Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires
Xavier Bofill-De Ros,
Wojciech K. Kasprzak,
Yuba Bhandari,
Lixin Fan,
Quinn Cavanaugh,
Minjie Jiang,
Lisheng Dai,
Acong Yang,
Tie-Juan Shao,
Bruce A. Shapiro,
Yun-Xing Wang,
Shuo Gu
Affiliations
Xavier Bofill-De Ros
RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
Wojciech K. Kasprzak
Basic Science Program, RNA Biology Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
Yuba Bhandari
Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
Lixin Fan
Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
Quinn Cavanaugh
RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
Minjie Jiang
RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
Lisheng Dai
RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
Acong Yang
RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
Tie-Juan Shao
RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
Bruce A. Shapiro
RNA Structure and Design Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
Yun-Xing Wang
Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
Shuo Gu
RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Corresponding author
Summary: MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low-grade glioma patient samples indicate that the alternative-miR-9 has a potential role in tumor progression. Furthermore, we provide evidence that distortion of pri-miRNA stems induced by asymmetric internal loops correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing. : By studying the processing of pri-miR-9 family, Bofill-De Ros et al. demonstrate that the tertiary structure of pri-miRNA triggers alternative biogenesis. Drosha cleaves pri-miR-9-1 at an additional site because of its distorted and flexible lower stem, generating a 5′ isomiR that regulates a distinct set of genes in low-grade glioma. Keywords: primary miRNA, miR-9, isomiRs, Drosha, microprocessor, RNA structure, paralogs
