sailing Craig at the tiller of Wind Therapy

Indiana University, Bloomington, IN

 

sample gatesIndiana University

 

 

RDR2   pol IV&II
In Arabidopsis, proteins of the 24nt siRNA pathway (red and green signals) colocalize in a nucleolar processing center (yellow signal). Image by Dr. Olga Pontes   Relative locations of RNA polymerases IV (green) and II (red) in an Arabidopsis nucleus. Image by Dr. Olga Pontes
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Welcome to the Pikaard lab

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. We are working to understand how specific subsets of rRNA genes are chosen for silencing or expression, and how these decisions are enforced or regulated.

The second focus of the lab concerns RNA polymerases IV and V (formerly 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 have 12 subunits, like DNA-dependent RNA polymerase II, and evolved as specialized forms of Pol II 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 generating transcripts at the target loci to be silenced. Our working hypothesis is 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. Current efforts are focused on understanding the biochemical activities of Pols IV and V, how they are recruited to their sites of action in the genome, and how they interact with other proteins to bring about targeted chromatin modifications.

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 Gordon and Betty Moore Foundation and is 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, National Science Foundation, Howard Hughes Medical Institute and the Gordon & Betty Moore Foundation. Any materials or opinions expressed at this site are those of the author(s) and do not necessaily reflect the views of our sponsors.

 

 
 

 
 

HIGHLIGHTS

Craig discusses nucleolar dominance and RNA Polymerases IV and V with Emilie Marcus, editor-in-chief of Cell, at the 77th Cold Spring Harbor Symposium.view the interview

RNA polymerases IV and V and the siRNA-directed DNA methylation pathway
RNA polymerases IV and V are plant-specific enzymes involved in siRNA-directed DNA methylation. Learn more.

Nucleolar Dominance
The silencing of one parental set of rRNA genes in a genetic hybrid is the epigentic phenomenon known as nucleolar dominance. Learn more

Vectors for epitope-tagging and fluorescent protein fusion in plants
Our Gateway-compatible plasmid vectors for Agrobacterium-mediated transformation, freely available from the Arabidopsis Biological Resource Center. Learn more.

NEWS STORIES:
1.New type of RNA polymerase discovered in plants,
2.Researchers find protein that silences genes,
3.Pathway toward gene silencing described in plants, 4.New gene silencing pathway found in plants.
5.Researchers solve piece of large-scale gene silencing mystery.
6. Plant RNA polymerases IV and V are special forms of RNA Polymerase II,
. 7. Pikaard named an HHMI-GBMF Investigator,
8. Subunit diversity alters RNA polymerase functions