Department of Biology

Program

Molecular, Cellular & Developmental Biology

Research Areas

• Chromatin, Chromosomes, and Genome Integrity
• Developmental Mechanisms and Regulation in Eukaryotic Systems
• Plant Molecular Biology

Education

Ph.D., Purdue University, 1985
Postdoctoral Research, Fred Hutchinson Cancer Research Center, Seattle

Awards

Fellow, American Association for the Advancement of Science

Research Description

We study the ways genes are activated and repressed, using techniques of genetics, biochemistry, genomics, cell biology and molecular biology. Our current research projects are focused on the roles played by chromatin modifying enzymes and noncoding RNAs in gene silencing and epigenetic phenomena.

Our favorite epigenetic phenomenon is nucleolar dominance, which occurs in genetic hybrids and describes the transcription by RNA polymerase I of ribosomal RNA (rRNA) genes inherited from only one of the progenitors. We have shown that the molecular basis for nucleolar dominance in Arabidopsis is the selective silencing of one parental set of rRNA genes. Nucleolar dominance operates on a scale of millions of basepairs of chromosomal DNA. In scope, it is second only to the inactivation of one X-chromosome that occurs in the somatic cells of female mammals - the molecular basis for the random splotches of different colors in the coats of calico cats. However, unlike X-inactivation, the choice of which set of rRNA genes to silence is not random, nor is it dictated by a maternal or paternal imprint.

We have shown that rRNA gene silencing involves concerted changes in DNA methylation and histone modification and we have proposed a model whereby DNA and histone modifications are each upstream of one another in a self-reinforcing, circular pathway. Members of the lab are identifying the chromatin modifying activities that are involved, using RNA interference (RNAi) to knock down the expression of targeted genes in A. suecica. Histone deacetylases and methylases, the de novo DNA methyltransferase DRM2, and two methylcytosine binding proteins have been identified.  Most recently, we found that nucleolar dominance is regulated by short interfering RNAs (siRNAs), suggesting that the “choice mechanism” has an RNA basis. We are making use of a variety of genetic, cytogenetic and biochemical approaches in order to understand the mechanism(s) of action of these chromatin modifying activities and how their actions are functionally intertwined.

The second focus of the lab concerns RNA polymerases IV and V and their roles in RNA-directed DNA methylation and chromatin modification. Pol IV and Pol V are plant-specific polymerases that localize in the nucleus. We have shown that both enzymes have 12 subunits and evolved as specialized forms of DNA-dependent RNA polymerase II, but specialize in noncoding RNA-mediated gene silencing pathways rather than mRNA biosynthesis. Pol IV is required for the production of 24 nt small interfering RNAs (siRNAs) that direct the silencing of repeated sequences in the genome via DNA methylation. Pol V facilitates siRNA mediated silencing by generating transcripts at the target loci to be silenced. Our studies indicate that Pol V transcripts serve as scaffolds for the binding of siRNAs associated with the protein ARGONAUTE4, thereby recruiting silencing complexes to the target genes. The details of how Pol IV, Pol V and siRNAs mediate transcriptional silencing are being pursued using a variety of genetic, biochemical, cytological, structural and genomic approaches.

Select Publications

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

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.

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.

Thomas S. Ream, Jeremy R. Haag, Andrzej Wierzbicki, Carrie D. Nicora, Angela Norbeck, Jian-Kang Zhu, Gretchen Hagen, Thomas J. Guilfoyle, Ljiljana Paša-Tolic and Craig S. Pikaard (2008). 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.

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.

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.

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.

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

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 120:613-62

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.

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