This study seeks to address one of the simplest questions that can be asked about an interconnected system; what happens to one process in the absence of the other process? This is a more difficult task than it would appear at first, due to the absence of small molecule inhibitors that can inhibit splicing globally in yeast cells. The first results chapter describes the adaptation of a system called the auxin induced degron (AID) to the task of inhibiting pre-mRNA splicing. This system appears to have several advantages over previous methods of inhibiting splicing and has many potential applications. Another hurdle to understanding what happens to transcription in the absence of splicing is the differential stability of pre-mRNA versus mRNA. At steady state the vast majority of transcripts of a specified gene will be mRNA transcripts. This means that even if you could rapidly inhibit splicing it would be a long time before all the pre-existing mRNA would turn-over. If you waited until specified mRNAs turned over it is likely that the cells would be very sick making it difficult to separate primary and secondary effects. The second results chapter shows the use of a metabolic labelling technique using a uracil analogue called 4-thiouracil (4SU). 4SU is added for an extremely short amount of time (1.5 min, 2.5 min, and 5 min) and the RNA produced during the labelling time is isolated by affinity purification. This allows us to study the kinetics of pre-mRNA splicing in wild-type cells and to seek correlations between splicing kinetics and gene architecture. The third results chapter combines the methods used in the previous two chapters to give a new technique called AID4U-seq. AID4U-seq allows for rapid inhibition of splicing and then the ability to isolate only the transcripts that were created after this inhibition came into effect. This should allow for examination of the primary consequences of blocking pre-mRNA splicing at multiple stages during spliceosome assembly. Additionally AID4U-seq is immediately applicable to the study of other areas of RNA processing. Defining the effects on the transcriptome of inhibiting splicing at multiple stages of assembly is an ambitious aim likely to require many more years of research. Therefore this thesis chiefly seeks to illustrate a novel strategy to begin dissecting a complex issue in which splicing, transcription, degradation and the post-transcriptional modification of histones are all likely to have roles.

I investigated two aspects of in vivo splicing that are poorly understood: spliceosome disassembly and recycling, and proofreading. To this end, I used the auxin-inducible degron (AID) to individually deplete several splicing factors in budding yeast and then I measured the effect on co-transcriptional spliceosome assembly through chromatin immunoprecipitation. In addition, using RNA next-generation sequencing, I measured the frequency of splicing errors following depletion or mutation of the fidelity factor, Prp22. I show that formation of the pre-spliceosome (the first stage of spliceosome assembly) is rapidly inhibited by global defects in late stages of spliceosome assembly. I demonstrate that this is due to the accumulation of arrested spliceosomes that sequester the splicing machinery and, as a result, causes a recycling defect. This suggests that spliceosomes that lack essential splicing factors are not always properly disassembled and recycled in vivo, and warns about potential systematic secondary effects when perturbing single components of the spliceosome. Secondly, I describe the development of a new version of the AID system for budding yeast, called the B-estradiol AID. To the best of my knowledge, an AID system for budding yeast that is fast-acting, tightly-controlled and gratuitous, was lacking until now. Lastly, I show that absence of Prp22 protein, which was previously proposed to play a role in splicing fidelity, correlates with more mistakes in 3’ss selection of many endogenous intron-containing transcripts in vivo. This provides indirect evidence to suggest that Prp22-dependent splicing proofreading is physiologically important. The data from this analysis will be useful in ongoing studies to try to identify common features that could improve our understanding of the mechanism of Prp22’s function in splicing proofreading.

Telomere dysfunction is a significant source of genomic instability and contributes to the development of cancer. The multi-protein complex shelterin binds telomeric DNA to mitigate telomere dysfunction and ensure overall telomere stability. In addition to shelterin, the telomeric cap includes the telomeric repeat-containing RNA, TERRA, which associates with telomeric proteins and the telomeric DNA itself, often forming RNA:DNA hybrids or R-loops. TERRA is most abundant in cancer cells that utilize the alternative lengthening of telomeres (ALT) pathway, where it has been suggested that TERRA R-loops act as a source of replication stress at telomeric DNA that ultimately contributes to the activation of the ALT mechanism. In an effort to evaluate the effect TERRA may have on the emergence of the ALT phenotype, we sought to identify the enzyme(s) that regulate TERRA degradation in mammalian cells. Here, we leveraged an auxin-inducible degron (AID) system to identify the 5’-3’ exoribonuclease XRN2 as a direct modulator of TERRA stability in mammalian cells. Following XRN2 depletion, we demonstrate a significant increase in TERRA on chromatin in both non-ALT and ALT-positive cell lines. While the stabilization of TERRA on chromatin alone was insufficient to drive replication stress and activation of ALT in telomerase cells, depletion of XRN2 in the ALT-positive context led to a significant increase in R-loops and DNA damage signaling at telomeric DNA. Thus, increased TERRA stability alone is unlikely to activate ALT but may instead exacerbate ALT activity. Taken together, we demonstrate that XRN2 regulates TERRA stability, that defects in TERRA metabolism can alter telomere stability, and dysfunction in both factors drive telomere dysfunction in cells that rely on the ALT pathway. / 2024-08-12T00:00:00Z

