The studies discussed in this thesis unify experimental and theoretical techniques, both established and novel, in investigating the problem of how a protein that binds specific sites on DNA translocates to, recognizes, and stably binds to its target site or sites. The thesis is organized into two parts. Part I outlines the history of the problem and the theory and experiments that have addressed the problem and presents an apparent incompatibility between efficient search and stable, specific binding. To address this problem, we elaborate a model of protein-DNA interaction in which the protein may bind DNA in either a search (S) mode or a recognition (R) mode. The former is characterized by zero or weak sequence-dependence in the binding energy, while the latter is highly sequence-dependent. The protein undergoes a random walk along the DNA in the S mode, and if it encounters its target site, must undergo a conformational transition into the R mode. The model resolves the apparent paradox, and accounts for the observed speed, specificity, and stability in protein-DNA interactions. The model shows internal agreement as regards theoretical and simulated results, as well as external agreement with experimental measurements. Part II reports on research that has tested the applicability of the two-mode model to the tumor suppressor transcription factor p53. It describes in greater depth the experimental techniques and findings up to the present work, and introduces the techniques and biological system used in our research. We employ single-molecule optical microscopy in two projects to study the diffusional kinetics of p53 on DNA. The first project measures the diffusion coefficient of p53 and determines that the protein satisfies a number of requirements for the validity of the two-mode model and for efficient target localization. The second project examines the sequence-dependence in p53's sliding kinetics, and explicitly models the energy landscape it experiences on DNA and relates features of the landscape to observed local variation in diffusion coefficient. The thesis closes with proposed extensions and complements to the projects, and a discussion of the implications of our work and its relation to recent developments in the field.

Gene expression is a fundamental process in the cell and is made up of two parts – the information flow from DNA to RNA, and from RNA to protein. Here, we examined specific sub-processes in Escherichia coli gene expression using newly available tools that permit genome-wide analysis. We begin our studies measuring mRNA and protein abundances in single cells by single-molecule fluorescence microscopy, and then focus our attention to studying RNA generation and degradation by high throughput sequencing. The details of the dynamics of gene expression can be observed from fluctuations in mRNA and protein copy numbers in a cell over time, or the variations in copy numbers in an isogenic cell population. We constructed a yellow fluorescent fusion protein library in E. coli and measured protein and mRNA abundances in single cells. At below ten proteins per cell, a simple model of gene expression is sufficient to explain the observed distributions. At higher expression levels, the distributions are dominated by extrinsic noise, which is the systematic heterogeneity between cells. Unlike proteins which can be stable over many hours, mRNA is made and degraded on the order of minutes in E. coli. To measure the dynamics of RNA generation and degradation, we developed a protocol using high throughput sequencing to measure steady-state RNA abundances, RNA polymerase elongation rates and RNA degradation rates simultaneously with high nucleotide-resolution genome-wide. Our data shows that RNA has similar lifetime at all positions throughout the length of the transcript. We also find that our polymerase elongation rates measured in vivo on a chromosome are generally slower than rates measured on plasmids by other groups. Studying nascent RNA will allow further understanding of RNA generation and degradation. To this end, we have developed a labeling protocol with a nucleoside analog that is compatible with high throughput sequencing.

Bacterial cells reproduce by doubling in size and dividing. The molecular control systems which regulate the cell cycle must do so in a manner which maintains a similar cell size over many generations. A cell can under conditions of fast growth conclude cell cycles in shorter time than the time required to replicate its chromosome. Under such conditions several rounds of replication are maintained in parallel and a cell will inherit replication processes which were initiated by an ancestor. To accomplish this the cell has to initiate and terminate one round of replication during each cell cycle. To investigate the effects of the cell cycle on gene-regulation in the gut bacterium Escherichia coli, an experimental method combining microfluidics, single molecule fluorescence microscopy and automated analysis capable of acquiring an arbitrary number of complete cell cycles per experiment was developed. The method allowed for the rapid exchange of the chemical environment surrounding the cells. Using this method it was possible to measure the dissociation time of the transcription factor molecule, LacI-Venus, from the native lactose operator sequence, lacO1, and an artificially strong operator, lacOsym, in vivo. The results indicated that regulation of gene-expression from the lactose operon does not occur at equilibrium in living cells. Furthermore, by studying the intracellular location of non-specifically interacting transcription factor molecules it was possible to determine that these do not form long-lived gradients inside the cell as was previously proposed. By studying the replication machinery and the origin of replication it was found that replication is initiated according to a cell volume per origin which did not vary over different growth conditions. Further, division timing was found to be determined by the initiation event to occur after a fixed time-delay. A consequence of this mode of regulation is an uncertainty relation between the size at birth and the cell cycle time, in which cells will vary more in in the cycle time during conditions of slow growth as compared to fast growth and vary more in birth length during conditions of fast growth as compared to slow growth.

