Date of Award

2019

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Biology

First Advisor

Gideon Dreyfuss

Second Advisor

Brian Gregory

Abstract

U1 snRNP (U1) functions in controlling transcription through both the splicing of introns and the suppression of premature cleavage and polyadenylation. The latter, termed telescripting, is the critical process that allows for the creation of full-length pre-mRNA. Reducing the level of available U1 in cells relative to pre-mRNA, either through global transcription up-regulation or functional U1 inhibition, causes widespread premature cleavage and polyadenylation (PCPA) from cryptic polyadenylation signals in introns. Through the development of novel analytical programs for large sequencing datasets, I identified the gene features that increase sensitivity to U1 inhibition and examined the size-function polarization of genomes that has occurred through intron expansion as a result of telescripting. By conducting a series of high-throughput sequencing experiments for both chromatin immunoprecipitation (ChIPseq) and RNA (RNAseq), I demonstrated that PCPA is co-transcriptional and that it is an evolutionarily conserved transcription regulation mechanism. I have shown that U1 inhibition caused PCPA selectively in large genes (median 39 kb in human), which were enriched for developmental and differentiation functions, while small genes were enriched for acute cell survival and stress response function are up-regulated under the same conditions. Importantly, I proved that PCPA susceptibility is evolutionarily conserved and has been a major driving factor in vertebrate intron size expansion. I demonstrated that this gene size-function polarization allows for large genes to sacrifice transcription during cell stress and activation, supplying small genes necessary for cell survival with RNA processing proteins that boost their mRNA productivity. Lastly, I have shown that minor U1 inhibition caused general and previously unannotated multi-exon skipping events that can sometimes occur between two, adjacent and same-stranded genes as a part of read through transcription including in disease relevant genes. These results highlight the importance of U1, not only as a mechanism of transcription regulation in all metazoans, but also as a primary contributor to the evolution of gene and genome structure.

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