My lab is interested in how genes can be selectively inactivated and how the silent state can be perpetuated through multiple rounds of cell division, and even from one generation to the next. One longstanding interest of the lab is the uniparental silencing of 45S ribosomal RNA (rRNA) genes in genetic hybrids, an epigenetic phenomenon known as nucleolar dominance. 45S rRNA genes are transcribed in the nucleolus by RNA polymerase I. There are thousands of nearly identical rRNA genes in the genome. At specific periods of development, most or all of these rRNA genes are presumably needed, but in most cell types the number of rRNA genes exceeds the physiological demands of the cell. Under these conditions, excess rRNA genes are selectively inactivated via mechanisms that involve methylation of the DNA and chemical modifications of the histone proteins that organize the DNA. My student and postdoctoral colleagues in the lab are working to understand the mechanisms responsible for selective rRNA gene silencing, focusing on new evidence that the silencing decisions are not made one rRNA gene at a time but are made on a multi-megabase, sub-chromosomal scale affecting hundreds of rRNA genes.
A second focus of my lab is to understand the functions of RNA polymerases IV and V in the RNA-directed DNA methylation pathway. RNA polymerases IV and V are plant-specific enzymes whose subunit compositions indicate that they evolved as specialized forms of DNA-dependent RNA polymerase II, the enzyme that makes protein-coding mRNAs. 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. The siRNAs bind to these Pol V transcripts in association with proteins that bring about the DNA methylation and histone modification of the associated chromatin, thus silencing genes transcribed by conventional RNA polymerases, including Pol II. New evidence indicates that specific chromatin modifications that can be perpetuated mark loci for Pol IV recruitment. We have thus proposed that epigenetic inheritance at these loci consists of at least two separable steps: the first accounting for specification and inheritance of silent locus identity and the second involving recruitment of Pol IV and the silencing machinery.