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Item Open Access Regulation of polarised trafficking by Klp98ABittleston, AliceDirectional trafficking of cargo, a hallmark of living cells, relies on a polarised landscape of microtubule tracks. Here, I studied how the regulation of an endosomal motor affects polarised trafficking, using the asymmetric division of *Drosophila* Sensory Organ Precursor (SOP) cells as a model system. In this pathway, the PI(3)P-binding kinesin-3, Klp98A biases the motility of signalling endosomes towards the posterior daughter cell. Since these endosomes contain the cell fate determinants Notch and Delta, this contributes to an asymmetric cell fate. Mechanistically, Klp98A-mediated transport is achieved along the microtubule-based anaphase-specific spindle midzone, termed the central spindle. During SOP division, the central spindle becomes asymmetric, with a higher density of microtubules on the anterior side. Since Klp98A is a plus-end directed motor, this biases the motility of early endosomes into the posterior daughter cell, towards which more microtubule plus-ends point. In this work, I focused on how the modulation of Klp98A activity can control polarised trafficking on three levels: i) via post-translational modifications, ii) through changes in microtubule binding, and iii) by polarising the microtubules Klp98A walks on. By first using an *in vitro* reconstitution with purified motors on micropatterned supported lipid bilayers containing PI(3)P, I investigated how Klp98A is activated. Lipid-binding was sufficient to induce activation of Klp98A, so I proceeded to use both enzymatic-induced proximity labelling and a candidate-based approach to identify possible regulators of Klp98A activity. *In vivo*, modulation of two enzymes, p-21 activated kinase 1 (Pak1) and Sirtuin 2 (Sirt2), resulted in symmetric endosome segregation despite an asymmetric landscape of microtubule tracks. In the case of Pak1, this endosomal phenotype appeared to arise due to a delay in the targeting of endosomes to the central spindle, either directly due to modulation of post-translational modifications on the motor itself or through an intermediary. Next, I focused on characterising how the loop 8 (L8) region of the Klp98A motor domain modulates its activity. This well-conserved loop within the kinesin-3 family is thought to be involved in microtubule binding and could thus be a central way by which the activity of this motor is regulated *in vivo*. To understand how L8 controls motor activity, I studied a previously isolated Klp98A mutant, Klp98A Δ6, which consists of a two amino-acid deletion and one amino-acid substitution within the L8 site. Strikingly, *in vivo*, Klp98A Δ6 localises to endosomes like the *wild-type* but leads to symmetric segregation of cell fate determinants in dividing SOP cells, phenocopying a complete loss of function of Klp98A. A combination of *in vitro* reconstitution, single-molecule assays and crystal-structure determination showed that, unexpectedly, Klp98A Δ6 retains wild-type microtubule binding affinity but is unable to move processively. The cause of this transport defect by Klp98A Δ6 is likely a consequence of a long-range structural rearrangement from the L8 site to the catalytic domain, preventing ATP hydrolysis independently of microtubule binding. Thus, it seems in *wild-type* Klp98A, L8 functions as a sensor, coupling microtubule binding to ATP hydrolysis. Lastly, I investigated how the asymmetry of the central spindle, which polarises Klp98A motility, is established and maintained during SOP cell division. I demonstrated that at the cell cortex, the Par complex promotes central spindle symmetry breaking. Downstream of that, I found that Elongator, originally identified as a regulator of translation, promotes the formation of an asymmetric central spindle. Here, Elongator is enriched on the anterior side of the spindle, where it stabilises microtubules. Altogether, this data sheds light on how polarised trafficking emerges from the synergistic effects of both the polarity within the network of microtubules and the local control of the activity of motors at the surface of endosomes.Item Open Access Studies of the MYM-type zinc finger protein ZMYM3Shapson-Coe, AlexanderRNase H2 is a trimeric ribonuclease that specifically degrades the RNA moiety of DNARNA hybrids. Mutations in RNase H2 result in Aicardi–Goutières syndrome (AGS), a rare inflammatory disorder notable for being a ‘mendelian mimic’ of congenital viral brain infection. Some AGS-associated mutations in the RNase H2B subunit do not affect the catalytic activity of the RNase H2 *in vitro* and are clustered together on the surface of the complex, suggesting a possible role for these residues in mediating important interactions of RNase H2. I set out to identify binding partner(s) of RNase H2B whose binding is impaired by this cluster of mutations, by screening for interactors of FLAG-tagged wild-type and mutant RNase H2B in HEK293T cells. In this work, I identify several members of a putative chromatin-silencing complex as novel RNase H2B binding partners whose binding is impaired by each mutation in this cluster, including: HDAC2, a histone deacetylase, LSD1, a histone demethylase, CoREST, a co-repressor of transcription, TFII-I, a transcription factor, and ZMYM3, an MYM-type zinc finger protein of unknown function. By making several truncation mutants of ZMYM3, I show that a C-terminal region containing a ‘PXP’ repeat motif mediates its interaction with RNase H2, and that the PXP-containing proteins ZMYM2 and ZMYM4 interact with RNase H2, whereas the PXP-null proteins ZMYM1 and ZMYM6 do not. By systematic truncation of the zinc fingers of ZMYM3 I also demonstrate that the first zinc finger mediates its interaction with TFII-I, while the eighth and ninth zinc fingers are each sufficient for its interaction with LDS1, HDAC2 and CoREST. These interaction sites implicate ZMYM3 as a novel type of scaffold protein mediating interactions between deacetylase, demethylase and RNase H-type enzymes. To better understand the function of ZMYM3, I generate a ZMYM3 knock-out mouse embryonic stem cell line, and show that ZMYM3 is not required for cell viability or DNA repair, and is not cell-cycle regulated. Given the association of ZMYM3 with various regulators of transcription, I hypothesised that ZMYM3 might be involved in regulating a set of transcripts through these associations. To test this, I compare the transcriptomes of ZMYM3 knock-out and wild-type mouse embryonic stem cell lines by RNA-Seq. While deletion of ZMYM3 has no effect on transcription globally in this context, ZMYM3-null cells express lower levels of the primary transcript of microRNA 142, a specific target of the AGS-associated dsRNA deaminase ADAR1. To better understand the *in vivo* function of ZMYM3, an ES cell line with a ZMYM3 exon flanked by loxP sites is generated, to allow the conditional deletion of ZMYM3 in a whole organism. The association of deacetylase, demethylase and RNase H-type enzymes raises the possibility that histone modification and degradation of DNA-RNA hybrids may be coordinated, and is therefore of potential importance for the field of chromatin biology. As the roles of these associations