The genome is structurally and functionally organized by the action of many proteins. However, RNAs also play an important role in genome organization within animal cells. These RNAs do not code for proteins, but rather, they act as structural molecules or enzymes to regulate gene organization and expression. Three classes of non-coding RNAs are relatively small: each is between 20 and 30 nucleotides in length. All of them function to repress transcriptional or post-transcriptional steps in gene expression. The microRNA class represses expression of protein-coding genes; the siRNA class represses the expression of genes encoded by viruses; the piRNA class represses the expression of transposable elements.
We use the model experimental system of Drosophila to study microRNAs and siRNAs, hoping to understand why these molecules have been selected for these functions rather than proteins. We use a variety of methods in our experiments, including small-RNA-seq and proteomics. We work closely with theorists in applied mathematics and physics to construct models that explain and predict our experimental data.
Some of the questions we are pursuing have to with the following. What is the purpose of the thousands of siRNAs that recognize endogenous protein-coding genes in the genome. Do microRNAs suppress the inherent biochemical stochasticity that underlies gene expression. How and why do small RNAs undergo phase transitions in the cytoplasm to form liquid droplets that sequester their target substrates.
The most abundant class of non-coding RNAs have member RNAs that are longer than 200 nucleotides, and they are called long non-coding RNAs or lncRNAs. Thousands of lncRNAs have now been catalogued in many eukaryotic species, and their ubiquity have led some to hypothesize that lncRNAs are fundamental to most biological processes in eukaryotes. That said, lncRNAs fail to display typical signals of evolutionary constraint that are taken as evidence of biological importance. A handful of lncRNAs have been shown to play key roles in biological processes as diverse as X-chromosome dosage compensation, nervous system development, and stem cell maintenance, and have been implicated in diseases such as cardiovascular disease and cancer. Further, these lncRNAs operate through diverse mechanisms. Some act as scaffolds for ribonucleoprotein complexes and some recruit proteins to chromatin; some act in cis to regulate transcription enhancers, while others can physically interfere with expression of neighboring genes.
We are using phylogenetics, single-molecule FISH, and CRISPR technologies to systematically explore the functions of lncRNAs in animal development. We want to deepen our understanding of the biological impact of the ubiquitous but poorly understood lncRNAs and how they function mechanistically.