Browsing by Subject "Gene Silencing"
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Item Communal Cell Death and P53 Mediated Transcriptional Control in Drosophila Melanogaster(2011-08-26T17:33:49Z) Link, Nichole Lynn; Abrams, JohnApoptosis is essential for all metazoan development. The key component that functions in apoptosis, the apoptosome, is a molecular machine that initiates caspase activation and is conserved throughout the animal kingdom. Drosophila strains that are mutated for genes encoding the apoptosome show pronounced defects in programmed cell death (PCD). Using a characteristic phenotype associated with mosaic animals, we conducted a screen in Drosophila to discover new regulators or effectors of the apoptosome. Using this model, we also discovered a unique communal form of cell death where large regions of epithelial cells are eliminated within minutes. We also produced 'saturation tile' arrays by digital optical chemistry for an unbiased sampling of transcriptional activity in the Drosophila genome. We found that the scope of unannotated transcriptional activity is extensive and widespread. A dominant population of noncanonical transcripts was stress-responsive and required p53, a master regulator of conventional stress-responsive target genes in vertebrates and invertebrates. This prompted us to examine stimulus dependent activity surrounding a single p53 enhancer in our tiled region. Through genetic analyses, we showed that this enhancer coordinates stimulus dependent induction of multiple genes spanning over 300kb throughout the Reaper region. Surprisingly, this same enhancer regulated a gene positioned across the centromere at distances over 20Mb and also controlled at least one gene mapping to a different chromosome. Chromosome conformation capture analyses placed this enhancer in close proximity to these distant targets in vivo through specific DNA looping and these interactions were influenced by p53. Therefore, a single p53 enhancer is necessary and sufficient for long range, multigenic regulation in cis and in trans.Item Transcriptional Gene Silencing in Mammalian Cells by MicroRNAs That Target Gene Promoters(2011-08-26T17:35:48Z) Younger, Scott Thomas; Corey, David R.A rich history exists for RNA-based regulation of gene transcription. It was reported more than a decade ago that RNA is capable of inducing DNA methylation and transcriptional gene silencing in plants. It was subsequently shown that small RNAs are involved in the establishment of heterochromatic regions of the yeast genome. More recently it has been demonstrated that small duplex RNAs designed to be complementary to gene promoters are potent regulators of gene transcription in mammalian cells. Potent and robust transcriptional regulation by designed small RNAs suggests the existence of endogenous mechanisms that facilitate recognition of gene promoters by small RNAs in mammalian cells. microRNAs (miRNAs) are endogenous small RNAs that regulate gene expression post transcriptionally through base complementarity to target sequences within 3’ UTRs of mRNA transcripts. In this body of work I test the hypothesis that miRNAs can also recognize sequences within gene promoters using two alternative approaches. In the first approach I computationally evaluate the potential for miRNAs to recognize gene promoters by performing a genome-wide survey of putative miRNA target sites within promoter sequences. In the second approach I use the well characterized human progesterone receptor (PR) gene as a model to experimentally validate that miRNAs possess the ability to regulate transcription in a cell culture system. Upon completion of this work I found that gene promoters are significantly enriched for miRNA target sites. Furthermore, the frequency of miRNA target sites within promoter sequences is comparable to their frequency within 3’ UTRs. I experimentally screened multiple miRNAs predicted to target the PR gene promoter, identified several that were capable of inhibiting transcription of the PR gene, and characterize the mechanism of transcriptional silencing. miRNAs have been understood to regulate gene expression at the post transcriptional level through recognition of 3’ UTRs within mRNA transcripts. My study extends miRNA function to recognition of sequences within gene promoters. Sequence specific recognition of gene promoters by miRNAs may complement protein transcription factors. In addition, the ability of small RNAs to rapidly evolve specificity for new sequences would have evolutionary advantages.