remain unknown, several functional models of these interactions are proposed, with a discussion of the possible reasons why disruption of these interactions may result in Aicardi–Goutières syndrome.Item Open Access The Logic of Innately Aversive Olfactory PathwaysMyers, PhilipAnimals must locate food to survive and appropriate sexual partners with whom to reproduce. At the same time they must avoid predators and pathogens that threaten their survival, or the survival of their offspring. Recognising salient environmental cues is therefore critical to fitness-related behaviours. In many cases, certain stimuli evoke stereotypical behavioural responses. These innate behaviours, in contrast to learned behaviours, are thought to be hardwired in the neural circuitry of an animal. How are these innate behavioural responses instantiated in the circuitry of the brain? We used the olfactory sensory circuit of a microbial odorant, geosmin, as a model to understand how an innately aversive olfactory signal is processed in the brain in order to produce an appropriate behavioural response. We used connectomics, functional imaging, and behavioural assays to determine the anatomy and function of this geosmin processing circuitry. Using behavioural assays, we show that the aversive response to geosmin is due to chemotaxis, and provide evidence of a post-mating switch in behavioural response to geosmin. We then show that geosmin is detected via a functionally segregated pathway in the sensory periphery until it reaches the central brain, where the signal diverges significantly, and use connectomics to show that this divergent connectivity is largely stereotyped. We then imaged the activity of one previously described third-order neuron downstream of the geosmin pathway to show that it integrates olfactory signals of similar ethological significance at its dendrites. We used connectomics to follow this circuit deeper into the brain, and discovered a previously unknown descending neuron that senses geosmin, and is required for the innate aversion to geosmin exhibited during egg-laying. Connectomics analysis showed that this cell converges with other descending neurons in the ventral nerve cord of the fly that are known to induce escape behaviours. We further find evidence of a learned innate interaction via memory input to this descending neuron, implicating this circuit in aversive memory recall. These findings extend our understanding of how aversive signals are processed by the brain by providing a functional and connectomic characterisation of an olfactory circuit all the way from the brain to the nerve cord.Item Embargo Structural and Biochemical Investigation of Fanconi Anemia Pathway ActivationSijacki, TamaraDNA interstrand-crosslinks (ICLs) are covalent links between complementary DNA strands that prevent their separation, interfering with fundamental cellular processes such as DNA replication and transcription. Consequently, these DNA lesions are highly toxic and the inability to repair them results in a severe genetic disease, Fanconi Anemia (FA), manifested by developmental impairment, bone marrow failure, and predisposition to various types of cancers. In healthy cells, a specialized cascade of DNA repair proteins comes together to establish the FA pathway that specifically recognizes and repairs DNA ICLs. Ubiquitination of the FANCD2-FANCI (D2-I) complex by a multi-subunit ubiquitin E3 ligase, the FA core complex, is a key step of the FA pathway. D2-I ubiquitination initiates ICL repair by recruiting endonucleases to remove the DNA lesion, which is subsequently repaired via homologous recombination and trans-lesion synthesis. Due to its immense importance in the FA pathway, D2-I ubiquitination has been thoroughly studied using genetic, cellular, biochemical, and structural tools. FANCI phosphorylation by the ATR DNA damage kinase stimulates D2-I ubiquitination in cells, which enables timely and coordinated FA pathway activation to ensure DNA repair fidelity. In this dissertation, I investigated the mechanism of this process by employing a triple-phosphomimetic FANCI. First, I confirmed the stimulatory effect of phosphomimetic FANCI on D2-I ubiquitination through in vitro ubiquitination assays using purified proteins. To elucidate the structural basis of this stimulation, I visualized different states of phosphomimetic D2-I using cryo-electron microscopy (cryo-EM). This revealed that phosphomimetic D2-I securely closes around double stranded DNA. Upon closure, target ubiquitination sites on D2-I become accessible, explaining how FANCI phosphorylation promotes D2-I ubiquitination. I further explored how phosphomimetic mutations affected biophysical properties and dynamics of the D2-I complex. Strikingly, while phosphomimetic mutations did not significantly alter DNA binding, in vitro ubiquitination assays suggested that phosphomimetic D2-I closes more readily in solution even in the absence of DNA. This is not due to increased binding of the phosphomimetic D2-I to the FA core complex. Instead, using quantitative crosslinking mass spectrometry, I discovered that phosphomimetic mutations locally alter the D2-I dimerization interface to prime the complex for closure. Thus, phosphomimetic mutations shift the conformational equilibrium of D2-I towards a closed state. Moreover, I observed that in the presence of DNA, phosphomimetic and wild-type D2-I exist in both open and closed states, however phosphomimetic D2-I has a higher preference for the closed conformation. Overall, the work presented in this thesis provides mechanistic insight into how an interplay between DNA binding and FANCI phosphorylation by the ATR kinase alters the conformational dynamics of the D2-I complex, promoting its closure and ubiquitination to activate the FA pathway.Item Open Access Encoded synthesis and evolution of clinically approved 2'-modified ribonucleic acidsFreund, NiklasXeno-nucleic acids (XNAs) are unnatural nucleic acids with altered sugar, phosphodiester backbone, or nucleobase components. 2'-modified nucleic acid chemistries, such as 2'-O-methyl-RNA (2'OMe-RNA) and 2'-O-2-methoxyethyl-RNA (MOE-RNA), have shown promise in clinical applications due to their enhanced properties like high antisense-binding affinity and increased biostability. However, conventional phosphor-amidite synthesis for these 2'-modified nucleic acids is limited in length, prevents parallel exploration of different sequences and modifications, and precludes evolution. This study aims to develop an encoded enzymatic synthesis approach using polymerase engineering to enable the efficient synthesis of 2'OMe-RNA and MOE-RNA. This approach opens up possibilities for the evolution and selection of modified aptamers and nucleic acid enzymes with therapeutic potential. First, I describe how structure-guided engineering on a thermophilic archaeal polymerase led to the identification and mutation of a two-residue nascent-strand steric gate near the active site. This modification alleviated steric clashes within the polymerase, enabling processive synthesis of 2'-modified nucleic acids, including mixed-chemistry 2'OMe-/MOE-RNA aptamers, and unlocking their evolution. Furthermore, a reverse transcriptase-free selection procedure was established for