RISCy business: regulation of microRNA function and processing by RNA binding proteins

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Wednesday, December 06, 2017 4:00pm - 5:00pm
Watson CIT - SWIG Boardroom (CIT241)

Jeremy Sanford
Associate Professor of MCD Biology
University of California Santa Cruz

RISCy business: regulation of microRNA function and processing by RNA binding proteins.

Accurate expression of human protein-coding genes requires coordinated actions of several large macromolecular machines, including chromatin remodelers, RNA polymerase II, the spliceosome and the ribosome. These machines are spatially separated within the cell allowing for multifaceted regulation of gene expression. Through decades of research, a detailed picture has emerged of transcriptional regulation and execution in the cell’s nucleus. However, exploration of post-transcriptional regulatory mechanisms, which govern the fate of newly synthesized RNA transcripts, continues to reveal unexpected layers of complexity. Key to managing this rich pool of information are the RNA binding proteins (RBPs). 

Given the central roles of RBPs in gene regulation, it is not surprising that their aberrant expression can be a driving force in diverse human diseases, including cancer. To begin unraveling the pathogenetic contributions of RBPs, it is critical to not only identify their target transcripts but also their mechanisms of action. In this talk, I will focus on two proto-oncogenes with very different roles in post-transcriptional gene regulation. Remarkably, both of these factors influence the activity of microRNAs another important class of post-transcriptional gene regulators.

The Insulin-like growth factor 2 mRNA binding protein 3 is a provocative RBP for several reasons. Most notably, IGF2BP3 is strongly expressed in both embryonic and cancerous tissue, but absent in healthy adult cells. There is also a strong correlation between elevated IGF2BP3 expression and the malignancy of many forms of cancer, including B-acute lymphoblastic leukemia and pancreatic cancer. Work from our lab, as well as Dinesh Rao’s laboratory at UCLA, demonstrate that enforced expression of IGF2BP3 in hematopoietic stem cells is sufficient to drive leukemia-like phenotypes in mice. In both human leukemia and pancreatic cancer cells we identified malignancy-associated transcripts bound directly to IGF2BP3. Single nucleotide resolution mapping of protein-RNA interactions revealed overlap between IGF2BP3 binding sites and with microRNA target sites. Using Ago2 immunoprecipitation assays, we discovered that IGF2BP3 influences the association of the RNA induced silencing complex (RISC) with mRNAs. Collectively our data suggest that IGF2BP3 amplifies oncogenic gene expression programs by modulating microRNA-mRNA targeting. 

Like IGF2BP3, the splicing factor SRSF1 is also a proto-oncogene that is amplified in many tumors. During a global survey of SRSF1-RNA interaction sites, we found a striking enrichment of crosslinking sites near the 5’ end of microRNA precursor transcripts. These data suggested the intriguing hypothesis that SRSF1 may participate in small RNA biogenesis. Through a combination of in vivo and in vitro assays, we provide evidence that SRSF1 promotes processing of several microRNAs, including miR10b, a potent oncogene. Our work reveals a potentially new determinant of microRNA biogenesis and delineates a cancer-relevant feedback loop between SRSF1 and miR10b.

In summary, our studies of these SRSF1 and IGF2BP3, demonstrate two distinct mechanisms through which microRNA activity can be controlled in the context of human disease. We imagine that both mechanisms could provide useful new therapeutic targets.