig S Pikaard
Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(25):14891-6.
1997: Julio Saez-Vasquez; Craig S Pikaard
Extensive purification of a putative RNA polymerase I holoenzyme from plants that accurately initiates rRNA gene transcription in vitro.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(22):11869-74.
1997: M Kermekchiev; J L Workman; Craig S Pikaard
Nucleosome binding by the polymerase I transactivator upstream binding factor displaces linker histone H1.
Molecular and cellular biology 1997;17(10):5833-42.
1997: ZJ Chen; Craig S Pikaard
Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance.
Genes & development 1997;11(16):2124-36.
1997: ZJ Chen; Craig S Pikaard
Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(7):3442-7.
1997: R J Gaudino; Craig S Pikaard
Cytokinin induction of RNA polymerase I transcription in Arabidopsis thaliana.
The Journal of biological chemistry 1997;272(10):6799-804.
1996: J H Doelling; Craig S Pikaard
Species-specificity of rRNA gene transcription in plants manifested as a switch in RNA polymerase specificity.
Nucleic acids research 1996;24(23):4725-32.
1996: Gregory Paul Copenhaver; Craig S Pikaard
Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution.
The Plant journal : for cell and molecular biology 1996;9(2):273-82.
1996: Gregory Paul Copenhaver; Craig S Pikaard
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 : for cell and molecular biology 1996;9(2):259-72.
1995: J H Doelling; Craig S Pikaard
The minimal ribosomal RNA gene promoter of Arabidopsis thaliana includes a critical element at the transcription initiation site.
The Plant journal : for cell and molecular biology 1995;8(5):683-92.
1994: C D Putnam; Gregory Paul Copenhaver; M L Denton; Craig S Pikaard
The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA.
Molecular and cellular biology 1994;14(10):6476-88.
1994: Gregory Paul Copenhaver; C D Putnam; M L Denton; Craig S Pikaard
The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids.
Nucleic acids research 1994;22(13):2651-7.
1994: Craig S Pikaard
Ribosomal gene promoter domains can function as artificial enhancers of RNA polymerase I transcription, supporting a promoter origin for natural enhancers in Xenopus.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(2):464-8.
1993: J H Doelling; R J Gaudino; Craig S Pikaard
Functional analysis of Arabidopsis thaliana rRNA gene and spacer promoters in vivo and by transient expression.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(16):7528-32.
1992: C D Putnam; Craig S Pikaard
Cooperative binding of the Xenopus RNA polymerase I transcription factor xUBF to repetitive ribosomal gene enhancers.
Molecular and cellular biology 1992;12(11):4970-80.