MOE-RNA aptamer selections, enabling re-selection of a 2'OMe-RNA VEGF aptamer in the MOE-RNA chemistry. Additionally, procedures for the de novo selection of Tau-binding RNA, 2'OMe-RNA, and MOE-RNA aptamers were established. These selection procedures involved pre-enrichment over four rounds, followed by deep screening using an Illumina HiSeq instrument. By advancing these aptamer selections further, this study lays the groundwork for the development of the first MOE-RNA aptamer and demonstrate the potential of encoded synthesis of 2'-modified nucleic acids in creating biostable aptamers using nucleic acid chemistries approved for human use.Item Embargo Mechanisms underlying substrate engagement by TRIM7 and TRIM21 and strategies for re-directing their E3 ligase activityLuptak, Jakub; Luptak, Jakub [0000-0002-9527-8755]The work presented in this thesis focuses on two members of the TRIM protein family: TRIM7 and TRIM21. Both proteins are ubiquitin E3 ligases that ubiquitinate and degrade substrates. My work on TRIM7 has uncovered a unique molecular mechanism of substrate selection and explains why TRIM7 is reported to interact with unrelated and diverse substrates, ranging from cellular proteins involved in metabolism to viral proteins. In summary, TRIM7 recognises a dipeptide motif at the C terminus of substrates, so if this sequence is exposed in the folded protein and the substrate is oligomeric, this results in substrate engagement in cells and subsequent degradation. The function of TRIM21 as a cytosolic antibody receptor has been firmly established – it can recognise antibody coated viruses that have managed to enter the cytoplasm and mediate their degradation. This feature of TRIM21 has also been exploited to develop a technology called Trim-Away, where antibodies against endogenous proteins can be introduced to the cytosol of cells, resulting in targeted degradation of these proteins. While it is understood that the RING-E3 domain of TRIM21 is essential for this degradation, along with a number of E2 enzymes, how and why the formation of a TRIM21:antibody:substrate ternary complex results in the degradation of each component is incompletely understood. I have developed and applied *in vitro* assays to monitor ubiquitination of proteins involved in physiological TRIM21 function and in Trim-Away experiments. In both cases, the role of N terminal ubiquitination is explored. Finally, I have developed degrader molecules based on the mechanistic rules underpinning TRIM21 activation. These molecules can be further used as tools for studying endogenous TRIM21 function and potentially developed into therapeutics.Item Embargo Characterization of endocytic escape pathway and its role in adaptive immunityKrawczyk, Patrycja AnnaIn dendritic cells, endocytic escape appears critical for the induction of cytotoxic T-cell responses against viruses and tumors, in a process termed cross-presentation. During cross-presentation, dendritic cells present exogenous antigens on MHC class I, and the predominant molecular model for it is one where exogenous antigens are first released from endosomes into the cytosol, and further processed like endogenous proteins for presentation on MHC class I. Endocytic escape of antigens appears to be the rate-limiting step of cross-presentation, yet we know very little about the molecular mechanisms involved. To identify the machinery involved in endocytic escape of proteins, the Kozik lab has established a genetic screening strategy where escape of a ribosome-inactivating protein, called saporin, is being followed. When saporin enters the cytosol, it causes translational arrest quantified using puromycin labelling of newly synthesized polypeptides. Using the saporin assay, the Kozik lab performed CRISPR/Cas9 genetic screen targeting 200 candidate genes. The screen yielded one strong hit: pore-forming protein, perforin-2 (*Mpeg1*; Macrophage-expressed gene 1) and we proposed perforin-2 forms pores in endolysosomal compartments, allowing for endocytic escape of saporin. The main aim of my PhD was to extend our understanding of mechanisms governing endocytic escape through perforin-2, to identify other members of endocytic escape pathway, and to study their role in cross-presentation. We demonstrated that perforin-2 activity might be regulated by proteolytic cleavage and set out to identify the protease involved. The cleavage depends on low pH and can be stimulated by a range of pathogen-associated molecular patterns. To identify the new players of the endocytic escape pathway, we employed a genome-wide CRISPR/Cas9 genetic screening approach, where we followed endocytic escape of either saporin or of another translation inhibitor, a small peptide AGAAMSH (here named Pep). The screen confirmed that *Mpeg1* is a main regulator of endocytic escape of saporin in MutuDCs, and we identified and validated multiple potential *Mpeg1* regulators, including proteins involved in trafficking and posttranslational modifications. Interestingly, the screen with use of Pep as a translation inhibitor identified largely different hits. Many of the negative regulation hits were mitochondrial proteins, especially complex I related, which might indicate the involvement of mitochondrial ROS in endocytic escape of Pep. Finally, we went to address whether any of the validated hits indeed play a role in cross-presentation. Using the B3Z T cell hybridoma-based cross-presentation assay, we did not observe defects in cross-presentation in *Mpeg1* knockouts, however, knockout of a negative regulator of saporin escape, *Sppl2a*, seemed to increase cross-presentation of soluble ovalbumin, whereas knockout of a negative regulator of Pep escape, *Chchd5*, might enhance cross-presentation of immune complexes of ovalbumin. We hope that further characterization and cross-presentation studies will shed more light on the role of validated hits in the endocytic escape pathways, and on how different endocytic escape pathways contribute to adaptive immunity.Item Embargo Quality control of protein complex assemblyCarrillo Roas, SaraAll cells contain numerous multi-subunit protein complexes of exceptional abundance and physiological importance. Prominent examples include the ribosome, proteasome, chaperonin, tubulin, haemoglobin, and many others. A major challenge for the cell is to synthesise individual subunits in the correct stoichiometry. Any imbalance in subunit synthesis results in excess unassembled “orphan” subunits lacking their interaction partner(s). Orphans are accentuated in disease states such as cancer where altered gene expression caused by aneuploidy is common. Acute aneuploidy is known to cause proteotoxicity, probably as a consequence of high orphan burden. How orphan subunits are targeted for degradation to maintain protein homeostasis remains an unanswered question for most of the cell’s major protein complexes. The work described in this thesis investigated how the seven beta subunits of the 20S core proteasome (named PSMB1-7) are targeted for degradation when produced in excess. I used a mammalian *in vitro* translation system to identify candidate interactors of nascent PSMB subunits and found several proteins related to the ubiquitin-proteasome system. Using fluorescent reporters of