In the Pikaard lab, we study how genes are turned on or off, using techniques of genetics, genomics, biochemistry, cell biology and molecular biology. Our current research projects are focused on the roles of chromatin modifying enzymes and noncoding RNAs in gene silencing and epigenetic phenomena.

An epigenetic phenomenon in which we are keenly interested is nucleolar dominance. This phenomenon occurs in genetic hybrids and describes the transcription by RNA polymerase I of ribosomal RNA genes inherited from only one of the progenitors. A similar phenomenon occurs in non-hybrids and brings about the silencing of nearly half of the 1500 rRNA genes present in a diploid Arabidopsis thaliana plant as the need for protein synthesis and ribosome production decreases during development. We have shown that nucleolar dominance and rRNA gene dosage control involve the selective silencing of specific sets of rRNA genes on a scale of millions of basepairs of chromosomal DNA. In scale, rRNA gene silencing is second only to the inactivation of one X-chromosome in somatic cells of female mammals, which is the basis for the random coat coloration of calico cats. But 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. Recently, we found that rRNA genes in Arabidopsis are chosen for silencing during development based on their chromosome affiliation, not their individual gene sequences. We are now working to identify the molecular basis for this chromosomal position-effect.

The second focus of the lab concerns RNA polymerases IV and V (initially known as Pol IVa and Pol IVb) and their roles in RNA-directed DNA methylation. Pol IV and Pol V are plant-specific polymerases that localize in the nucleus. We've shown that Pols IV and V each have 12 subunits, like DNA-dependent RNA polymerase II, and evolved as specialized forms of Pol II that are dedicated to the production of noncoding RNAs. In the RNA-directed DNA methylation pathway, Pol IV is required for the production of 24 nt small interfering RNAs (siRNAs) that direct the silencing of transposons and other repeated sequences in the genome via DNA methylation. We have shown that Pol V facilitates siRNA mediated silencing by collaborating with an RNA-dependent RNA polymerase, RDR2, to generate short double-stranded RNAs that are the precursors of 24 nt siRNAs. The siRNAs then guide the silencing machinery to complementary DNA sequences transcribed by Pol V. Current efforts are focused on understanding the biochemical activities of the enzymes and RNAs that carry out RNA-directed DNA methylation.

Where we are located: The Pikaard laboratory is located in the Biology Department at Indiana University, in Myers Hall Room 300.

Affiliations: Craig Pikaard is an Investigator of the Howard Hughes Medical Institute and is a Distinguished Professor and the Carlos O. MIller Professor of Plant Growth and Development in the Departments of Biology and Molecular & Cellular Biochemistry at Indiana University.

Our Funding: The Pikaard lab's research is supported by funding from the National Institutes of Health and Howard Hughes Medical Institute. Any materials or opinions expressed at this site are those of the author(s) and do not necessaily reflect the views of our sponsors.