Dr. Jack Keene
Professor, Department of Molecular Genetics and Microbiology, Duke University
Hosted by Dr. Howard Lipshitz
April 11th @ 4PM
1 King’s College Circle, Medical Sciences Building, Room 4171

RNA binding proteins (RBPs) are highly conserved in metazoans while transcription factors are far less conserved. This conservation of RBPs is hypothetically due to the need for coordination of global gene expression by RNA regulons that coordinate ribonomic regulators of regulators. Thus, RBPs control each other’s levels while each RBP also controls a larger subset of overlapping mRNA targets. RNA regulons are probabilistic and agile, and are coordinated via RNP codes. Techniques to identify global mRNA targets of RNA-binding proteins (RBPs) need to address regulatory mechanisms by discriminating non-regulatory RBP interactions. We have developed RNA-protein enrichment techniques based on probabilistic principles to identify and discriminate functional RNA binding motifs (RNP codes) from nonfunctional motifs. This approach can help quantify strength of binding, thus yielding continuous metrics that change during different biological conditions. We will describe experiments using HuR, RBM38 and Tra2 RBPs and explore their putative combinatorial interactions and potential cooperativity of binding. We suggest that cooperative and/or competitive binding by two or more RBPs can affect binding strength at regulatory RNP codes.  For example, RBM38 appears to cooperate with HuR and with Tra2, but Tra2 and HuR do not appear to cooperate with one another. Therefore, our procedure DO-RIP-seq can reveal sites of RBP binding that may cooperate or compete for binding on a transcriptome-wide scale. Our goal is to derive quantitative metrics of RNA targeting under different conditions that indicate regulatory RNP codes governing dynamic RNA regulons. This approach provides a gateway to compare and quantify regulatory RBP binding events within RNP complexes under varying biological conditions.