PSMB subunit degradation in cells depleted of individual candidates, I found that the E3 ubiquitin ligases KCMF1 and UBR4 are required for efficient degradation of unassembled PSMB subunits. Biochemical assays showed that KCMF1 and UBR4 form a stable complex that physically interacts with nascent PSMB subunits. Moreover, using a cell-based flow cytometry assay, I determined which domains of KCMF1 and UBR4 are required for effective degradation of PSMB subunits. Analysis of orphans from other protein complexes showed that the KCMF1-UBR4 complex was also required for efficient degradation of PSMC5 (a 19S proteasomal subunit) and CCT4 (a chaperonin subunit). This was unexpected because orphaned PSMC5 and CCT4 were recently shown to be multiply mono-ubiquitinated by the E3 ubiquitin ligases HERC1 and HERC2, respectively. This led to the hypothesis that the KCMF1-UBR4 complex might build ubiquitin chains on pre-ubiquitinated orphans, thereby improving their recognition by the proteasome. *In vitro* reconstitution of orphan ubiquitination by the KCMF1-UBR4 complex showed that substrate pre-ubiquitination is both necessary and sufficient to create a KCMF1-UBR4 substrate. This reconstitution system revealed that the KCMF1-UBR4 complex builds K48-linked polyubiquitin chains and helped to define the key domains on both ubiquitin and UBR4 involved in substrate recognition. UBR4 mutants impaired in substrate recognition *in vitro* were also impaired in substrate degradation in cell-based assays. These results support a model in which the KCMF1-UBR4 E3 ligase complex acts as a chain elongator for orphaned subunits that are mono-ubiquitinated by a priming ligase. Elongation by the KCMF1-UBR4 complex generates K48 polyubiquitin chains that are ultimately required for efficient degradation by the proteasome. The KCMF1-UBR4 complex may therefore represent a general quality control pathway for the degradation of many types of orphan subunits. Consistent with this model, a wide range of cancer cells are observed to be strongly reliant on KCMF1 and UBR4 for their fitness.Item Embargo Crosstalk between natural killer cells and cancer associated fibroblasts in the tumour microenvironmentNunes Rodrigues, LeonorCancer is a deadly disease where malignant cells proliferate and avoid elimination by the immune system. Although natural killer (NK) cells, of the innate immune response, recognise and eliminate cancer cells, their cytotoxic function is often impaired in the tumour microenvironment. Indeed, difficult to treat solid cancers, like pancreatic cancer, are rich in cancer associated fibroblasts (CAF) which support tumour growth and suppress immune cell functions. Overcoming barriers like CAF-derived immune suppression in the solid tumour microenvironment remains a challenge. Successful restraint of CAF has proven challenging due to their complex intratumoral heterogeneity and plasticity. However, the potential exploitation of NK cell cytotoxicity remains attractive in the field of cancer immunotherapy. This work aimed to investigate the crosstalk between CAF and NK cells and to identify potential targets in solid tumours, thus improving NK cell cytotoxicity and reducing tumour growth. Initial flow cytometry and imaging analysis of mouse models of solid tumours revealed NK cell dysfunction within the tumours, characterised by an immature and less cytotoxic profile as compared to more mature blood circulating NK cells. Moreover, within the tumours, NK cells interacted closely with CAF defined by expression of platelet derived growth factor receptor alpha (PDGFR-⍺), while being distant from myofibroblastic CAF. Investigation of the roles of distinct CAF populations *in vitro* and *ex vivo* by flow cytometry and quantitative PCR, revealed that TGF-β-driven CAF (myofibroblastic) were strong NK cell modulators, in contrast to inflammatory CAF and healthy fibroblasts. Furthermore, *in vitro* assays revealed that pancreatic CAF-derived factors suppressed NK cell functions, in contrast to healthy fibroblasts. Comparative mass spectrometry and ELISA revealed CAF increased secretion of extracellular matrix proteins osteopontin, laminin and perlecan, but also the lipid metabolite prostaglandin E2 (PGE2). Blocking CAF-derived PGE2 *in vitro* restored NK cell functions such as tumour killing capacity and granzyme B secretion. *In vivo*, targeting this crosstalk by blocking PGE2 receptors EP2 and EP4 with antagonists reduced tumour growth and restored NK and T cell derived granzyme B. This work revealed unknown and contrasting roles for CAF populations in NK cell anti-tumour function, suggesting that targeting myofibroblastic CAF and derived factors like PGE2 could be relevant to improving intratumoral NK cell cytotoxicity in difficult to treat cancers such as pancreatic cancer.Item Open Access Interaction between form and fate during human neural developmentChiaradia, IlariaGenetics instructs on cell differentiation. Controlled cell differentiation over time and space determines the formation of complex tissue structures. Tissue architecture is permissive to tissue function. Little is known about whether tissue architecture influences cell fate acquisition. We sought to investigate the interaction between shape and fate during neural development. We relied on cerebral organoids as a tractable *in vitro* system where tissue shape can be manipulated following several complementary approaches and tissue identity assessed by transcriptomics. We first discovered key protocol variables that contribute to differences in organoid morphology. We designed a pipeline to quality- screen organoids based on their morphological features. Morphology alone can predict organoid cytoarchitecture and transcriptional proximity to the *in vivo* developing brain. Organoids with complex morphology display more and larger ventricles with thicker progenitor layer. They better resemble the transcriptome of foetal brain. Organoids with poor morphology and cytoarchitecture display an aberrant cell repertoire with fewer basal progenitors and upper-layer neurons. They fail to undergo proper developmental trajectories of events. Neurons maintain the signature of progenitors. Progenitors express neuronal genes early on. We observed a similar dysmaturity as in cortical dysplasia. We perturbed cytoarchitecture by mechanical dissociation-reaggregation of the organoid. We achieved a controlled morphology by encapsulating the organoid in hydrogel. Both perturbation paradigms resulted in aberrant cytoarchitecture and cells with a poised neuron/progenitor identity. We demonstrated that cell positioning influences cell fate. Next, we showed neural network dynamics in mature organoids. Organoids with poor morphology display isotropic neural networks. Overall, we demonstrated how shape influences fate during neural development.Item Open Access Mechanisms of TRIM21-directed intracellular degradationRhinesmith, TylerThe cytosolic antibody receptor TRIM21 has been studied for more than a decade for its role in mediating antibody-dependent neutralization of nonenveloped viruses. The presence of antibodies in the cytosol is abnormal—by binding them and initiating inflammatory signaling cascades, TRIM21 acts as a danger sensor and intracellular effector of humoral