Genome-Wide Approaches To Study Rna Secondary Structure

The central hypothesis of molecular biology depicts RNA as an intermediary conveyor of genetic information. RNA is transcribed from DNA and translated to proteins, the molecular machines of the cell. However, many RNAs do not encode protein and instead function as molecular machines themselves. The most famous examples are ribosomal RNAs and transfer RNAs, which together form the core translational machinery of the cell. Many other non-coding RNAs have been discovered including catalytic and regulatory RNAs. In many cases RNA function is tightly linked to its secondary structure, which is the collection of hydrogen bonds between complimentary RNA sequences that drives these molecules into their three dimensional structure. Over the last decade, technology for determining the sequence of DNA and RNA has advanced rapidly, making transcriptome-wide expression profiling fast and widely available. In this dissertation, I discuss recent efforts to leverage this powerful technology to study, not just RNA expression, but several other aspects of RNA function. In particular, I focus on three tightly linked aspects of RNA biology: RNA-secondary structure, RNA cleavage, and regulatory small RNAs. I introduce a database for integrating, comparing, and contrasting techniques for determining RNA secondary structure including a technique developed in my dissertation laboratory. Additionally, I discuss a newly improved technology capable of detecting RNA cleavage events. Finally, I integrate RNA secondary structure probing and RNA cleavage detection to interrogate a family of genes important for eukaryotic small RNA-mediated silencing. These diverse analyses are just a few examples of the vast promises offered by adapting RNA-sequencing technology to probe RNA function across many cellular processes

網羅的構造予測及び再現性を考慮したハイスループット構造解析によるRNA二次構造の全体像の解明

学位の種別: 課程博士審査委員会委員 : （主査）東京大学教授 浅井 潔, 東京大学准教授 木立 尚孝, 東京大学教授 津田 宏治, 東京大学講師 笠原 雅弘, 京都大学教授 阿久津 達也University of Tokyo(東京大学

Genomics-Based Studies Identify Cis And Trans Acting Post-Transcriptional Regulators

The identity of every organism is stored in its genetic material. Each gene is transcribed into an intermediate RNA molecule, which undergoes complex processing before translation into a functional protein. RNA processing is controlled by RNA binding proteins (RBPs). Each RBP binds to and regulates the processing, stability, and translation of hundreds to thousands of RNA targets, thereby making these proteins essential for organismal development. RBPs bind to their targets by recognizing both the RNA sequence and secondary structure, which is the interaction between complementary RNA sequences within a single molecule. These interactions can be regulated by changing the chemical makeup of RNA nucleotides via covalent modification, thereby altering the secondary structure and RBP-binding of an RNA molecule. Therefore, the interplay between covalent modifications, secondary structure, and RNA-protein interactions regulates the processing and regulation of each RNA transcript. In this dissertation, I have examined these cis and trans acting post-transcriptional regulators to determine their role in RNA processing. To do this, we have applied a next generation sequencing technique to globally identify RNA-protein interactions and RNA secondary structure in the nuclei of Arabidopsis seedlings. This work has revealed a strong anti-correlation between RNA structure and protein binding. We next utilized this same technique to help identify RBPs that regulate root hair cell development. Hair cells are located on the root epidermis and are responsible for the uptake of water and nutrients from the environment. Therefore, increasing hair cell number can increase plant survival. During this work, we identified two RBPs that regulate root hair cell fate, one of which functions in the phosphate starvation response pathway. These findings reveal novel pathways involved in this developmental process. Finally, we examined the role of covalent modifications in RNA processing. By identifying modifications across the nuclear and cytoplasmic transcriptomes, we found broad populations of modifications corresponding to altered stability. These results illustrate the various regulatory roles held by covalent modifications. Together, this work has advanced the field of post-transcriptional regulation using the model plant Arabidopsis thaliana, by identifying fundamental features of RNA processing, and has raised many questions for future studies to address

Post-Transcriptional Regulation Of The Eulkaryotic Transcriptome By The Covalent Rna Modicication N6-Methyladenosine

