Research Spotlight

Dr. Craig Pikaard

Biology Department
Washington University

St. Louis, MO 63130

Research interests: In most offspring there are genes that are expressed from the chromosomes inherited from only one parent. Often a maternal or paternal imprint dictates which allele will be active. However, this is not the case for the uniparental expression of ribosomal RNA (rRNA) genes in genetic hybrids. This epigenetic phenomenon, known as nucleolar dominance, occurs both in plants and animals but is best studied in plants because non-sterile hybrids can be generated. The Pikaard lab has shown that rRNA gene silencing involves concerted changes in both DNA methylation and histone modification and has 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 involved in this repression cycle, using RNA-interference to knock down the expression of targeted genes. Two histone deacetylases, one DNA methyltransferase and several methylcytosine binding proteins have been identified in the screens thus far. They 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 to understand how their actions are intertwined to comprise an epigenetic on-off switch.

A second emphasis in the Pikaard lab is the characterization of nuclear RNA polymerase IV (pol IV), whose atypical catalytic subunits were first identified by Craig during the annotation of the newly completed Arabidopsis genome sequence in 2000. There are two forms of Pol IV which play non-redundant roles in the production of small interfering RNAs (siRNAs) and the subsequent siRNA-directed DNA methylation and silencing of repeated genomic sequences, including transposable elements. Acting in a pathway that includes Dicer-like 3 (DCL3), argonaute 4 (AGO4) and RNA-dependent RNA polymerase 2 (RDR2), pol IV function is required to maintain the normal organization of the chromatin within the nucleus. Consequently, disruption of the pol IV catalytic subunits causes heterochromatin dispersal. By combining genetic and cytological analyses, the Pikaard lab has determined the order of events in the Pol IV-dependent nuclear siRNA pathway and, in collaboration with the lab of Steve Jacobsen, identified a putative siRNA processing center located in the nucleolus. Current priorities in the Pikaard lab include purifying pol IVa and Pol IVb to homogeneity, determining their complete subunit structures, determining their template requirements (e.g. DNA vs. RNA) and identifying their transcripts or enzymatic products.


References:
Lawrence RJ, Earley K, Pontes O, Silva M, Chen ZJ, Neves N, Viegas W, Pikaard CS. (2004) A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Molecular Cell13:599-609.

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.

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.

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.