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Dr. John Kim, The Johns Hopkins University

“Two cases of protein RNA interactions: Transgenerational gene silencing and glycolytic body formation”

My lab is interested in addressing these basic questions: What are small RNAs, how are they made, and what do they do? What are RNA-binding proteins, how do they bind RNA, and to what extent do they collaborate with known small noncoding pathways? We have addressed these questions rigorously first by using genome-wide approaches and, when necessary, developing new methodologies. This strategy has delivered in many unexpected ways. To identify new genetic small RNA pathways, we performed genome-wide screens revealing collaboration between splicing and endo-siRNA biogenesis. To define the landscape of 3’UTR isoforms, the targets of microRNAs, we developed the polyA-capture method and discovered a remarkable diversity of 3’UTR isoforms expressed during development. Finally, we developed the gPAR-CLIP method to globally interrogate how RNAs are bound by proteins, and, conversely, we developed an RNP purification method to define the “RBPome”. These genomic surveys have then allowed us to return to the genetics and organismal phenotypes to more deeply understand underlying gene regulatory mechanisms. This coupling of genomic and proteomic strategies with genetic, biochemical, and molecular approaches led us to identify specific RBP:small RNA complexes critical for genome defense, germline immortality, and animal development. For example, we discovered an unexpected process of glycolytic body formation that illustrates the diverse nature and underlying principles of RBP:RNA interactions. There is still much work to do, but we have developed a solid foundation of new methods and knowledge from which we will continue to gain fundamental, and in many cases, unexpected insights into basic mechanisms.