immunity. In addition to antibody binding, TRIM21 is a ubiquitin E3 ligase, an enzyme which catalyzes the formation of polymers of the protein ubiquitin around target substrates. When viruses coated in non-neutralizing antibodies escape into the cytosol, TRIM21 binds and decorates the complex with these polyubiquitin chains. Polyubiquitin is a highly-conserved protein post- translational modification with a number of important roles, including the initiation of degradative processes and antiviral genetic programs. Polyubiquitin-coated TRIM21:antibody:virus complexes are degraded by the cell, thus neutralizing viral infection. Its ability to bind generic immunoglobulins has allowed TRIM21 to be developed into the targeted protein degradation technology Trim-Away, whose intracellular mechanism is thought to mirror that of antibody-coated virions. Prior to the work presented here, the specific mechanistic steps following TRIM21-antibody binding had been established in some detail, and were believed to involve the sequential action of ubiquitin E2 conjugating enzymes UBE2W and UBE2N, which cooperated with TRIM21 to catalyze the formation of a specific type of linear polyubiquitin chain linked through lysine 63 on ubiquitin. This was thought to lead to the recruitment of the segregase p97/VCP and the 26S proteosome which together disassembled and degraded the encapsidated virion. In this thesis, I describe my efforts to define the sequential enzymatic mechanism of TRIM21 degradative signaling in greater detail. I report data from a series of biochemical and in-cell experiments which are not consistent with a role for UBE2W in polyubiquitin chain priming on TRIM21 during adenoviral neutralization. Then, I detail my development of two proximity-proteomics screens and a whole-genome CRISPR/Cas9 knockout screen for TRIM21 interacting partners, in both Trim-Away and adenovirus neutralization contexts. Collectively, the data from these experiments led me to hypothesize that the TRIM21 mechanism is plastic, and sensitive to substrate features and intracellular context. The whole-genome screen and follow up validatory experiments were consistent with a new model for TRIM21-adenoviral neutralization—rather than processing through the proteasome, intracellular adenoviruses coated with antibodies are degraded by selective autophagy following polyubiquitin deposition by TRIM21. Taken together, this work represents a clear advancement in understanding how TRIM21 targets substrates for proteolysis, and opens several new lines of inquiry into how the protein affects adaptive immunity at the cellular level.Item Embargo Genome-Wide and Multi-Scale Mapping of DNA Supercoiling in Differentiating Human Stem CellsPerez, ConsueloThe molecular programme of every cell is encoded in its genome. Human cells must organise and compact their genetic material at multiple levels to accommodate the two-meter-long DNA within the confined nuclear space of six microns. Chromatin folding is not only a cellular need, but is also crucial for gene regulation, and coordinates the precise rewiring of gene expression programmes in every cell type during developmental transitions. Therefore, our genome works in a dynamic rather than a static manner, allowing feedback between function and structure. However, how exactly the genome reaches a functional equilibrium in a particular cell type and the mechanisms for maintaining such balance remain incompletely understood. Increasing understanding of the genome topology derived from mathematical descriptions, *in silico* and *in vitro* studies, to single-molecule approaches and functional experiments in cells, has revealed that the free energy stored as twist in the DNA molecule can be used to facilitate key biological processes. Accordingly, changes in the winding of DNA, known as supercoiling, were shown to impact gene expression and chromosome architecture. Nonetheless, its intrinsic dynamic and multifaceted nature, together with experimental limitations, have hindered the study of the timing and factors orchestrating supercoiling formation and dissolution across human chromosomes. This thesis explores the cellular processes responsible for introducing DNA supercoiling, and its remodelling by topoisomerase enzymes, and addresses how supercoiling underlies chromatin contacts and genome organisation during cell fate transitions. Initially, we mapped DNA supercoiling dynamics genome wide by adapting bTMP-seq (Naughton et al., 2013, Achar et al., 2020) to high-throughput sequencing. This approach offered increased resolution compared to previous studies and allowed us to interrogate the entire human genome. By then integrating this dataset with a chromatin conformation capture Hi-C map, we studied DNA supercoiling across multiple scales: from kilobase genes, through larger-scale topologically associating domains, to megabase epigenomic compartments. Crucially, we observed the formation of supercoiling domains throughout the genome and revealed their temporal remodelling due to transcriptional activity and topoisomerase-mediated relaxation across cell differentiation. In summary, our multi-omic study revealed widespread supercoiling dynamics in differentiating human stem cells, which likely contribute to the chromatin environment for gene regulation during developmental transitions, in conjunction with previously well-described chromatin features.Item Embargo Investigating tau propagation in situBehr, Tiana SophiaThe abnormal assembly of tau protein in neurons is the pathological hallmark of multiple neurodegenerative diseases, including Alzheimer’s disease (AD). In AD, tau assembly begins in the locus coeruleus and transentorhinal cortex, and progresses over years to connected regions in the limbic system and neocortex. Cellular and in vivo models of tau assembly suggest that prion-like propagation may underlie this progression, including the intracellular trafficking, intercellular transfer and seeded aggregation of assembled tau. However, the underlying molecular mechanisms are poorly understood. The goal of my thesis was to investigate tau propagation in situ. I focussed on characterising the ultrastructural context of assembled tau filaments at different stages of propagation, including their subcellular localisation and molecular interactions. To achieve this, I employed electron cryo-tomography (cryo-ET), a powerful technique that allows the visualization of biological samples at molecular resolution in near-native conditions. I wanted to study tau propagation in a disease relevant context. I first focused on human tissue and then developed a neuronal cell model of propagation to enable further investigation. In the first chapter of my thesis, I investigated the association of assembled tau with brain extracellular vesicles (EVs). This association has been documented in AD and has been linked to the clearance and propagation of assembled tau. However, the molecular species of assembled tau and how they associate are not known. By performing cryo-ET on EVs isolated from AD patient brain, I discovered tau filaments enclosed within the lumen of large EVs. I also observed multiple novel molecular interactions of filaments, including molecules that tether filaments to the EV limiting