RNA, the Epicenter of Genetic Information

The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers

Development of bioinformatics tools and studies in biomedical association networks for the analysis of human genetic diseases

Fecha de lectura de Tesis Doctoral: 18 de marzo 2019.El presente trabajo de tesis doctoral se centra en el análisis en red y desarrollo de herramientas bioinformáticas para la determinación de las causas que dan lugar a las enfermedades con base genética. Mediante el análisis de sistemas de red se pueden asociar fenotipos patológicos y las regiones del genoma que potencialmente sean su causa a partir de información de pacientes. Estas asociaciones fenotipo-genotipo pueden emplearse para el desarrollo de herramientas de apoyo al diagnóstico genético de pacientes con un cuadro fenotípico complejo, de manera que puedan dar información sobre las regiones del genoma que potencialmente estén afectadas en un paciente a partir de sus fenotipos patológicos observados. Del mismo modo, estas regiones asociadas a fenotipos patológicos pueden analizarse para determinar los elementos funcionales del genoma que sean la causa de la enfermedad. Este análisis incluye tanto genes como elementos reguladores, ya que se ha demostrado que un 80% de las enfermedades caracterizadas mediante análisis del genoma completo han sido asociadas a regiones no codificantes del genoma, en las cuales se encuentran los elementos reguladores. Una vez determinados los elementos funcionales existentes en las regiones del genoma asociadas a fenotipos patológicos, se pueden determinar los sistemas biológicos que estén afectados en el paciente. Sin embargo, no todos los genes tienen anotaciones funcionales que muestren a qué sistemas afectan. Esta funcionalidad viene dada por el producto génico, las proteínas, que a su vez constan de dominios que les confieren su función y/o estructura. De nuevo, mediante análisis de red se pueden asociar dominios de proteínas con anotaciones funciones a partir de información de proteínas, con el fin de poder usar esas asociaciones dominio-función para predecir la posible función desconocida de proteínas en base a sus dominios

A MATTER OF STYLE.HOW MAP THINKING AND BIO-ONTOLOGIES SHAPE CONTEMPORARY MOLECULAR RESEARCH

ABSTRACT The aim of this thesis is to provide an epistemic analysis of the transformations occurring in contemporary biological research by considering the relation between molecular biology and computational biology. In particular, I will focus on bio-ontologies, as the tool which incarnates at best the new face of biomedical research. Such a choice is not arbitrary. By appealing to the notion of style of reasoning and way of knowing, I will show that bio-ontologies exemplify the rise and success of map thinking as the signature of a new way of doing molecular biology, while the theoretical tenets, established more than 30 years ago, still maintain their epistemic prominence. This is neither to say that experimentalism will disappear from science, nor that the experiments power will be diminished but rather that experiments will have a new role in the architecture of scientific efforts, precisely because of the increasing importance of classificatory approaches. Therefore, such a transition within biomedical research is indeed radical and profound but it does not involve paradigm shifts but rather a change in the practice. In this sense, it is a matter of style

Cereal Genomics II

During the last decades, major advances have been made in the field of cereal genomics. For instance, high-density genetic maps, physical maps, QTL maps and even draft genome sequence have become available for several cereal species. This has been facilitated by the development of next generation sequencing (NGS) technologies, so that, it is now possible to sequence genomes of hundreds or thousands of accessions of an individual cereal crop. Significant amounts of data generated using these latest NGS technologies created a demand for computational tools to analyse this massive data. These developments related to technology and the tools, along with their applications not only to plant and genome biology but also to breeding have been documented in this volume. The volume, entitled “Cereal Genomics II”, therefore supplements the earlier edited volume “Cereal Genomics” published in 2004. The new volume has updated chapters, from the leading authorities in their fields, on molecular markers, next generation sequencing platform and their use for QTL analysis, domestication studies, functional genomics and molecular breeding. In addition, there are also chapters on computational genomics, whole genome sequencing and comparative genomics of cereals. The book should prove useful to students, teachers and young research workers as a ready reference to the latest information on cereal genomics

Susceptibility to late onset hearing loss: an investigation into genetic variation at the Brn-3c locus.