A microscopia de fluorescência é uma das técnicas mais poderosas disponíveis atualmente, uma vez que proporciona uma combinação excepcional de alta sensibilidade na detecção, alta especificidade, além de ser consideravelmente não invasiva. Avanços recentes permitiram a detecção em resolução de subdifração, o que eleva sua potencialidade de investigação de um maior número de sistemas e, consequentemente, de avanço científico. O estudo de novas sondas fluorescentes é de fundamental importância para a aplicação em métodos avançados de microscopia óptica. Na primeira vertente da pesquisa, Capítulo 2, foi realizado o estudo fotofísico de uma série de compostos bisarilados derivados do anidrido maleico e de maleimidas sintetizados pela reação de Heck-Matsuda. Visando o aprimoramento do design dessas moléculas, foi realizada a ciclização fotoquímica de tais compostos, resultando em moléculas com anéis condensados, nomeados como derivados de fenantreno, as quais proporcionaram maior estabilidade fotoquímica. A dinâmica do estado excitado remete ao efeito push-pull, em que há um deslocamento de carga notável, mas não completo. Para os compostos com a substituição 4-hidroxifenil foi observado um processo de deslocamento de carga combinado com uma transferência de próton no estado excitado assistida por solvente. Ademais, o estudo dos compostos derivados de fenantreno em microscopia confocal demonstrou que as propriedades locais do solvente afetam a dinâmica de relaxação de fluorescência em diferentes meios condensados e que os mesmos são passíveis de serem aplicados a técnicas avançadas de microscopia de fluorescência. A segunda vertente desta tese, Capítulo 3, explora um sistema biológico em nível de uma única molécula. Especificamente, este capítulo concerne à investigação de uma metodologia ótima para a marcação fluorescente de DNA em sequência específica, através de microscopia de fluorescência com super-resolução. As reações foram conduzidas utilizando uma metodologia de marcação de duas etapas, de acordo com o princípio mTAG. Na primeira etapa, grupamentos contendo alquino terminal, azida ou amina primária são transferidos do cofator análogo ao S-adenosil-L-metionina para o DNA através de uma enzima metiltransferase. Foi utilizada a enzima M.TaqI, a qual tem como alvo a sequência 5\'- TGCA -3\' para modificação. Na segunda etapa é realizado o acoplamento do fluoróforo aos sítios funcionais do plasmídeo (pUC19) através de reações químicas bioortogonais, tais como reação click catalisada por cobre (CuAAC), reação click na ausência de cobre (SPAAC) e acoplamento do grupo amina primária com NHS-éster. Também foi desenvolvida uma metodologia direta de uma etapa, na qual o fluoróforo é diretamente transferido do cofator análogo para o DNA em uma única etapa reacional. Para acompanhar o desempenho das reações foi desenvolvido um ensaio single-molecule para a contagem do número de moléculas de corante ligadas a plasmídeos individuais. A topologia dos plasmídeos após a marcação foi investigada por imagens de AFM em alta resolução. A combinação de ambas as análises demonstrou que a reação SPAAC assim como a reação direta de uma etapa promoveram uma marcação fluorescente quase completa e a técnica de AFM confirmou que o acoplamento de fluoróforos não induziu danos à estrutura dos plasmídeos, os quais preservaram sua morfologia nativa, superenrolada. Além disso, os plasmídeos marcados foram aplicados com sucesso a procedimentos de transfecção em células de mamíferos, indicando que o DNA reteve sua capacidade de codificar informação genética, mesmo na presença de fluoróforos ligados. / Fluorescence microscopy is one of the most powerful techniques currently available, since it provides the unique combination of a high sensitivity in detection, a high specificity, and a considerable non-invasiveness. Recent developments have allowed the detection at a sub-diffraction resolution, which elevates its potentiality to investigate several systems and hence to go further in science. The study of new fluorescent probes is crucial for the application in advanced methods in optical microscopy. In the first extent of this research, Chapter 2, a photophysical study of maleic anhydride and maleimide derivatives, synthesized by the Heck-Matsuda reaction, was performed. Aiming at the improvement of the design of these molecules, a photochemical cyclization was carried out, resulting in molecules with condensed rings, termed as phenanthrene derivatives, which promoted more photochemical stability. The excited state dynamics rely on the push-pull effect, in which a notable, but not complete, charge shift takes place. For the compounds with a 4-hydroxyl substituent, a charge shift combined with an excited state solvent-assisted proton transfer was observed. Additionally, the confocal microscopy study of the phenanthrene derivatives showed that the local properties of the solvent modulate the fluorescence relaxation dynamics in condensed media and hence