Post-Transcriptional regulation of the eukaryotic transcriptome by the covalent RNA modification N6-methyladenosine Stephen James Anderson Brian Gregory Once a messenger RNA molecule is transcribed, a myriad of RNA fate decisions must be made. How these fate decisions are made is often unclear, and elucidating factors determining these fate outcomes is an essential task in order to fully understand gene regulation. One poorly- understood but undoubtedly important factor in post-transcriptional gene regulation is the covalent modification of ribonucleotides. Much like DNA can have chemical groups added to a nucleotide within its primary sequence, RNA can be modified in a similar manner. These covalent modifications of RNA are a ubiquitous feature found within the RNA of all organisms. Dozens of these modifications have been described to date, yet the function or importance of most of these modifications remains unclear. One crucial RNA modification is N6-methyladenosine (m6A), as it is the most abundant known non-cap modification within the eukaryotic transcriptome. In this work, we characterize the role of m6A in the Arabidopsis transcriptome using various sequencing methods that demonstrate that m6A is an abundant mark that is largely maintained across differing Arabidopsis tissues and developmental stages. This prevalent mark promotes transcript stability in mNRAs involved in many important and diverse biological processes, such as salt stress. The absence of this mark results in endonucleolytic cleavage and degradation of the transcript in a highly specific and local manner. We further demonstrate that this modification modulates secondary structure throughout the transcriptome, and that m6A is associated with changes in RNA-binding protein association. Lastly, we turn our view to how an association between m6A and the m6A-specific binding protein YTHDC1 influences the development and transcriptome-wide splicing and polyadenylation pattern in the mouse germline. We demonstrate that in the absence of YTHDC1, widespread developmental, splicing, and polyadenylation defects occur, resulting in non-functional gametes. In total, this work greatly expands our knowledge and understanding of the biological importance and mechanisms of m6A-mediated post-transcriptional regulation

Integrative computational approaches to study protein-nucleic acid interactions

Interactions between proteins and nucleic acid molecules are central to the cellular regulation and homeostasis. To study them, I employ a wide range of computational analysis methods to integrate genomic data from many types of experiment. This thesis has three parts. In the first part, I explore the patterns of indels created by CRISPR-Cas9 genome editing. By thorough characterisation of the precision of editing at thousands of genomic target sites, we identify simple sequence rules that can help predict these outcomes. Furthermore, we examine the role of the structural chromatin context in fine-tuning Cas9-DNA interactions. In the second part, I explore methods to study protein-RNA interactions. I use comparative computational analyses to assess both the data quality of, and data analysis methods for, different crosslinking and immunoprecipitation (CLIP) technologies. I then develop new methods to analyse data generated by hybrid individual-nucleotide resolution CLIP (hiCLIP). By tailoring computational solutions to an understanding of experimental conditions, I improve the overall sensitivity of hiCLIP, and ultimately feedback to drive ongoing experimental development. In the third part, I focus on the Staufen family of double-stranded RNA binding proteins and using hiCLIP data to define transcriptome-wide atlases of RNA duplexes bound by these proteins both in a cell line and in rat brain tissue. Through integration with other data sets, both publicly available and newly generated, I derive insights into their function in RNA metabolism, and in how these interactions change during the course of mammalian brain development with putative roles in ribonucleoprotein complex formation. In summary, I present a range of tailored computational methods and analyses developed to understand interactions between proteins and nucleic acids; aiming to link these interactions to functional outcomes

Studium úlohy Antibakterií a hub účastnícch se degradace rostlinné biomasy kombinací biochemických a moderních sekvenčních metod

Dead plant biomass is a key pool of carbon in terrestrial ecosystems. Its decomposition in soil environments is thus an essential process of the carbon cycle. Fungi are considered to be the primary decomposers in soil ecosystems because of their physiological adaptations and enzymatic apparatus composed from highly effective oxidative and hydrolytic enzymes. Many recent works show that in addition to fungi, bacteria may also play a significant role in lignocellulose decomposition and among bacteria, the members of the phylum Actinobacteria are often regarded to significantly contribute to cellulose and lignocellulose decomposition. This thesis is focused on the evaluation of the role that fungi and Actinobacteria play in dead plant biomass degradation. First, it explored mechanisms involved in degradation, in particular the enzymatic breakdown of major lignocellulose components as cellulose, hemicelluloses and lignin. Enzymatic apparatus of the saprotrophic fungus Fomes fomentarius was explored both in vitro as well as in vivo. Several Actinobacteria were isolated from soil and comparative experiments, investigating production of hydrolytic enzymes, were carried out to track the transformation of polysaccharides and lignin by these strains. To explain the roles of lignocellulose decomposers in...Odumřelá rostlinná biomasa je klíčovým zdrojem uhlíku v pevninských ekosystémech, a proto je její rozklad významný pro koloběh tohoto prvku na zemi. Mezi nejvýznamnější rozkladače jsou řazeny především houby, a to zejména díky schopnosti produkovat vysoce účinné oxidativní a hydrolytické enzymy. Mnoho současných prací dále ukazuje, že kromě hub mohou být dalšími důležitými rozkladači celulózy a lignocelulózy také bakterie, zejména zástupci kmene Actinobacteria. Tato disertační práce je zaměřena na zhodnocení role hub a aktinobakterií při rozkladu odumřelé rostlinné biomasy. V rámci jejího řešení byly nejdříve zkoumány mechanismy tohoto rozkladu, týkající se především rozkladu hlavních komponent lignocelulózy: celulózy, hemicelulóz a ligninu, pomocí extracelulárních enzymů. U saprotrofní houby Fomes fomentarius byl důkladně popsán enzymový aparát a to jak in vitro, tak in vivo. Schopnost produkce hydrolytických enzymů byla dále testována u aktinobakterií izolovaných z půdy a u vybraných kmenů byly provedeny experimenty sledující osud polysacharidů a ligninu v průběhu jejich dekompozice. Aby bylo možno objasnit úlohu rozkladačů lignocelulózy v komplexních prostředích, jako je půda, bylo zkoumáno jejich zastoupení ve společenstvech hub a bakterií se speciálním zaměřením na aktinobakterie. K dosažení...Department of Genetics and MicrobiologyKatedra genetiky a mikrobiologieFaculty of SciencePřírodovědecká fakult

