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Please use this identifier to cite or link to this item: http://arks.princeton.edu/ark:/88435/dsp01v405sd495
Title: Small RNAs and Genome Defense: Silencing and Licensing in the P Granules of C. elegans
Authors: McEnany, John
Advisors: Wingreen, Ned
Meir, Yigal
Department: Physics
Class Year: 2021
Abstract: Small RNAs are essential for many organisms to maintain proper gene expression across multiple generations. Piwi-interacting small RNAs, or piRNAs, are small RNAs associated with gene silencing, especially of deleterious transposons. The piRNAs of Caenorhabditis elegans, unlike those found in many other organisms, lack obvious transposon targets and are not immediately necessary to maintain transposon silencing. Based on their low binding specificity, many researchers hypothesize that C. elegans piRNAs are capable of associating with the entire genome, acting as a wide net of silencing. This silencing pathway competes with a more specific licensing system that maintains a “memory” of prior gene expression, driven by the CSR-1 Argonaute protein and its siRNA guides. Both of these systems are localized to the perinuclear P granules of germ cells, suggesting that newly transcribed mRNAs are sent to P granules to be vetted by the silencing and licensing systems before translation. However, there has been little investigation into how piRNAs achieve such broad coverage, or how target recognition in the P granule actually operates. We use the piRNA binding site identification tool pirScan as well as an original, functional metric of piRNA distance to locate possible binding sites across the genome, comparing large-scale piRNA affinity for genes and transposons. We show that piRNAs can bind to most of the genome via near-random coverage of sequence space, with only moderate enrichment of transposon and gene binding sites compared to random controls. We then conduct a biophysical analysis of target recognition in the P granules, presenting a system where Argonautes combine 1D and 3D diffusion to find their targets so that they can classify a candidate transcript as self or nonself in a 15-minute timeframe. We propose that phase transitions between compartments separated by intrinsically disordered proteins are vital to this classification process, allowing self transcripts to leave the P granule while nonself transcripts are separated for downstream silencing, and suggest experiments that could further investigate this hypothesis.
URI: http://arks.princeton.edu/ark:/88435/dsp01v405sd495
Type of Material: Princeton University Senior Theses
Language: en
Appears in Collections:Physics, 1936-2023

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