such dyes can be potential candidates for use in advanced fluorescence microscopy techniques. The second extent of this thesis, Chapter 3, explores a biological system at the single-molecule level. Specifically, this chapter concerns to an investigation of an optimal sequence-specific DNA fluorescent labelling, using super-resolution fluorescence microscopy. The reactions were performed using a two-step methodology, according to the mTAG approach. In the first step, moieties containing a terminal alkyne, azide, or primary amine group are transferred from an S-adenosyl-L-methionine analogue cofactor to the DNA by a methyltransferase enzyme. Herein, the enzyme M.TaqI was used, which targets the 5\'- TCGA -3\' sequence for modification. In the second step, a fluorophore is coupled to the functional sites of the plasmid (pUC19) using bio orthogonal reactions, such as the click reaction catalysed by copper (CuAAC), the copper-free click reaction (SPAAC), and the amino-to-NHS-ester coupling reaction. A direct one-step approach in which the fluorophore is directly transferred to the DNA from the analogue cofactor in a single reaction step, was also developed. A single-molecule assay was developed for counting the number of fluorophores associated with the individual plasmids. The topology of the plasmids after labelling was also investigated by high-resolution AFM imaging. Combining both analysis, the SPAAC as well as the direct one-step reactions were found to promote near-complete labelling and the AFM showed that the fluorophore coupling did not damage the structure of the plasmids and that their native, supercoiled, morphology was preserved. Moreover, labelled plasmids were successfully applied for transfection into mammalian cells, implying that the DNA retained its ability to encode genetic information, even while carrying bound fluorophores.

La microscopie de molécule unique (single-molecule microscopy, SMM) regroupe un ensemble de techniques pour la biologie moléculaire et cellulaire permettant de visualiser le mouvement de molécules biologiques individuelles. Néanmoins, les techniques SMM imposent de fortes contraintes en ce qui concerne les luminophores utilisés. Récemment, un nouveau luminophore appelé «particule à conversion ascendante» (upconverting nanoparticles, UCNP) a attiré l'attention de la communauté scientifique en raison de son émission efficace de lumière visible après une excitation par de la lumière infrarouge. Cette propriété fait des UCNPs un luminophore très intéressant pour les applications biologiques : l'excitation infrarouge permet d'éliminer l’autofluorescence, généralement associé à une excitation dans la gamme du visible. De plus, la photostabilité extrême des UCNP et l’absence de photoclignotement sont également de précieux atouts pour les expériences SMM. L’objectif de cette thèse était d’adapter les UCNPs aux applications SMM, avec le but ultime d’exploiter leurs propriétés uniques pour améliorer les performances des expériences SMM. Au cours du projet, les protocoles de dispersion des UCNPs dans des tampons aqueux ont été optimisées pour conserver une bonne monodispersité des particules; l'efficacité des UCNPs dans les expériences de transfert résonant d'énergie en particule unique a été estimée; des protocoles pour l'imagerie d'UCNPs uniques ont été développés; et la preuve de concept de l'utilisation des UCNPs dans des expériences de suivi de molécules uniques à la surface de cellules vivantes a été réalisée. Finalement, ces résultats forment une base solide pour de futures expériences SMM utilisant les UCNPs. / Single-molecule microscopy (SMM) is a powerful set of techniques for molecular and cell biology that allows visualizing the movement of individual biological molecules, but has strict requirements towards the utilized luminophores. Recently, a new luminophore called upconverting particles (UCNPs) gained attention of the research community due to their efficient emission of visible light upon excitation with infrared light. This property makes UCNPs a valuable luminophore for biological applications due to the elimination of autofluorescence background, commonly associated with regular visible light excitation. Extreme photostability of UCNPs and absence of sporadic photoswitching are also valuable for SMM experiments. The objective of this thesis was to adapt UCNPs to SMM applications, with the ultimate goal of exploiting their unique properties towards superior performance of SMM experiments. During the project, protocols for dispersing UCNPs in aqueous buffers were streamlined to provide superior particle monodispersity; the efficiency of UCNPs in single-molecule resonance energy transfer experiments was estimated; protocols for single-molecule imaging with UCNPs were developed; and a proof-of-concept system for targeted single-molecule tracking with UCNPs in live cells was demonstrated. Overall, these findings will serve as a foundation towards robust SMM assays based on UCNPs.

