Abstract
The ribonuclease III enzyme Drosha has a central role in the biogenesis of microRNA (miRNA) by binding and cleaving hairpin structures in primary RNA transcripts into precursor miRNAs (pre-miRNAs). Many miRNA genes are located within protein-coding host genes and cleaved by Drosha in a manner that is coincident with splicing of introns by the spliceosome. The close proximity of splicing and pre-miRNA biogenesis suggests a potential for co-regulation of miRNA and host gene expression, though this relationship is not completely understood. Here, we describe a cleavage-independent role for Drosha in the splicing of an exon that has a predicted hairpin structure resembling a Drosha substrate. We find that Drosha can cleave the alternatively spliced exon 5 of the eIF4H gene into a pre-miRNA both in vitro and in cells. However, the primary role of Drosha in eIF4H gene expression is to promote the splicing of exon 5. Drosha binds to the exon and enhances splicing in a manner that depends on RNA structure but not on cleavage by Drosha. We conclude that Drosha can function like a splicing enhancer and promote exon inclusion. Our results reveal a new mechanism of alternative splicing regulation involving a cleavage-independent role for Drosha in splicing.
Highlights
MicroRNAs are short non-coding RNAs that mediate posttranscriptional gene silencing by base-pairing with target mRNAs
We found that the Microprocessor can bind and cleave exon 5, which precludes inclusion of the exon in the mRNA
Our results suggest that the Microprocessor has a role in splicing that is distinct from its role in miRNA biogenesis
Summary
MicroRNAs (miRNAs) are short non-coding RNAs that mediate posttranscriptional gene silencing by base-pairing with target mRNAs. The production of mature miRNAs occurs through a series of processing steps beginning with cleavage from the primary RNA transcript by the Microprocessor complex, which is minimally composed of the ribonuclease (RNase) III enzyme Drosha and the RNA binding protein DGCR8 [1,2,3,4,5,6]. Cleavage of an RNA transcript by Drosha in the Microprocessor complex occurs cotranscriptionally. The process by which non-coding introns are removed and exons are ligated together by the macromolecular spliceosome complex, occurs cotranscriptionally. Processing of intragenic miRNAs by the Microprocessor must occur in the context of splicing. The mechanisms that dictate the coordination of splicing and miRNA processing are not clearly understood
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