Cryptic reservoirs of micro-eukaryotic parasites in ecologically relevant intertidal invertebrates from temperate coastal ecosystems unveiled by a combined histopathological, ultrastructural, and molecular approach

271 p.La mayoría de los eucariotas son organismos unicelulares (protistas), muchos de ellos pertenecientes a linajes que divergieron temprano en la historia evolutiva de este Dominio de organismos nucleados. Microscópicos, enormemente diversos y fenotípicamente convergentes, su clasificación cladística ha sido históricamente compleja, dejando atrás un extenso registro de taxones y de términos parafiléticos y polifiléticos. Teniendo que investigar atributos estructurales, celulares, biológicos y ecológicos en un mundo de rápidas interacciones y difícilmente accesible a simple vista, la protistología es particularmente dependiente de la sistemática. Ésta permite inferir rasgos de especies crípticas a partir de especies evolutivamente relacionadas.Las moléculas de ADN (y ARN), representan un "registro" preciso de estos eventos de diversificación, que preceden incluso a los más antiguos registros fósiles. En los últimos años, la maduración de los métodos de filogenia molecular, catalizados por una mayor accesibilidad a la secuenciación de próxima generación (NGS), está permitiendo resolver preguntas e hipótesis sobre la evolución y la especiación de estos organismos micro-eucariotas que no se habían podido responder mediante otros métodos. Por una parte, arboles filogenéticos construidos mediante concatenaciones de cientos, incluso miles de genes, están permitiendo rastrear la historia evolutiva de los linajes protistas hasta el último ancestro común de todos los eucariotas (LECA). Concomitantemente, análisis moleculares basados en genes e incluso fragmentos cortos (especialmente 18S rRNA), recuperados principalmente de matrices ambientales u orgánicas (eDNA o ADN ambiental), están revelando una ¿caja de Pandora¿ de diversidad micro-eucariota. Ésta diversidad ¿oculta¿ está transformando nuestra percepción de los protistas en la cadena trófica y la estructura ecológica. En el medio marino, sus papeles como autótrofos, heterótrofos (predadores, saprófitos, parásitos) o mixótrofos crece en importancia día a día. El aumento simultáneo de diversidad e importancia ha sido particularmente pronunciado entre los linajes de parásitos protistas, que adaptados a la vida dentro de un huésped son más inaccesibles y morfológicamente indistinguibles que sus homólogos de vida libre. Muy competitivo como estilo de vida, el parasitismo ha evolucionado de forma independiente varias veces en prácticamente todos los grupos eucariotas, en algunos incluso cientos de veces. De hecho, es posible que el efecto parapátrico que implica una existencia endosimbiótica, haya exacerbado la especiación entre los parásitos, que representan la que posiblemente sea la más común estrategia de consumo entre los organismos vivos. Es más, el número de especies crípticas que están, a día de hoy, siendo descubiertas en la mayoría de los linajes de parásitos protistas sigue aumentando abruptamente o apenas comienza a mostrar una desaceleración. Cabe destacar, que el descubrimiento de esta diversidad oculta, incluidas las especies crípticas, va más allá de la escalada en el número de especies; afecta los estudios sobre biología celular, ciclos biológicos, y ecología. Inexorablemente, esta fuerza mostrada por los métodos de análisis y secuenciación del ADN está abriendo una brecha entre la diversidad genética existente y nuestra comprensión de la morfología, patología, transmisión y posibles hospedadores de los parásitos protistas que la constituyen. Este desequilibrio es particularmente evidente entre los parásitos que infectan linajes de invertebrados, los cuales, salvo algunos taxones con interés comercial, permanecen en gran parte sin analizar, a pesar de constituir un grupo mucho más diverso que los vertebrados. Por una parte, es lógico que los parásitos protistas causantes de infecciones en especies marinas de interés comercial (peces, bivalvos, crustáceos¿) hayan sido priorizadas, pero hay que tener en cuenta que muchos de