A microscopia de fluorescência é uma das técnicas mais poderosas disponíveis atualmente, uma vez que proporciona uma combinação excepcional de alta sensibilidade na detecção, alta especificidade, além de ser consideravelmente não invasiva. Avanços recentes permitiram a detecção em resolução de subdifração, o que eleva sua potencialidade de investigação de um maior número de sistemas e, consequentemente, de avanço científico. O estudo de novas sondas fluorescentes é de fundamental importância para a aplicação em métodos avançados de microscopia óptica. Na primeira vertente da pesquisa, Capítulo 2, foi realizado o estudo fotofísico de uma série de compostos bisarilados derivados do anidrido maleico e de maleimidas sintetizados pela reação de Heck-Matsuda. Visando o aprimoramento do design dessas moléculas, foi realizada a ciclização fotoquímica de tais compostos, resultando em moléculas com anéis condensados, nomeados como derivados de fenantreno, as quais proporcionaram maior estabilidade fotoquímica. A dinâmica do estado excitado remete ao efeito push-pull, em que há um deslocamento de carga notável, mas não completo. Para os compostos com a substituição 4-hidroxifenil foi observado um processo de deslocamento de carga combinado com uma transferência de próton no estado excitado assistida por solvente. Ademais, o estudo dos compostos derivados de fenantreno em microscopia confocal demonstrou que as propriedades locais do solvente afetam a dinâmica de relaxação de fluorescência em diferentes meios condensados e que os mesmos são passíveis de serem aplicados a técnicas avançadas de microscopia de fluorescência. A segunda vertente desta tese, Capítulo 3, explora um sistema biológico em nível de uma única molécula. Especificamente, este capítulo concerne à investigação de uma metodologia ótima para a marcação fluorescente de DNA em sequência específica, através de microscopia de fluorescência com super-resolução. As reações foram conduzidas utilizando uma metodologia de marcação de duas etapas, de acordo com o princípio mTAG. Na primeira etapa, grupamentos contendo alquino terminal, azida ou amina primária são transferidos do cofator análogo ao S-adenosil-L-metionina para o DNA através de uma enzima metiltransferase. Foi utilizada a enzima M.TaqI, a qual tem como alvo a sequência 5\'- TGCA -3\' para modificação. Na segunda etapa é realizado o acoplamento do fluoróforo aos sítios funcionais do plasmídeo (pUC19) através de reações químicas bioortogonais, tais como reação click catalisada por cobre (CuAAC), reação click na ausência de cobre (SPAAC) e acoplamento do grupo amina primária com NHS-éster. Também foi desenvolvida uma metodologia direta de uma etapa, na qual o fluoróforo é diretamente transferido do cofator análogo para o DNA em uma única etapa reacional. Para acompanhar o desempenho das reações foi desenvolvido um ensaio single-molecule para a contagem do número de moléculas de corante ligadas a plasmídeos individuais. A topologia dos plasmídeos após a marcação foi investigada por imagens de AFM em alta resolução. A combinação de ambas as análises demonstrou que a reação SPAAC assim como a reação direta de uma etapa promoveram uma marcação fluorescente quase completa e a técnica de AFM confirmou que o acoplamento de fluoróforos não induziu danos à estrutura dos plasmídeos, os quais preservaram sua morfologia nativa, superenrolada. Além disso, os plasmídeos marcados foram aplicados com sucesso a procedimentos de transfecção em células de mamíferos, indicando que o DNA reteve sua capacidade de codificar informação genética, mesmo na presença de fluoróforos ligados. / Fluorescence microscopy is one of the most powerful techniques currently available, since it provides the unique combination of a high sensitivity in detection, a high specificity, and a considerable non-invasiveness. Recent developments have allowed the detection at a sub-diffraction resolution, which elevates its potentiality to investigate several systems and hence to go further in science. The study of new fluorescent probes is crucial for the application in advanced methods in optical microscopy. In the first extent of this research, Chapter 2, a photophysical study of maleic anhydride and maleimide derivatives, synthesized by the Heck-Matsuda reaction, was performed. Aiming at the improvement of the design of these molecules, a photochemical cyclization was carried out, resulting in molecules with condensed rings, termed as phenanthrene derivatives, which promoted more photochemical stability. The excited state dynamics rely on the push-pull effect, in which a notable, but not complete, charge shift takes place. For the compounds with a 4-hydroxyl substituent, a charge shift combined with an excited state solvent-assisted proton transfer was observed. Additionally, the confocal microscopy study of the phenanthrene derivatives showed that the local properties of the solvent modulate the fluorescence