membrane. These findings suggest that tau filaments are selectively packaged within EVs in AD. Using single particle electron cryo-microscopy (cryo-EM), I found that the filaments contained distinct anionic molecules compared to tau filaments within intracellular inclusions. These results reveal the molecular species and structures of assembled tau associated with brain EVs in AD, as well as how they associated with EVs. This will guide future investigations of the mechanisms of assembled tau secretion, and inform biomarker and therapeutic strategies targeting extracellular tau. In the second chapter, I investigated tau assembly at the synapse in AD. Synaptic dysfunction is the earliest manifestation of neurodegeneration. Evidence suggests that this may be driven by tau assembly directly at the synapse. How assembled tau contributes to synaptic dysfunction is not known. In addition, synapses may mediate the intercellular transfer of assembled tau during propagation. I analysed synaptosomes isolated from AD patient brain. Using cryo-ET, I found tau filaments in the cytoplasm of pre-synapses. The filaments associated with one another, as well as with vesicles. The filaments were also tethered to the plasma membrane and were decorated with globular densities, similar to the interactions that I observed in brain EVs. These results provide insights into disease mechanisms of tau assembly and guide future studies to ultimately understand synapse dysfunction in AD. In the third chapter of my thesis, I established a neuronal cell culture model of tau propagation compatible with in situ studies using cryo-ET. Observations made in AD patient brain tissue relate directly to disease. However, they only provide static snap shots of tau assembly and propagation, whereas these are dynamic processes. Therefore, a model system that recapitulates tau propagation is important to further investigate observations made in human brain. I induced tau propagation in primary mouse hippocampal neurons by incubation with purified tau filaments from AD patient brain. I introduced strategies for the fluorescent labelling of tau filaments and for neuronal culture on EM grids in order to make this model system compatible with fluorescent live cell imaging, correlative light and electron cryomicroscopy and cryo-ET. These results lay the foundation for future in situ studies of dynamic propagation events. During the course of this thesis, I established cryo-ET of human brain tissue to investigate the subcellular localisation of assembled tau and its molecular interactions at different stages of propagation. This revealed tau filaments within EVs and pre-synapses, and identified their tethering to the limiting membranes of these compartments. I then developed a model system to enable in situ studies of dynamic tau propagation events. This work sets the foundations for future studies of the molecular mechanisms of tau assembly and will guide therapeutic strategies and biomarker development to target assembled tau in AD.Item Embargo Identifying regulators of natural killer cell development through CRISPR screening of common lymphoid progenitorsMurphy, JaneNatural Killer (NK) cells are cytotoxic lymphocytes that perform a key role in the innate immune response, lysing abnormal host cells such as those that are cancerous or virally infected. They are the prototypic member of the innate lymphoid cell (ILC) family, which also comprises the functionally divergent ILC1s, ILC2s, ILC3s and lymphoid tissue inducer (LTi) cells. Most NK cells arise from progenitors in the bone marrow (BM), from which other ILCs are also derived. However, the precise signals that specify the commitment of ILC progenitors to the NK cell lineage are poorly characterised. The aim of this thesis was to study the transcriptional networks and BM niche factors that promote NK cell development from uncommitted BM progenitors, using the mouse as a model organism. Pooled CRISPR screens were performed by culturing CRISPR-edited primary common lymphoid progenitors in vitro to generate NK cells and ILC2s, so that the regulators unique to each lineage could be discovered. Reassuringly, this approach identified previously studied regulators of NK cell development such as *Nfil3*, *Runx3* and *Eomes*. Additional putative regulators, such as *Tcf3* (encoding E2A), *Rere*, *Bach1* and *Zfp652* were identified and validated using arrayed CRISPR screens. Due to the known role of *Tcf3*/E2A in the decision between the innate and adaptive lymphocyte lineages, this was an attractive target for further study. Using a novel *Tcf3FLAG* mouse strain, E2A protein was detectable in progenitors but not mature ILC subtypes. However, transcriptional analysis revealed that *Tcf3* was expressed by mature NK cells so a conditional knockout of *Tcf3* in NK cells/ILC1s was generated and characterised. Fewer NK cells in these mice produced effector molecules such as granzyme B, and mice challenged with B16F10 melanoma cells had more lung metastasis. Finally, the developmental niche of ILCs was studied using immunohistochemistry of bone cryosections, and the role of Notch signalling as a potential regulator of E2A was studied. Overall, the work presented in this thesis adds to our knowledge of innate lymphopoiesis, with potential implications for how this might be distorted in systemic diseases such as cancer or targeted therapeutically.Item Embargo Investigation of enteric neuron and type 2 lymphocyte interactions at homeostasis and during Nippostrongylus brasiliensis infectionKo, MichelleType 2 lymphocyte responses are vital for mediating immunity to parasitic helminths and establishing wound repair. Key lymphocytes – type 2 innate lymphoid cells (ILC2s) and T helper 2 (Th2) cells – express the effector cytokines IL-4, IL-5, and IL-13 which drive the canonical “weep and sweep” responses that are critical for resistance to parasitic helminth infections. Emerging evidence indicates neuropeptides, such as Neuromedin U (NMU), as salient regulators of ILC2s. The bona fide sources of these neuropeptides has not been verified, with reciprocal interactions between ILC2s and distinct enteric neuronal populations not yet explored. In this thesis, a population of murine enteric neurons was identified as a meaningful player in the regulation of type 2 lymphocyte responses in steady-state conditions and after infection with *Nippostrongylus brasiliensis* (*N. brasiliensis*). Analysis of publicly available single cell RNA-sequencing data revealed one subset of enteric cholinergic neurons, termed NMU-ergic neurons, which express genes encoding known regulators of ILC2s (*Nmu*, *Calcb*, *Chat*) as well as molecules (*Il13ra1*, *Il4ra*, *Il7*) not previously implicated in intestinal neuro-immune interactions. Generation of a mouse strain, *NmuCre-iRFP670*, enabled the interrogation of how NMU-ergic neurons regulate type 2 immunity. Confocal microscopy imaging of tissues from an *NmuCre-iRFP670* fate mapper revealed that ILC2s closely associate with enteric NMU-ergic in either steady-state conditions or after infection with *N. brasiliensis*. Conditional deletion of *Il4ra* or *Il7* in NMU-ergic neurons established novel mechanisms of intestinal neuro-immune interactions. Flow cytometric analysis of