A high-throughput 3' UTR reporter screening identifies microRNA interactomes of cancer genes
Gert Van Peer1, Evelien Mets1, Shana Claeys1
1Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium.
Introduction:
Despite the established contribution of deregulated microRNA (miRNA) function to carcinogenesis, relatively few miRNA-cancer gene interactions have been validated, making it difficult to appreciate the true complexity of miRNA-cancer gene regulatory networks.
Results:
In this effort, we identify miRNA interactomes of 17 well-established cancer genes, involved in various cancer types, through a miRNome-wide 3' UTR reporter screening. Using a novel and performant strategy for high-throughput screening data analysis, we identify 390 interactions, quadrupling the size of the known miRNA interactome for the cancer genes under investigation. Clear enrichments of established and predicted interactions underscore the validity of the interactome data set. Interactomes appear to be primarily driven by canonical binding site interactions. Nonetheless, non-canonical binding sites, such as offset 6mer and seed-mismatched or G:U wobble sites, also have regulatory activity, albeit clearly less pronounced. Furthermore, we observe enhanced regulation in the presence of 3' supplementary pairing for both canonical and non-canonical binding sites.
Conclusions:
Altogether, the cancer gene-miRNA interactome data set represents a unique resource that will aid in the unraveling of regulatory miRNA networks and the dynamic regulation of key protein-coding cancer genes. In addition, it uncovers aspects of the functional miRNA binding site's architecture and the relative contributions of different binding site types.
Insights
This study identified 390 microRNA (miRNA) interactions with 17 cancer genes, significantly expanding the known miRNA interactome. These findings reveal insights into miRNA binding site architecture and regulation of cancer genes.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- MicroRNAs (miRNAs) play a crucial role in cancer development, but their interactions with cancer genes are not fully understood.
- Existing knowledge of miRNA-cancer gene regulatory networks is limited, hindering a comprehensive understanding of their complexity.
Purpose of the Study:
- To identify and characterize the miRNA interactomes of 17 well-established cancer genes across various cancer types.
- To expand the known miRNA-cancer gene interactions and investigate the underlying regulatory mechanisms.
Main Methods:
- Utilized a miRNome-wide 3' UTR reporter screening approach.
- Employed a novel strategy for high-throughput screening data analysis to identify miRNA-gene interactions.
- Validated interactions through enrichment analysis of known and predicted binding sites.
Main Results:
- Identified 390 novel miRNA-cancer gene interactions, quadrupling the known interactome for the studied genes.
- Demonstrated that canonical binding site interactions are the primary drivers of these interactomes.
- Revealed regulatory activity from non-canonical binding sites (e.g., offset 6mer, seed-mismatched, G:U wobble) and enhanced regulation with 3' supplementary pairing.
Conclusions:
- The generated cancer gene-miRNA interactome dataset is a valuable resource for studying miRNA regulatory networks and cancer gene regulation.
- The study provides insights into the functional architecture of miRNA binding sites and the relative importance of different binding site types.
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