relaxation dynamics in condensed media and hence such dyes can be potential candidates for use in advanced fluorescence microscopy techniques. The second extent of this thesis, Chapter 3, explores a biological system at the single-molecule level. Specifically, this chapter concerns to an investigation of an optimal sequence-specific DNA fluorescent labelling, using super-resolution fluorescence microscopy. The reactions were performed using a two-step methodology, according to the mTAG approach. In the first step, moieties containing a terminal alkyne, azide, or primary amine group are transferred from an S-adenosyl-L-methionine analogue cofactor to the DNA by a methyltransferase enzyme. Herein, the enzyme M.TaqI was used, which targets the 5\'- TCGA -3\' sequence for modification. In the second step, a fluorophore is coupled to the functional sites of the plasmid (pUC19) using bio orthogonal reactions, such as the click reaction catalysed by copper (CuAAC), the copper-free click reaction (SPAAC), and the amino-to-NHS-ester coupling reaction. A direct one-step approach in which the fluorophore is directly transferred to the DNA from the analogue cofactor in a single reaction step, was also developed. A single-molecule assay was developed for counting the number of fluorophores associated with the individual plasmids. The topology of the plasmids after labelling was also investigated by high-resolution AFM imaging. Combining both analysis, the SPAAC as well as the direct one-step reactions were found to promote near-complete labelling and the AFM showed that the fluorophore coupling did not damage the structure of the plasmids and that their native, supercoiled, morphology was preserved. Moreover, labelled plasmids were successfully applied for transfection into mammalian cells, implying that the DNA retained its ability to encode genetic information, even while carrying bound fluorophores.

Des matériaux ayant des propriétés émissives spécifiques peuvent être obtenus par l'organisation contrôlée de fluorophores aux échelles moléculaire, nano- et micro-métrique. Dans ce travail, l'émission de lumière bleue polarisée est obtenue par l'auto-assemblage hautement anisotrope de n-acènes alcoxylés en nano-rubans. Des techniques de microscopie de fluorescence ont été utilisées pour déterminer le mécanisme de leur croissance et ont été combinées à la cristallographie aux rayons X pour déterminer l'empilement moléculaire dans les nano-objets. L'étude a révélé que la formation des nano-rubans est induite non seulement par le mécanisme de maturation d'Ostwald très commun, mais aussi par une croissance par attachement orienté rarement démontré dans des systèmes organiques. En plus des techniques plus courantes, la microscopie en polarisation de fluorescence de molécules uniques a contribué à caraxctériser l'emplilement moléculaire, bien que les nano-objets à haute densité en chromophore constituent des échantillons très difficiles à étudier. Dans ce travail, les propriétés des nano-rubans ont été contrôlées au niveau microscopique par les conditions de croissance, ainsi que par l'addition de dopants. Ainsi, en combinant différentes molécules et une réaction photochimique sous microscopie, des rubans à motifs colorés sub-micrométriques ont été obtenus. Par ailleurs, l'assemblage orthogonal a été exploité pour développer des réseaux interpénétrés. Ces derniers se distinguent par une émission à double couleur, un transfert d'énergie entre objets et une électroluminescence aux jonctions. / Materials with specific emissive properties can be obtained by the controlled organization of fluorophores at the molecular, nano- and microscales. In this work, polarized blue light emission is achieved by the highly anisotropic self-assembly of alkoxylated n-acenes into nano-ribbons. Fluorescence microscopy techniques were used to determine the growth mechanism and were combined to X-ray crystallography to determine the molecular packing in the nano-objects. The study revealed that the formation of the nano-ribbons is induced not only by the very common Ostwald ripening mechanism but also by an oriented attachnment growth, rarely observed with such evidence in organic systems. Besides more common techniques, single molecule fluorescence polarization microscopy contributed to characterize the molecular packing, although the nano-objects with high chromophore density represent very challenging samples. In this work, the properties of the nano-ribbons have been controlled at the microscopic level by the growth conditions, as well as by the addition of dopants Thereby, combining different molecules and photochemistry at the sub-micrometer scale under the microscope, colorful patterned ribbons could be obtained. In addition, orthogonal assembly was exploited to grow interpenetrated networks. The latter demonstrated dual color-emission, as well as inter-object energy transfer and electroluminescence at junctions.