estos micro-eucariotas tienen ciclos de vida complejos, en los que pequeños invertebrados actúan muchas veces como vectores o reservorios. Descubrir y contextualizar estas asociaciones puede ser determinante a la hora de comprender cuándo y dónde puede variar la presión y capacidad infectiva de algunas de estas infecciones en la comunidad o huéspedes específicos. Al mismo tiempo que su diversidad e importancia aumenta, la inclusión progresiva de parásitos en modelos ecológicos está experimentando variaciones de gran alcance en la dinámica poblacional de las especies animales, vegetales o fúngicas en los ecosistemas. En consecuencia, las asociaciones entre parásitos y hospedadores se investigan cada vez más como una parte importante de la estructura de la comunidad, y no exclusivamente como una "molestia" para el ser humano y sus intereses. Por desgracia la inclusión de parásitos en modelos ecológicos está siendo lastrada por un profundo desconocimiento de estas interacciones. A diferencia de los organismos multicelulares, que han podido ser observados por científicos y aficionados durante siglos, la distribución espaciotemporal de la mayoría de los organismos unicelulares sigue siendo un profundo misterio. No obstante, dadas sus importantes funciones como vectores, huéspedes intermediarios y reservorios, una comprensión mucho más profunda del patobioma (patógenos asociados a un hospedador) y su variabilidad espacio-temporal es de suma importancia para un mayor poder de predicción de los factores de presión causantes de epidemias o zoonosis en el huésped, la población y el medioambiente.En este contexto, la hipótesis de este estudio plantea que especies de invertebrados comunes en la zona inter-mareal de ecosistemas costeros en climas templados son reservorios crípticos de un número significativo de parásitos micro-eucariotas (protistas) de interés para el medio y los recursos marinos. Eldescubrimiento progresivo de estas asociaciones ocultas de parásitos-huéspedes (mediante exámenes combinando técnicas histopatológicas, ultraestructurales y moleculares) permite una mejor comprensión de la morfología, patología, biología celular y ciclo de vida de dichos patógenos, lo que a su vez consiente un seguimiento más estrecho de los factores y presiones que promueven epidemias y zoonosis en una escala espacio-temporal.PIE:Plentziako Itsas Estazio

Discovery of Molecules that Modulate Protein-Protein Interactions in the Context of Human Proliferating Cell Nuclear Antigen-Associated Processes of DNA Replication and Damage Repair

Integral to cell viability is the homotrimeric protein complex Proliferating Cell Nuclear Antigen (PCNA) that encircles chromatin-bound DNA and functionally acts as a DNA clamp that provides topological sites for recruitment of proteins necessary for DNA replication and damage repair. PCNA has critical roles in the survival and proliferation of cells, as disease-associated dysregulation of associated functions can have dire effects on genome stability, leading to the formation of various malignancies ranging from non-Hodgkin’s lymphoma to skin, laryngeal, ocular, prostate and breast cancers. Here, a strategy was explored with PCNA as a drug target that may have wider implications for targeting protein-protein interactions (PPIs) as well as for fragment-based drug design. A design platform using peptidomimetic small molecules was developed that maps ideal surface binding interaction sites at a PPI interface before considering detailed conformations of an optimal ligand. A novel in silico multi-fragment, combinatorial screening approach was used to guide the selection and subsequent synthesis of tripeptoid ligands, which were evaluated in a PCNA-based competitive displacement assay. From the results, some of the peptoid-based compounds that were synthesized displayed the ability to disrupt the interaction between PCNA and a PIP box-containing peptide. The IC50 values of these compounds had similar or improved affinity to that of T2AA, an established inhibitor of PCNA-PIP box interactions. The information gained here could be useful for subsequent drug lead candidate identification