BrnSc (BrnS.l, POU4F3) encoding a POU domain transcription factor is a candidate gene for late onset sensorineural hearing loss, which is exhibited by a large proportion of the ageing population. To identify common sequence variants at the Brn-3c locus mutation scanning of the BrnSc cDNA, intron and 5'-flanking region was performed by PCR-SSCP analysis in 45 members of the general population. Seven polymorphic sites were identified of which five within the Bm-Sc 5'-flanking region appear common. A functional screening approach utilising in-vitro assays suggests that at least three common sequence variants in the Brn-Sc 5'-flanking region could have a functional affect: -566(GT)i7-23, -1391A>C and a complex multi-allelic poly-G polymorphism at - 3432 that exhibits multiple variations in length together with single base substitutions within the guanine repeat. The -3432poly-G polymorphism modifies the binding affinity of an OC-2 derived nuclear protein and there is convincing evidence that this is the transcription factor SP1. Use of purified human recombinant SP1 protein, in-vitro translated SP1 and in-vitro translated SP3 confirms that the -3432polyG polymorphism modulates a high affinity SP family binding site and evidence suggests that this alters the regulation of the BrnSc promoter when SP1 levels are limiting, p<0.05. Moreover, the data suggest a functional interaction between the -3432poly-G polymorphism and the -566(GT)i7.23 repeat which associate to determine the response of the Brn-3c gene to SP1. Similarly, evidence suggests that the variant allele, -1391C has a reduced affinity for an OC-2 derived nuclear protein and this is consistent with a significant decrease in basal activity of the Brn-Sc promoter, pC were genotyped for a pilot association study but allelic frequencies were not found to significantly differ between the patient and control populations examined (by %2 analysis). Further large-scale population studies are required to establish whether these common sequence variants are associated with late onset hearing loss

Orchestration of the neural stem cell fate by NRF2 and TAZ

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Medicina, Departamento de Bioquímica. Fecha de lectura: 11-10-2019Neurogenesis is a multiple step process that must be tightly regulated or otherwise results in pathological events. Therefore, a deep characterization of the molecular mechanisms that control the biology of neural stem/progenitor cells (NSPCs) will provide a better understanding of the role of neurogenic niches and new therapeutic strategies for neurodegenerative diseases and brain tumours. In this thesis we have analyzed the regulation of NSCs fate by the transcription factor Nuclear factor (erythroid-derived 2)-like 2 (NRF2), which is considered a master regulator of cellular homeostasis, and the Transcriptional co-activator with PDZ-binding motif (TAZ), a major effector of the Hippo pathway. NRF2 controls the expression of a wide battery of cytoprotective genes that have a tremendous impact on physiological responses such as inflammation, senescence or metabolism. However, its relevance in neurogenesis is just starting to be unveiled. On the other hand, TAZ is a major effector of the Hippo pathway, which plays a key role in tissue homeostasis and organ size control by regulating tissue-specific stem cells. However, the implication of TAZ in neurogenesis has not been analyzed. In this study, we have identified NRF2 as a regulator of hippocampal NSCs self-renewal and differentiation. We show that genetic manipulation of NRF2 results in the modulation of NSPCs differentiation and proliferation capacity. To assess the functional relevance of NRF2 in neurogenesis under pathological conditions, we analyzed the impact of NRF2 deficiency in neurogenesis of the subgranular zone (SGZ) of the hippocampus in a mouse model of Alzheimer´s Disease (AD). We found that NRF2 deficiency results in an accelerated loss of NSCs, loss of synaptic plasticity measured as long term potentiation (LTP) and impaired the execution of cognitive tasks. At the molecular level, we have identified NRF2 enhancer sequences, termed Antioxidant Response Elements (AREs), in the promoter region of the TAZ coding gene. Consequently, we show that genetic and pharmacological manipulation of NRF2 results in the modulation of TAZ gene expression in NSPCs. These findings open a new window to understand the molecular mechanisms underlying NRF2 function in stemness. We have also established a novel role of TAZ as repressor of neuronal differentiation, based on the transcriptional repression of SOX2 and the basic helix-loop-helix (bHLH) factors ASCL1, NEUROG2 and NEUROD1. Data mining of The Cancer Genome Atlas showed a negative correlation between TAZ and the expression of these proneurogenic factors in lower grade gliomas and glioblastomas. We found that TAZ favours glioblastoma CSCs tumorigenic capacity and that genetic modulation of TAZ in these cells inversely correlated with proneurogenic genes expression. Due to the relevance of these proneurogenic factors in the ablation of glioblastoma cancer stem cells (CSCs), this novel TAZ/proneurogenic factors axis may have important implications in the development of this type of brain tumours. The characterization of molecular mechanism governing NSPCs fate provides new insights to harness these cells for brain repair. Overall, this thesis describes a novel role of NRF2 and TAZ in the control of neural stem cell fate, suggesting a new strategy to combat brain pathology

