This competitive renewal proposes to continue our work on the post-transcriptional regulation of the hundreds of human mRNAs that are controlled by the double-stranded (ds)RNA-binding protein Staufen (STAU). Over the last <4 years we have followed up our discovery of STAU1-mediated mRNA decay (SMD). During SMD, mRNAs that harbor a STAU1-binding site (SBS) in their 3'-untranslated regions (3'UTRs) are degraded when translation terminates (usually normally, i.e., not prematurely) upstream of the SBS. We have shown that SMD is critical for cell motility, myogenesis and probably most cellular processes. We have expanded what defines a human SBS to include intermolecular duplexes formed by base-pairing between an Alu element within a mRNA 3'UTR and a complementary Alu element within (i) one or more cytoplasmic long non-coding (lnc)RNAs, thereby defining new roles for Alu elements and lncRNAs, which we call 1/2sbs-RNAs, and/or (ii) one or more mRNAs, thereby defining an exciting new function for mRNAs. Alu elements, which are a type of small interspersed element (SINE), are restricted to primates. Our finding that these new and complex Alu functions also apply to the SINEs of mouse, coupled with our computational and statistical analyses, support the notion that orthologous human and mouse genes have independently acquired and maintained 3'UTR SINEs for the purpose of triggering SMD. In related studies, we have determined the X-ray crystal structure of the human STAU1 dimerization interface, which involves interactions between a new motif that we call the STAU- swapping motif (SSM) and a degenerate dsRNA-binding domain. We have reported that STAU1 dimerization promotes SMD by augmenting STAU binding to the RNA helicase UPF1. In fact, both STAU1 and its paralog STAU2 activate SMD by activating UPF1 helicase activity in a mechanism that requires ATP hydrolysis without increasing UPF1 ATPase activity. We have found that STAU1 also binds inverted-repeated Alu elements (IRAlus) within mRNA 3'UTRs to allow mRNA export to, and translation in, the cytoplasm rather than activate SMD. In this proposal, AIM 1 is to identify new human-gene products that mediate SMD using a haploid genetic approach. This approach is an important complementation to our on-going identification of proteins (using mass spectrometry) and, when appropriate, 1/2sbs-RNAs and mRNAs (using RNA-seq) that associate with the SBSs of individual SMD targets.
AIM 2 is to define how human Staufen proteins affect RNA metabolism via (i) 3'UTR IRAlus, and (ii) the convergent evolution of human and mouse SINEs.
AIM 3 will mine RNA-seq data identifying mRNAs that (i) are upregulated by 1/2sbs-RNA1 siRNA or 1/2sbs-RNA2 siRNA - data indicating that 1/2sbs-RNA1 regulates Wnt signaling - and/or (ii) co-purify with either 1/2sbs-RNA.
This aim will also examine the mechanism of STAU-mediated UPF1 activation. In sum, we have shown that STAU is key to several post-transcriptional regulatory pathways affecting hundreds of human genes that, when improperly expressed, cause disease. We will continue to unravel how STAU paralogs contribute to cellular homeostasis.

Public Health Relevance

This proposal aims to extend our understanding of how human protein-encoding genes are regulated via pathways that affect processing of the intermediate 'messenger' mRNA. Remarkably, regulatory factors include not only the RNA-binding protein Staufen but another type of RNA - so-called long noncoding RNAs that do not encode protein but contain repetitive elements that were initially thought to be cellular 'junk'. We will investigate the complex network of how Staufen regulates human gene expression, often but not always in collaboration with long noncoding RNAs via the repetitive elements, to maintain proper cellular physiology and to prevent disease.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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Molecular Genetics A Study Section (MGA)
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Bender, Michael T
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University of Rochester
School of Medicine & Dentistry
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Elbarbary, Reyad A; Miyoshi, Keita; Myers, Jason R et al. (2017) Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G1/S phase transition. Science 356:859-862
Elbarbary, Reyad A; Miyoshi, Keita; Hedaya, Omar et al. (2017) UPF1 helicase promotes TSN-mediated miRNA decay. Genes Dev 31:1483-1493
Elbarbary, Reyad A; Maquat, Lynne E (2017) Distinct mechanisms obviate the potentially toxic effects of inverted-repeat Alu elements on cellular RNA metabolism. Nat Struct Mol Biol 24:496-498
Gleghorn, Michael L; Zhao, Jianbo; Turner, Douglas H et al. (2016) Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation. Nucleic Acids Res 44:8417-24
Elbarbary, Reyad A; Lucas, Bronwyn A; Maquat, Lynne E (2016) Retrotransposons as regulators of gene expression. Science 351:aac7247
Elbarbary, Reyad A; Maquat, Lynne E (2016) Coupling pre-mRNA splicing and 3' end formation to mRNA export: alternative ways to punch the nuclear export clock. Genes Dev 30:487-8
Maquat, Lynne E (2016) Eukaryotic antisense ahead of its time. Nat Rev Mol Cell Biol 17:204
Maquat, Lynne E (2015) The amazing web of post-transcriptional gene control: the sum of small changes can make for significant consequences. RNA 21:488-9
Gong, Chenguang; Maquat, Lynne E (2015) Affinity purification of long noncoding RNA-protein complexes from formaldehyde cross-linked mammalian cells. Methods Mol Biol 1206:81-6
Elbarbary, Reyad A; Maquat, Lynne E (2015) CARMing down the SINEs of anarchy: two paths to freedom from paraspeckle detention. Genes Dev 29:687-9

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