The regulation of gene expression is vital for healthy development and physiology, and many diseases are caused by or associated with changes in gene expression. In the past decade, a tremendous amount of information has been gathered regarding transcriptional control by transcription factors that bind directly to regulatory DNA sequences in or around their target genes. In addition, microRNAs that control gene expression post-transcriptionally have been studied extensively. However, functional and biochemical information about the vast majority of RNA binding proteins has been lacking despite clear evidence of their importance in development and disease. A major factor contributing to our limited understanding of post- transcriptional control by RNA binding proteins is a shortage of appropriate technologies that start with an important mRNA, for instance corresponding to a disease gene of interest, and identify the RNA binding proteins with which this mRNA interacts. In the proposed project, we will develop a novel, high-throughput method for the detection and identification of RNA-protein interactions. We have provisionally named this technology "RNA-associated protein interaction detection" (RAPID). RAPID is based on translation and mimics endogenous RNA binding protein activity. We will first develop and apply RAPID to RNA-protein interactions in the nematode Caenorhabditis elegans because it provides a highly suitable model for further in vivo studies, and because we have clone resources such as the ORFeome available, which contains numerous full-length RNA binding protein-encoding clones. Successful completion of this project will provide the research community with a novel and broadly applicable method to detect RNA-protein interactions in an unbiased and high-throughput manner. We envision applying RAPID to the genome-scale detection of such interactions to further our understanding of complex gene regulatory networks. The methodology and RNA binding protein resource that we will develop for C. elegans will provide an important blueprint for the creation of similar resources in other model organisms and humans.

Public Health Relevance

The regulation of gene expression is vital for healthy development and homeostasis and many diseases are caused by or associated with changes in gene expression. In recent years, tremendous progress has been made in the study of individual RNA binding proteins and how they affect gene expression. However, the genome encodes hundreds of such proteins, and methods that enable the characterization of many at one time are lacking. The proposed project is to develop a novel technology that will be broadly applicable for the functional and large-scale characterization of RNA binding proteins, and will impact both the fields of systems biology of gene expression and researchers that study one or a few disease-relevant human genes.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Exploratory/Developmental Grants (R21)
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Special Emphasis Panel (ZRG1-GGG-B (02))
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Feingold, Elise A
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University of Massachusetts Medical School Worcester
Schools of Medicine
United States
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Tamburino, Alex M; Ryder, Sean P; Walhout, Albertha J M (2013) A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda) 3:297-304