In recent years, the primary emphasis of the Meyers lab has become genomic analysis using novel sequencing technologies. This includes analyses of mRNA and small RNA using high-throughput, parallel, short-read sequencing technologies. Specific areas of research include the use of these technologies to quantify levels of gene expression in Arabidopsis and rice. These data are being used to identify novel transcripts, to study small RNAs, microRNA targets, alternatively-polyadenylated transcripts, to identify antisense transcripts and to understand the relationship between physical position of a gene and its expression level. The data are being analyzed to determine patterns of gene expression under different developmental conditions, for example to identify tissue-specific gene expression. We have also created several databases with query & analysis tools to enable the use of these data for the scientific community. Our original and most popular site is available by clicking on this text: Arabidopsis MPSS but we’ve also developed a number of other organism-specific variants of this page, as well as version for SBS data. These studies are centered around the use of novel genomics tools and bioinformatics approaches to address fundamental questions of gene expression (mRNA and small RNA) in plants.
The Meyers lab also studies disease resistance genes in plants. The Nucleotide Binding Site-Leucine Rich Repeat (NBS-LRR) proteins encoded by many resistance genes provide the first line of defense in many specific plant-pathogen interactions. Approximately 150 of these proteins are encoded in the Arabidopsis Col-0 genome; 50 contain an N-terminal coiled-coil (CC) domain and 100 contain an N-terminal Toll-like (TIR) domain. We study sequence variation and function in this class of genes, with the long-term goal of understanding the relationship between sequence, structure and protein function. Of particular interest to the lab are two additional groups of genes that encode Toll-like proteins but lacking the LRR, as these are similar to a class of adapter proteins that signal in animal defense responses. The TIR-NBS (TN) and TIR-X (TX) proteins are closely related to the TIR-NBS-LRR proteins that mediate recognition of some plant pathogens, yet the TN and TX proteins have no demonstrated role in signaling. We are studying the role of these two families of proteins in plant biology. Signal pathways recently identified in animal systems may provide a useful model for the function of the TX and TN proteins. The distribution of the NBS-LRR and TX/TN families of proteins in different plant genomes is unusual, as there are very few TIR-like proteins in grass genomes (rice, wheat, corn, etc.), but they are quite abundant in dicot genomes (Arabidopsis, soybean, pine tree, etc). We are also interested in why these differences exist, what it tells us about the mechanisms of signaling in disease resistance in these diverse plants, and how which plant species show these differences in resistance related-proteins.