Browsing by Subject "Models, Genetic"
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Item Context-Dependent Function of the Splicing Factor hnRNP L(2010-11-02) Motta-Mena, Laura Beatriz; Lynch, Kristen W.Based on the number of genes impacted (~95% of humans genes), alternative splicing is one of the most extensively used mechanisms for generating proteomic diversity and cellular complexity. Splicing of pre-mRNAs is carried out by a highly specialized, RNA-based macromolecular enzyme known as the spliceosome. The spliceosome is made up of 5 small nuclear RNP (snRNP) complexes (U1, U2, U4/U6, and U5), all of which consist of a uridine-rich snRNA and multiple proteins. Importantly, the spliceosome is not a pre-formed enzyme but instead forms through the step-wise assembly of the snRNP complexes on the pre-mRNA. Mechanistically, the selection of exons or splice sites during alternative splicing occurs by modulating the assembly of the spliceosome on a pre-mRNA. Ultimately, the decision to include or exclude an exon into the final mRNA is based on the integration of both the synergistic and antagonistic forces between groups of protein regulators and between protein regulators and the snRNP complexes. An excellent model system to illustrate the mechanisms of alternative splicing, as well as the physiologic significance of this mode of regulation, is the human CD45 gene. HnRNP L binds to a motif present in both CD45 variable exons 4 and 5 to affect their coordinate repression. Previously, it was shown that hnRNP L regulates exon 4 by stalling the U1 and U2 snRNPs in a non-permissive A-like exon-defined spliceosomal complex. Here, we show that, in contrast to its direct repression of exon 4, hnRNP L represses exon 5 by countering the activity of a neighboring splicing enhancer element. As the splice sites flanking exon 4 and 5 are distinct, we directly examined the effect of varying splice site strength on the mechanism of hnRNP L function. Remarkably, binding of hnRNP L to an exon represses strong splice sites but enhances weak splice sites. A model in which hnRNP L stabilizes snRNP-binding can explain both effects in a manner determined by the inherent snRNP-substrate affinity. Overall, these findings demonstrate that context can fundamentally alter the activity of a splicing regulatory protein and can therefore impact our predictions of splicing patterns and mechanisms of splicing regulation.Item A Tool-Box for Quantifying the Relationship Between Gene Expression, Nutrient Conditions, and Cellular Growth Rate in Bacteria(2020-08-01T05:00:00.000Z) Mathis, Andrew David; Mishra, Prashant; Lin, Milo; Reynolds, Kimberly A.; Ross, Elliott M.A central aspect of the genotype to phenotype problem is relating changes in gene expression to cellular division (or growth rate). The relationship between gene expression and growth rate can be complex, nonlinear, and dependent on environmental conditions, however, most high-throughput studies condense this complexity into a single discrete measurement per gene. This greatly limits the utility of high-throughput screening data in applications like rational engineering of cellular systems, modeling of cellular behavior, and genetic screening for specific phenotypes. I developed a series of techniques, based on highthroughput CRISPR interference gene knockdowns, to more continuously quantify the effects of gene expression and nutrient condition on bacterial growth rate. These techniques allow high-throughput titration of gene expression, precise modulation of environment conditions, and corresponding quantification of growth rate, epistasis, and gene-by-environment interactions all in the same experiment. Using these techniques, I have demonstrated that epistasis can explain co-evolution between a pair of enzymes, that gene by environment interactions are often specific to certain gene expression regimes, and that the sign and magnitude of epistasis can be dependent gene expression levels. In sum, these techniques are an essential step towards developing predictive models that relate gene expression, nutrient condition, and growth rate.