lymphocytes following *Il4ra* deletion in NMU-ergic neurons unveiled an interesting mechanism by which type 2 cytokines can affect NMU-ergic neuronal regulation of ILC2 and Th2 cell responses across different mucosal sites during infection with *N. brasiliensis*. Furthermore, flow cytometric analysis of lymphocyte populations following *Il7* deletion in NMU-ergic neurons demonstrated that these neurons represent a novel and important source of IL-7 for lymphocytes at steady-state conditions, but not during *N. brasiliensis* infection. To further dissect the dynamic interactions between NMU-ergic neurons and ILC2s, a chemogenetic system using Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) was established using the *NmuCre-iRFP670* strain. The establishment and study of *NmuCre-iRFP670* strain has elucidated a significant intestinal neuro-immune circuit for the regulation and potentiation of type 2 immune responses.Item Embargo Molecular Mechanisms of SURF4- mediated Protein SecretionMaldutyte, JulijaProtein secretion is an essential process that drives organelle biogenesis, cell growth and communication. Once synthesised and processed in the Endoplasmic Reticulum (ER), secretory proteins are incorporated into transport carriers that are generated by the COPII coat. Efficient and accurate cargo incorporation into ER-derived carriers is driven by transmembrane cargo receptors. ER export receptors are especially important for secretion of soluble cargo as they provide a transmembrane bridge to the cytosolic COPII coat. This study focused on SURF4, a cargo receptor for soluble cargo. I characterised the spectrum of SURF4 clients in HEK-293TREx and Huh7 cells using mass spectrometry. Amongst the top hits, I identified many oligomeric Ca2+-binding proteins, including Cab45 and NUCB1. Using *in vitro* translation and sitespecific photo-crosslinking, I showed direct co-translational SURF4 engagement with the cargo via an N-terminal ER-ESCAPE motif, exposed after signal peptide cleavage. This result supports a fast-export mechanism for preventing improper cargo oligomerization in an early organelle, and for the first time shows a cargo receptor can interact with an unfolded and incompletely translated client. Furthermore, with the aid of structural prediction-guided mutagenesis and site-specific cross-linking, I mapped a putative ER-ESCAPE interaction surface on SURF4 to an ER lumen-facing pocket. Additionally, my work examined SURF4 interactions with the COPII cargo adaptor, SEC24. Whereas Cab45 and NUCB1 use SEC24C/D isoforms, a previously described SURF4 cargo, PCSK9, which exposes ER-ESCAPE after propeptide autocleavage, exclusively employs SEC24A. I show that this discrepancy is due to a PCSK9 requirement for a co-receptor, TMED10. Using a protein-protein interaction assay and various SEC24 and SURF4 binding mutants, I showed that SURF4 uses C-terminal hydrophobic and acidic amino acids to bind the B-site on SEC24C. Conversely, SEC24A recognises a cytosolic loop on SURF4 via the D-site, while the B-site is likely occupied by TMED10 cytosolic tail. Finally, knock-down of TMED10 both reduced the SURF4-SEC24A interaction and abrogated PCSK9 secretion. Altogether, my PhD work defined the SURF4 cargo repertoire and described the biochemical basis for differential cargo recruitment into COPII vesicles.Item Open Access Using Translational Switching to Investigate the SCN ClockworkMcManus, DavidThe suprachiasmatic nucleus (SCN) of the hypothalamus is the principal clock driving circadian rhythms of physiology and behaviour that adapt mammals to environmental cycles. Timekeeping in the SCN is underpinned by a self-sustaining cell-autonomous transcriptional/translational delayed feedback loop (TTFL), whereby negative regulators inhibit their own transcription. The positive regulators CLOCK and BMAL drive transcription of the negative regulators Period1/2 and Cryptochrome1/2 via E-BOX regulatory sequences. PER/CRY mediated repression of BMAL/CLOCK closes the feedback loop allowing the cycle to begin again every 24 hours. In the SCN, synchronisation of the individual cell-autonomous clocks is achieved by circuit level signalling mediated via interneuronal neuropeptidergic interactions, as well as communication between astrocytes and neurons. The result is a robust SCN network that allows timekeeping to be maintained even when SCN are cultured as organotypic slices ex vivo. Thus, the SCN provides a highly tractable model for studying circadian timekeeping. In a formal sense, the TTFL motif is readily compatible with limit-cycle models, where the oscillation of key components (called state variables) entirely underpins the phase of the oscillation. In Neurospora and Drosophila the negative regulators Frequency (FRQ) and Period (Per) have been identified as state variables of their respective TTFLs. However, the identity of state variables in the SCN, or indeed if the simple limit cycle model is even compatible with SCN circadian oscillations, is less clear. Key to testing a component for a role as a state variable is reversible and conditional expression of a transgenic copy. By using genetic code expansion (GCE), it is possible to create translational switches whereby the translation of a transgene is conditional on the provision of a non-canonical amino acid. Incorporation of an ectopic amber stop codon (TAG) into the coding sequence of a gene of interest causes premature termination of translation and prevents generation of a functional protein. However, an orthogonal amino-acyl-tRNA synthetase/tRNACUA pair that specifically incorporates a non-canonical amino acid (ncAA) at the amber stop codon allows translational read-through when the amino acid is present. Delivery of this pair into the SCN, along with a translationally switchable gene of interest, can be achieved by use of adeno-associated virus (AAV) vectors, and ncAA can be added to culture medium. In this work I developed novel translationally switchable Bmal1 (tsBMAL1) and Period2 (tsPER2), as well as using a translationally switchable copy of CRY1 (tsCRY1) developed previously in the lab, to investigate the SCN clockwork. First, I show how generation of tsBMAL1 provided conditional and reversible control of transgenic expression in the SCN. Bmal1 knockout mice show behavioural arrhythmicity, however SCN slices from p10 mice showed low amplitude and highly variable oscillations. Reversible tsBMAL1 expression following AlkK provision reorganised the noisy oscillations and induced stable circadian rhythms. Then, by using tsCRY1 and tsPER2 constructs, I assessed the extent to which either CRY1 or PER2 could be considered state variables and the limits of the limit cycle model to describe circadian rhythmicity in organotypic SCN slices. I conclude that both CRY1 and PER2 display some of the hallmarks of state variables found in simpler limit cycle systems like the Neurospora clock but are also acting within a more complex cycle that underpins SCN timekeeping.Item Embargo DNA Translesion Synthesis Factors are Essential for Mammalian Embryonic Germ Cell DevelopmentShah, PranayGerm cells are responsible for the transmission of genetic and epigenetic information between generations and hence alterations to the genome can have effects across