Research
mRNAs carry genetic information from the nucleus to the cytoplasm, where they are translated into proteins. Their spatial organization therefore determines where proteins are produced and, in turn, how cells and organisms develop. Remarkably, the polarized distribution of even a single mRNA can determine cell morphology, establish an organism’s body plan, and specify cell lineages across metazoans, and its disruption can cause human disease. Understanding spatially organized mRNAs and their regulation is thus essential for understanding development and disease. Our long-term goal is to understand how organisms harness spatially organized mRNAs to promote development and how their disruption causes disease.
We combine in vivo quantitative and super-resolution microscopy, genetics, RNA structure probing, and next-generation sequencing to define the molecular mechanisms that organize and regulate mRNAs in their native cellular environments. We aim to understand how spatial information encoded in mRNAs is interpreted to produce cellular and developmental outcomes, and how disrupting mRNA organization contributes to disease. We focus on three questions:
Mechanisms of mRNA localization to RNA granules. RNA granules organize mRNAs and RBPs to regulate post-transcriptional gene expression, play essential roles in development and neuronal function, and are associated with diseases including neurodegeneration, cancer, and viral infection. How specific mRNAs are selected for localization remains poorly understood. We study this question using Drosophila germ granules and a human cell line system we developed that recapitulates mRNA localization to simplified germ granules. Combining this system with RNA libraries, structure probing, high-throughput sequencing, and mutagenesis, we aim to identify the sequence and structural elements that drive localization. Because germ granule localization is highly specific despite the broad RNA-binding activity of the RBPs involved, this system will also reveal how RBPs selectively recruit mRNAs. Ultimately, we aim to define the principles of mRNA selection in germ granules and apply them to other RNA granules, such as P-bodies and stress granules, to understand how distinct granules establish their characteristic mRNA compositions.
Mechanisms and function of mRNA clusters. We showed that within RNA granules, mRNAs from the same gene self-organize into homotypic clusters. Their presence across species suggests a conserved, intrinsic property of mRNAs. We showed that mRNAs use a clustering code that integrates multiple RNA features and defined how intermolecular base pairing and RNA structure contribute; we are now investigating the role of RBPs. Homotypic clustering is highly selective and may allow mRNAs to concentrate when needed while remaining dispersed otherwise. Indeed, mRNA concentration within clusters can increase more than 5,000-fold, suggesting that clusters may also concentrate RNA regulators and thereby alter post-transcriptional reactions. Using quantitative imaging, we are determining how clustering regulates translation, mRNA degradation, and mRNA enrichment within RNA granules.
RNA quality control associated with spatially organized mRNAs. We found that RNA sequences that promote clustering through intermolecular base pairing also decrease mRNA expression, impair protein accumulation, and ultimately disrupt Drosophila development. Our unpublished data show that this effect is conserved in mammalian cells and suggests a unique RNA quality control pathway that specifically detects such RNA sequences. Using fly and mammalian cell systems with RNA and protein screens, we aim to identify how this pathway recognizes and regulates mRNAs that contain sequences that promote intermolecular base pairing. Because base pairing-prone sequences are common in retroviruses, where they drive genome organization and virion assembly, our work may also reveal how host cells distinguish cellular from viral RNAs.
