Normal & Disease-Associated RNA Decay
The pioneer translation initiation complex
is functionally distinct from but structurally
overlaps with the steady-state translation
initiation complex. View Enlargement
Research in the Maquat lab focuses on RNA decay pathways, largely in human cells, and their relevance to human diseases. One pathway, called nonsense-mediated mRNA decay (NMD) or mRNA surveillance, surveys all newly synthesized mRNAs during what we call a "pioneer" round of translation. This round of translation involves mRNA that is associated with the cap-binding protein heterodimer CBP80 and CBP20 (and variants thereof). It is distinct from the type of translation that supports the bulk of cellular protein synthesis and that involves a different cap-binding protein, eukaryotic initiation factor (eIF) 4E. As a rule, if translation terminates more than ~50-55-nucleotides upstream of an exon−exon junction that is marked by what we call a splicing-dependent “mark” or exon-exon junction complex (EJC), then the mRNA will be subject to NMD. By the time CBP80 and CBP20 have been replaced by eIF4E, the EJC “mark” has been removed so that the mRNA is largely immune to NMD. Studies in progress will significantly advance our understanding of the mRNA-binding proteins, translation factors and nucleases that trigger NMD. Moreover, we are now putting our mechanistic findings to use by designing and developing therapies to abrogate or promote NMD with the goal of lessening the severity of nonsense-generated diseases. A remarkable one-third of inherited or acquired diseases are nonsense-generated.
NMD is much more than a quality-control mechanism. During the course of our studies, we have found that NMD is regulated by cells as a means to adapt to changing environments. As an example, breast cancer cells given the frontline chemotherapeutic doxorubicin (also sold under the trade name Adriamycin, among others) initiate the caspase-mediated cleavage of the key NMD factor – the ATP-dependent RNA helicase UPF1 – so as to up-regulate the ~10% of normal mRNAs that are natural NMD targets, among which as those encoding pro-apoptotic proteins. We have found that exposing breast-cancer cells to a drug that inhibits NMD, subsequently washing away the drug, and then treating cells with doxorubicin augments the rate and magnitude of cell death. This knowledge may be useful when developing future cancer treatments. We have also found that NMD is hyperactivated in Fragile X Syndrome, which is the most common single-gene cause of inherited intellectual disability, and we are working to understand the mechanism of inhibition. Remarkably, we have also found connections between transcriptional co-activators and the pioneer translation initiation complex, and we are currently extending mechanistic connections we have made between pre-mRNA splicing in the nucleus and mRNA translation and decay in the cytoplasm all the way back to transcription initiation.
Model of Phosphorylated UPF1 repressing translation
initiation on an NMD target. View enlargement
Over the past 15 years, our discovery and subsequent work on the mechanism of Staufen (Stau)-mediated mRNA decay (SMD) has uncovered new roles for cytoplasmic long non-coding RNAs (lncRNAs) and retrotransposon-derived short interspersed elements (SINEs) in post-transcriptional gene regulation. These SINEs include human Alu elements and mouse B1, B2, B4 and ID elements. We have shown that NMD and SMD are competitive pathways in ways that contribute to cellular homeostasis and also differentiation. We continue to define new cellular roles for SINEs as sites for nucleating intermolecular base-pairing between different mRNAs, between mRNAs and lncRNAs, and between different lncRNAs. We are additionally extending our studies of inverted-repeat Alu elements (IRAlus) and how competitive binding among the many nuclear and cytoplasmic double-stranded RNA binding proteins influence nuclear and cytoplasmic IRAlus-containing RNA metabolism.
Most recently, we have discovered a new microRNA decay pathway that is mediated by Tudor-SN. This pathway, which we call TumiD, promotes G1-to-S phase transition by degrading microRNAs that degrade mRNAs encoding proteins that promote this transition. We are currently working on how TumiD is regulated.