Investigating the coding region determinant binding protein-RNA interaction in vitro, in cells and in silico.

The Coding Region-Determinant Binding-Protein (CRDBP) belongs to a family of RNA-binding proteins involved in embryogenesis and oncogenesis. Accumulative evidence suggests that the physical interaction with target mRNAs is a critical determinant for CRDBP function. The goal of this study is to better understand the CRDBP-RNA interaction. The role of the glycine-X-X-glycine motif in each of the KH domains of CRDBP for RNA binding in vitro, in cells and in vivo was investigated. Smaller RNA fragments of c-myc, MITF, MAPK4 and β-TrCP1 bound by CRDBP were determined and used for in silico analysis. Overall, the results showed that the G-X-X-G motif in the KH domains of CRDBP are critical for RNA binding, and that the KH domains play differential roles in binding different RNA molecules. The mapped smaller RNA regions aid in discovering inhibitory molecules and in silico analysis leading to improved approach for understanding the CRDBP RNA interaction. --Leaf ii.