Transkription är stokastisk, där utbrottsmässiga episoder av RNA-transkription genererar RNA-molekyler. Trots att detta är en kärndel av eukaryotiskt liv, är lite känt om hur DNA-bindande transkriptionsfaktorer och transkriptionella kofaktorer formar gen-specifik transkriptionell utbrottskinetik. Syftet med detta examensarbete var att tyda rollerna hos kofaktorerna Med14 och P300/CBP inom transkriptionell utbrottskinetik. För detta ändamål användes Auxin inducible degron systemet för snabb nedbrytning av Med14 eller P300/CBP-proteiner i HCT116-celler, följt av Smart-seq3xpress single cell-RNA-sekvensering. Ett särskild fokus i denna avhandling var även att utvärdera förmågan att härleda direkta  genuttrycksförändringar genom analys av introniska reads – detta då introner ko-transkriptionellt splitsas och dess nyttjande skulle fånga effekter av mycket närliggande transkription. Resultaten visar en tidsberoende minskning av introniskt innehåll och en nedreglering av genuttryck för majoriteten av generna i de behandlade cellinjerna, medan opåverkade kontroller inte visar sådana trender. Utbrottskinetikresultaten indikerar att det inte finns någon korrelation mellan P300/CBP-pertuberade cellers geners ursprungliga utbrottsstorlek och några trender i genuttryckets relativa förändring, medan detsamma kan sägas för Med14-pertuberade cellers geners utbrottsfrekvens. Svaga trender från P300/CBP-påverkade cellers utbrottskinetik och uttrycksändring kan antyda att deras utbrottsfrekvens och inte utbrottsstorlek har påverkats. Resultaten antyder att perturbationen var framgångsrik och att P300/CBP inte påverkar utbrottsstorlek samt att Med14 kan reglera utbrottsfrekvensen för alla påverkade gener i lika hög grad. Vidare forskning behövs inom utbrottskinetikdata för att utöka vår förståelse av denna studies implikationer gällande Med14:s och P300/CBP:s reglerande roller på transkriptionella utbrott. / Transcription is stochastic with episodes of RNA transcription generating bursts of RNA molecules. Despite being a core part of eukaryotic life, little is known about how DNA-binding transcription factors and transcriptional co-factors shape gene-specific transcriptional bursting kinetics. The aim of this thesis was to decipher the roles of the co-factors Med14 and P300/CBP in transcriptional burst kinetics. To this end, the Auxin inducible degron system was used for rapid Med14 or P300/CBP protein degradation in HCT116 cells, followed by Smart-seq3xpress single-cell RNA-sequencing. A particular focus of this thesis was to evaluate the abilities to infer direct gene expression changes by analysis of intronic reads – since introns are co-transcriptionally spliced and would capture very recent transcription. Results show a time dependent decrease of intronic contents and a downregulation in gene expression for a majority of genes in the perturbed cell lines, while unperturbed controls show no such trends. Bursting kinetics results indicate that there is no correlation between P300/CBP perturbed cells’ gene’s original bursting size and any trends in gene expression fold change while the same can be said for Med14 perturbed cell’s gene’s burst frequency. Weak trends from P300/CBP perturbed cells’ bursting kinetics and expression fold change could imply that their bursting frequency and not bursting size has been affected. The results imply that the perturbation was successful and that P300/CBP does not affect bursting size as well as that Med14 could regulate bursting frequency for all affected genes to an equal degree. Further research is needed into the bursting kinetics data to expand our understanding of this study’s implications regarding regulatory roles of Med14 and P300/CBP on transcriptional bursting.