Der eukaryotische Zellzyklus ist auf allen Ebenen der Genexpres- sion reguliert. Sowohl breit angelegte genetische Screens als auch funktionale Studien zu den beteiligten Proteinen haben unser Ver- ständnis dieses fundamentalen Prozesses geprägt. In dieser Arbeit behandle ich räumliche Aspekte der post-transkriptionalen Regulation des Zellzyklus, die mit lichtmikroskopischen Einzelzell- und Einzel- molekülmethoden experimentell zugänglich werden. Insbesondere untersuchte ich die subzelluläre Lokalisierung der messenger RNA von CLB2, einem zentralen Regulator der Mitose im eukaryotischen Modellorganismus Saccharomyces cerevisiae (Bierhefe). Frühere Studien zeigten, dass diese RNA sich im Laufe des vegetativen Zellwachstums in der entstehenden Tochterzelle, der Knospe, anreichert. Mithilfe modernster Fluoreszenzmikroskopie charakterisierte ich die Bewe- gung und Verteilung einzelner CLB2 messenger RNA-Moleküle auf Zeitskalen von Millisekunden bis hin zur Generationszeit dieser He- fen. Ich zeigte, dass sich mit Hilfe von Multifokusmikroskopie unter Verwendung optimierter Fluoreszenzmarker und der Entwicklung objektiver Analysemethoden die Bewegung einzelner RNA-Moleküle zwischen Mutterzelle und Knospe nachvollziehen lässt. Dazu präsen- tiere ich eine Methode um die beobachteten Trajektorien der messenger RNA mathematischen Analysen der Systembiologie zugänglich zu machen. Weiterhin gab die Beobachtung der Verteilung einzelner CLB2 messenger RNA Moleküle über den Zellzyklus hinweg mittels einer neuartigen Lichtblattmikroskopie (Lattice Light Sheet Microscopy) Hinweise auf eine bisher unbekannte Dynamik in der Lokalisierung dieser messenger RNA. Die hier entwickelten Methoden ermöglichen eine quantitative Untersuchung räumlicher Aspekte der posttranskrip- tionalen Zellzyklusregulation. / The eukaryotic cell cycle is regulated on all levels of gene expression. Genetic screens and functional studies of the involved proteins have shaped our understanding of this fundamental process. In this thesis I use single cell and single molecule light microscopy methods to investigate spatial aspects of post-transcriptional cell cycle regulation. I investigated the subcellular localization of CLB2 mRNA, a central regulator of mitosis in the eukaryotic model organism Saccharomyces cerevisiae (baker’s yeast). Previous studies have shown that that this messenger RNA is enriched in the emerging daughter cell, the bud, during vegetative growth. Using pre-commercial fluorescence micro- scopes I characterized the dynamics and partitioning of single CLB2 mRNA on time scales from milliseconds to the generation time of this yeast. I demonstrate that using aberration corrected multifocus mi- croscopy, optimized fluorescent markers, and here developed objective analysis methods, the translocation of single mRNA molecules be- tween mother and bud can be observed. In addition, I report a method to make these trajectories available for the mathematical approaches of Systems Biology. Further, the observation of single CLB2 mRNA partitioning throughout the cell cycle with the use of lattice light sheet microscopy suggested a previously unknown localization behavior of the transcript. The methods developed here enable a quantitative analysis of spatial aspects of post-transcriptional cell cycle regulation.