generations. Faithful propagation of the genome is therefore of unique importance as mutations in the germline are the source of genetic variation on which evolution acts but also the drivers of sporadic, severe inherited diseases. Thus, the balance between generating genetic diversity and minimising the risk of genetic disorders is critical. However, the regulation of this balance and mechanisms for maintaining germline genome stability are incompletely understood. DNA mutations can arise from errors in replication, mis-repair of damaged DNA or the action of error-prone pathways such as DNA translesion synthesis (TLS). TLS enables DNA replication to be completed when the replication machinery stalls at impediments. In order to bypass these blocks, specialised factors are employed to ensure the completion of replication. However, due to properties of the factors involved in TLS, this occurs at the potential cost of introducing DNA mutations. The results presented in this thesis find that core components of the TLS pathway are essential in the mammalian germline but dispensable for the growth and homeostasis of somatic tissues. We find that these factors are required for fertility due to a role in primordial germ cells (PGCs). Development of PGCs entails extensive cell proliferation and in the absence of TLS initiation (PcnaK164R/K164R or Rev1-/-) or extension (Rev7-/-) there is a >150-fold reduction in PGC number. Consistent with a role for TLS, PGCs in mutant embryos accumulate unresolved DNA damage and have abnormal cell cycle kinetics which are found to be unique to the germ cell compartment. Loss of PGCs in TLS-deficient embryos temporally coincides with epigenetic reprogramming. During this process, wildtype PGCs alter histone tail modifications and lose the majority of DNA methylation marks. Strikingly, we find that in the absence of TLS factors there is a failure of DNA demethylation implicating this pathway in the successful loss of methylation marks. Moreover, mutant PGCs fail to activate the germ cell transcriptional program, preventing the progression of PGC development. The findings, therefore, reveal a role for TLS factors in shaping germline genome stability and ensuring correct DNA demethylation in PGCs.Item Open Access Identification of host factors required for cytosol entry by Shigella flexneri: Results of a genome-wide CRISPR/Cas9 screenO'Donovan, ConorThe Gram-negative bacterial pathogen *Shigella flexneri* remains a globally significant cause of morbidity and mortality. *Shigella* induces its uptake into colonic epithelial cells via a short-lived vacuole, and lyses the vacuole membrane to gain entry to the host cytosol. As a professional cytosol-dwelling pathogen, *Shigella* then overcomes cell-autonomous host defences to establish its replicative niche, before spreading into adjacent enterocytes. Although cytosol entry is a key step in its cellular pathogenesis, the mechanisms by which *Shigella* achieves this are not fully understood. To identify essential host factors and key pathways required by *Shigella* in the early stages of its pathogenesis, I developed and carried out a genome-wide CRISPR/Cas9 knockout screen using a tissue culture model of epithelial cell infection. I used a hierarchical validation method which combined arrayed high-content microscopy and semi-automated image analysis to confirm a novel set of host factors which facilitate *Shigella* infection. I then established in greater detail the roles of three of the major identified hits, using a further panel of microscopy, flow cytometry and intracellular replication assays. I showed that the multifunctional protein KHDRBS1, known to act as a signalling adaptor and regulator of inflammatory responses, facilitates cytosol entry and replication by *Shigella*. I showed that the transcriptional regulator YY1 is also required for cytosol entry and replication. Both KHDRBS1 and YY1 are likely to act indirectly in *Shigella* infection by their impact on host processes. The adaptor protein (AP)-3 subunit AP3M2 is involved in protein sorting in the post-Golgi endosomal network. I showed that AP3M2 is required for *Shigella* invasion and cytosol entry, and that it enriches transiently in the vicinity of the bacterial entry focus. Lastly, I found that AP3M2 is also targeted by *Shigella* for degradation in a host proteasome- dependent manner, along with additional subunits of the AP-2 and AP-3 complexes. Overall, this work identifies and characterises three novel host factors required for the cellular pathogenesis of *Shigella* infection, and provides a dataset that better informs our understanding of the host-*Shigella* interface. These findings complement current models of invasion and vacuole rupture by *Shigella*, and will help to direct the rational development of improved vaccination and therapeutic strategies.Item Open Access Structural studies of the in vitro assembly of tau and α-synuclein amyloidsLövestam, SofiaNeurodegenerative diseases are characterised by the accumulation of filamentous protein aggregates, which are composed of amyloids. Cryo-EM studies of amyloid filaments isolated from human brains have revealed that specific conformers of tau and α-synuclein are associated with different diseases. These findings suggest that specific molecular mechanisms underlie the formation of filaments in the different diseases. However, studying the molecular mechanisms of amyloid assembly in *post mortem* brains is difficult to study. In my PhD research, I studied the molecular mechanisms of amyloid formation for tau and α-synuclein by developing in vitro amyloid assembly reactions that replicate the same structures as observed in diseased brains. My results are divided into three parts. First, I describe the seeded assembly of recombinant α-synuclein filaments with seeds from brains with Multiple System Atrophy (MSA), and show that seeded assembly does not necessarily replicate the structures of the seeds. The results in this section have important implications when interpreting seeded assembly assays. In the future, it will be important to identify the factors that determine which structures are formed in seeded aggregation experiments. Second, I focused on the *in vitro* assembly of tau. I identified truncated tau constructs, lacking the N- and C-termini, and the *in vitro* assembly conditions, which can accurately replicate disease-relevant folds observed in Alzheimer’s Disease (AD) and Chronic Traumatic Encephalopathy (CTE). These findings are the first to describe the formation of disease specific structures of any amyloid, using recombinant protein *in vitro*. The conditions identified in this study can be used for the development of high affinity binders which are specific to the AD and CTE folds. Finally, I studied the time-resolved filament formation of tau into AD and CTE filament folds. I show that tau filament formation is a step-wise and dynamic process, characterised by the formation of initial intermediate filaments, which I call First Intermediate Amyloids (FIAs), that subsequently mature into AD and CTE folds through a variety of later intermediate amyloid structures. This study is the first to provide a tangible structural characterisation of intermediates of amyloid filament formation.