Abstract
The essential Drosophila RNA-binding protein Brain Tumor (Brat) represses specific genes to control embryogenesis and differentiation of stem cells. In the brain, Brat functions as a tumor suppressor that diminishes neural stem cell proliferation while promoting differentiation. Though important Brat-regulated target mRNAs have been identified in these contexts, the full impact of Brat on gene expression remains to be discovered. Here, we identify the network of Brat-regulated mRNAs by performing RNA sequencing (RNA-seq) following depletion of Brat from cultured cells. We identify 158 mRNAs, with high confidence, that are repressed by Brat. De novo motif analysis identified a functionally enriched RNA motif in the 3' untranslated regions (UTRs) of Brat-repressed mRNAs that matches the biochemically defined Brat binding site. Integrative data analysis revealed a high-confidence list of Brat-repressed and Brat-bound mRNAs containing 3'UTR Brat binding motifs. Our RNA-seq and reporter assays show that multiple 3'UTR motifs promote the strength of Brat repression, whereas motifs in the 5'UTR are not functional. Strikingly, we find that Brat regulates expression of glycolytic enzymes and the vacuolar ATPase complex, providing new insight into its role as a tumor suppressor and the coordination of metabolism and intracellular pH.
Overview
- The study focuses on the Drosophila RNA-binding protein Brain Tumor (Brat) and its role in controlling embryogenesis and differentiation of stem cells. The hypothesis being tested is the impact of Brat on gene expression, particularly its regulation of specific genes. The methodology used for the experiment includes RNA sequencing (RNA-seq) following depletion of Brat from cultured cells. The primary objective of the study is to identify the network of Brat-regulated mRNAs and their underlying mechanisms.
Comparative Analysis & Findings
- The study compares the outcomes observed under different experimental conditions, specifically the depletion of Brat from cultured cells. The results show that Brat represses 158 mRNAs with high confidence, and de novo motif analysis identified a functionally enriched RNA motif in the 3' untranslated regions (UTRs) of Brat-repressed mRNAs that matches the biochemically defined Brat binding site. Integrative data analysis revealed a high-confidence list of Brat-repressed and Brat-bound mRNAs containing 3'UTR Brat binding motifs. The study also shows that multiple 3'UTR motifs promote the strength of Brat repression, whereas motifs in the 5'UTR are not functional. Strikingly, the study finds that Brat regulates expression of glycolytic enzymes and the vacuolar ATPase complex, providing new insight into its role as a tumor suppressor and the coordination of metabolism and intracellular pH.
Implications and Future Directions
- The study's findings have significant implications for the field of research and clinical practice, as they provide new insight into the role of Brat as a tumor suppressor and the coordination of metabolism and intracellular pH. The study identifies a network of Brat-regulated mRNAs and their underlying mechanisms, which can be further explored in future research. The study also suggests that Brat regulates expression of glycolytic enzymes and the vacuolar ATPase complex, which can be further investigated in the context of tumor suppression and metabolic regulation. The study highlights the importance of understanding the role of RNA-binding proteins in gene expression and their impact on cellular processes.