Les ARNm sont des molécules centrales pour la régulation des gènes, aidant à convertir l'information génétique stockée dans l'ADN en protéines fonctionnelles. En tant que polymère simple brin, mesurant des centaines à des milliers de nucléotides, les ARNm peuvent former des structures secondaires et tertiaires étendues formant des particules appelés ribonucléoprotéines messagères (RNPm) en s’assemblant avec des protéines. L'organisation 3D des (pré-)RNPm influence de nombreux aspects de leur métabolisme, incluant la régulation de leur maturation, de leur export et de leur traduction dans le cytoplasme. Malgré leur importance, notre compréhension de l'organisation structurelle des (pré-)RNPm in vivo, et des principes qui la régissent est minime. Au cours de ma thèse, j'ai analysé l'organisation des (pré-)mRNP en développant une vision centrée sur l'ARN. Pour cela, j'ai mis en place une approche combinant l'hybridation in situ d'ARN monomoléculaire (smFISH) avec la microscopie à illumination structurée (SIM) et l'ai utilisée pour étudier l'organisation des mRNP dans le noyau et le cytoplasme. Nos résultats suggèrent que l'organisation (pré-)mRNP varie à différents stades de sa vie. Nous montrons que l'empaquetage (pré-)mRNP commence de manière co-transcriptionnelle, avec des introns organisés en conformations compactes. Cette organisation est modifiée au cours de la transcription au fur et à mesure que la polymérase se déplace le long du gène, assemblant finalement un intron avec les extrémités à proximité l’une de l’autre, d'une manière dépendante du spliceosome, suggérant que l'organisation co-transcriptionnelle des introns pourrait être critique pour déterminer son excision. Une fois libérés, les mRNP ont une organisation linéaire compacte dans le nucléoplasme et éventuellement une conformation en tige. L'organisation d’un mRNP dans le cytoplasme est influencée par sa traduction. Alors que la traduction ouvre les mRNP, la séparation des extrémités de l'ARNm, l'inhibition de la traduction et la libération de ribosomes, ou le recrutement dans les granules de stress, donnent aux mRNP une structure très compacte. Fait intéressant, nous trouvons rarement des ARNm avec les extrémités 5' et 3' à proximité, ce qui suggère que la traduction en boucle fermée n'est pas un état universel pour tous les ARNm en cours de traduction. Ensemble, nos résultats fournissent une image essentielle de l'organisation du mRNP dans les cellules et souligne le rôle important de la conformation du RNPm dans la régulation de la traduction et de la maturation d’une RNPm. / mRNAs act as the central molecules in gene regulation, helping convert the genetic information stored in the DNA to functional proteins. As a single-stranded polymer, hundreds to thousands of nucleotides in length, mRNAs can form extensive secondary and tertiary structures and, together with proteins, are packaged into assemblies called messenger ribonucleoproteins (mRNPs). The 3D organisation of (pre-)mRNPs influences many aspects of what happens to them, including regulating their processing, export and translation in the cytoplasm. Despite their significance, our understanding of the structural organisation of (pre-)mRNPs in vivo is minimal, as is our comprehension of the principles that govern it. During my PhD, I have developed an RNA-centric view on (pre-)mRNP organisation. For this, I have established an approach combining single-molecule RNA in situ hybridisation (smFISH) with structured illumination microscopy (SIM) and used it to study mRNP organisation in the nucleus and cytoplasm. Our results suggest that (pre-)mRNP organisation is altered at various stages during its lifetime. We show that (pre-)mRNP packaging starts co-transcriptionally, with introns organised into compact conformations. This organisation is altered during the course of transcription as the polymerase travels along the gene, finally assembling an intron with the ends in proximity in a spliceosome dependent manner, suggesting that co-transcriptional intron organisation could be critical in determining its excision. Once released, mRNPs have a compact linear organisation in the nucleoplasm and possibly a rod-like conformation. mRNP organisation in the cytoplasm is influenced by its translational status. While translation opens up mRNPs, separating the ends of the mRNA, translation inhibition and release of ribosomes, or recruitment to stress granules result in mRNPs having a highly compact structure. Interestingly, we rarely find mRNAs with the 5’ and 3’ ends in proximity, suggesting that closed-looped translation is not a universal state for all translating mRNAs. Together, our results provide a unique and essential view of mRNP organisation in cells and reveal important insight into the role of mRNP conformation in regulating translation and mRNP processing.