The SHAPE-MaP experiment to identify RNA structures of pri-mir-142 variants

MicroRNAs (miRNAs) are short non-coding RNAs that play essential roles in RNA silencing and gene regulation. The human Microprocessor (MP) is the key factor to initiate miRNA biogenesis by cleaving primary microRNAs (pri-miRNAs). However, the Microprocessor alone cannot precisely and efficiently cleave all pri-miRNAs; thus, it requires cofactors to assist its cleavage. SRSF3 interacts with CNNC in pri-miRNAs, enhancing the MP cleavage. However, it is unknown if SRSF3 can function with other non-CNNC motifs and if secondary structure might influce CNNC function. In addition, function of SRSF7, a paralog of SRSF3, in the SR proteins family, in miRNA biogenesis is largely unknown. In this study, by conducting the high-throughput pri-miRNA cleavage assays for the MP with SRSF3 or SRSF7 and randomized pri-miRNAs, we discovered that SRSF7 also stimulate MP clevage. Futhermore, we found that both SRSF3 and SRSF7 can function with some non-CNNC motifs and with CNNC motifs with certain secondary structures. Furthermore, we also demonstrated that SRSF7 and SRSF3 governed the cleavage sites of the Microprocessor in human cells. Our findings disclose the roles SRSF7 in miRNA biogenesis, demonstrate a compresenhive moleucalr mechanism of SFSF3 and SRSF7 in enhancing cleavage of MP and described in more detail the RNA-binding features of SRSF7 and SRSF3. Overall design: The SHAPE-MaP experiment to identify RNA structures of pri-mir-142 variants