The role of Dichaete in transcriptional regulation during Drosophila embryonic development

Sox domain genes encode a family of developmentally important transcription factors conserved throughout the Metazoa. The subgroup B, which includes the mammalian Sox1, 2 and 3 proteins and their Drosophila counterparts Dichaete and SoxNeuro, are particularly important for the development of the nervous system where they appear to play conserved roles in neuronal specification and differentiation. Despite years of detailed study we still have a relatively poor idea of how Sox proteins function on a genome wide scale and the aim of my PhD work was to explore this aspect using the fly group B protein, Dichaete. A number of studies have shown that Dichaete performs a variety of critical functions during development and a few individual regulatory targets have been defined, however, at the start of my work no genome-wide data on Dichaete action were available. While such data emerged from large scale initiatives during my work, a systematic analysis of Dichaete action was lacking. Here I describe the first detailed genomic analysis of Dichaete activity, with a particular focus on three areas: finding the locations of Dichaete binding in the genome, a prediction of potential Dichaete cofactors and an analysis of Dichaete effects on gene expression. To address the issue of where Dichaete binds in the genome, I generated whole genome DamID data for embryos and followed this with a detailed comparative analysis, combining my data with three newly published ChIP-chip datasets. The combined studies identify thousands of binding regions, mostly in the vicinity of developmentally important genes. The binding profiles were found to be consistent with Dichaete acting on enhancer regions and also suggest a role in facilitating RNA Polymerase II pausing. The analysis also identified a Dichaete binding motif closely matching that found with in vitro studies. By combined ChIP and DamID datasets I generated a very high confidence core Dichaete binding dataset, which should be of considerable use in future studies. To identify potential Dichaete cofactors, I compiled the available embryonic transcription factor binding data from the Berkeley Drosophila Transcription Network and mod- ENCODE projects, and identified significant overlaps with the core Dichaete binding data. A number of the proteins highlighted in this analysis have known roles during neuroblast development, including Hunchback and Krüppel, transcription factors involved in temporal specification of neuroblast division, and Prospero, which plays a key role in neuroblast differentiation. The analysis suggests that Dichaete has a role during early neuroblast divisions, where it likely interacts with Hb and Kr to maintain neuroblast pluripotency. This is a role consistent with previous studies in Drosophila larval neuroblasts and is analogous to neural functions of Sox2 in mammals. My analysis suggests that Dichaete acts on the same target genes as Prospero but in an antagonistic role, with Dichaete preventing stem cell differentiation and Prospero promoting it. To examine the effects of Dichaete on gene expression, a number of microarray transcript profiling studies were performed, including a global study with Dichaete null mutants, and tissue specific studies in the CNS midline and neuroblasts via the use of dominant negative constructs. Whole transcriptome expression profiling data was combined with the binding data to establish a set of high confidence potential Dichaete targets, both for specific tissues and more globally during neurogenesis. Specific high confidence targets were found, including bancal during nervous system development. It was also concluded that Dichaete is likely to prevent cell cycle exit by repressing the apoptosis genes grim, hid and reaper, as well as the differentiation genes prospero and miranda. An extensive list of potential Dichaete direct targets was generated and can be used for validation and future research.This work was supported by a Medical Research Council scholarship

Genomics-Assisted Crop Improvement, Vol 1: Genomics Approaches and Platforms

Genomics research has great potential to revolutionize the discipline of plant breeding. This two-volume set provides a critical assessment of genomics tools and approaches for crop breeding. Volume 1, entitled "Genomics Approaches and Platforms", illustrates state-of-the-art genomics approaches and platforms presently available for crop improvement. Volume 2, entitled "Genomics Applications in Crops", compiles crop-specific studies that summarize both the achievements and limitations of genomics research for crop improvement. We hope that these two volumes, while providing new ideas and opportunities to those working in crop breeding, will help graduate students and teachers to develop a better understanding of the applications of crop genomics to plant research and breeding