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Post-transcriptional regulation is a key mechanism of eukaryotic cells to
regulate gene expression. It recently became apparent that pancreatic beta
cells rapidly produce insulin in response to glucose stimulation by means of
post-transcriptional regulation.
The polypyrimidine tract binding protein 1 (PTBP1) is a messenger-RNA-binding protein and a known important regulator of insulin secretion. A recent proteome-wide screen for post-transcriptionally regulated components of the insulin secretory machinery identified 63 candidates. To investigate which of these candidates were post-transcriptionally regulated by PTBP1, we devised a computational method which combines RNA structure prediction with sequence motif scanning and evolutionary conservation to identify PTBP1 binding sites on candidate messenger RNAs. Applied to a benchmark set of five mRNAs known to be regulated by PTBP1, the algorithm successfully found significant binding sites in all benchmark mRNAs. Applied to 63 candidate mRNAs found in the screen, a ranked list of 11 high confident potential PTBP1 binding sites was obtained. Their experimental validation is ongoing. Regulation at the RNA level has become an increasingly significant area of research. Our method to predict protein-RNA interaction is generic and can be adapted to different RNA sequence or structure motifs. Understanding the molecular mechanisms that regulate the biogenesis and turnover of insulin in relationship to metabolic demands paves the way for new therapies in diabetes mellitus. Currently, more than 200 million people worldwide suffer from diabetes, and this number is likely to increase by 50% in the next 15 years. |
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