Background: The pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is one of the world's most important pests of cotton. Insecticide sprays and transgenic cotton producing toxins of the bacterium Bacillus thuringiensis (Bt) are currently used to manage this pest. Bt toxins kill susceptible insects by specifically binding to and destroying midgut cells, but they are not toxic to most other organisms. Pink bollworm is useful as a model for understanding insect responses to Bt toxins, yet advances in understanding at the molecular level have been limited because basic genomic information is lacking for this cosmopolitan pest. Here, we have sequenced, de novo assembled and annotated a comprehensive larval midgut transcriptome from a susceptible strain of pink bollworm. Findings: A de novo transcriptome assembly for the midgut of P. gossypiella was generated containing 46,458 transcripts (average length of 770 bp) derived from 39,874 unigenes. The size of the transcriptome is similar to published midgut transcriptomes of other Lepidoptera and includes up to 91 % annotated contigs. The dataset is publicly available in NCBI and GigaDB as a resource for researchers. Conclusions: Foundational knowledge of protein-coding genes from the pink bollworm midgut is critical for understanding how this important insect pest functions. The transcriptome data presented here represent the first large-scale molecular resource for this species, and may be used for deciphering relevant midgut proteins critical for xenobiotic detoxification, nutrient digestion and allocation, as well as for the discovery of protein receptors important for Bt intoxication.

Alcoholism is a complex neurological disorder characterized by loss of control in limiting intake, compulsion to seek and imbibe ethanol, and chronic craving and relapse. It is suggested that the characteristic behaviors associated with the escalation of drug use are caused by long-term molecular adaptations precipitated by the drug’s continual administration. These lasting activity-dependent changes that underlie addiction-associated behavior are thought, in part, to depend on new protein synthesis and remodeling at the synapses. It is well established that mRNA can be transported to neuronal distal processes, where it can undergo localized translation that is regulated in a spatially restricted manner in response to stimulation. Through two avenues of investigation, the research herein demonstrates that behavioral responses to ethanol result, at least in part, from alterations in the synaptic transcriptome which contribute to synaptic remodeling and plasticity. The synaptoneurosome preparation was utilized to enrich for RNAs trafficked to the synapse. Two complementary methods of genomic profiling, microarrays and RNA-Seq, were used to survey the synaptic transcriptome of DBA/2J mice subjected to ethanol-induced behavioral sensitization. A habituating expression profile, characteristic of glucocorticoid-responsive genes, was observed for a portion of synaptically targeted genes determined to be sensitive to repeated ethanol exposure. Other ethanol-responsive genes significantly enriched for at the synapse were related to biological functions such as protein folding and extra-cellular matrix components, suggesting a role for local regulation of synaptic functioning by ethanol. In a separate series of experiments, it was shown that altered trafficking of Bdnf, an ethanol-responsive gene, resulted in aberrant ethanol behavioral phenotypes. In particular, mice lacking dendritically targeted Bdnf mRNA exhibited enhanced sensitivity to low, activating doses and high, sedating doses of ethanol. Together these experiments suggest that ethanol has local regulatory effects at the synapse and lays the foundation for further investigations into the role of the synaptic transcriptome in ethanol-responsive behaviors. Supported by NIAA grants R01AA014717, U01 AA016667 and P20AA017828 to MFM, F31AA021035 to MAO, and NIDA T32DA007027 to WLD.

Rice blast disease is caused by the filamentous ascomycete fungus Magnaporthe oryzae and is the most destructive disease of cultivated rice. The pathogen elaborates a specialized infection structure called the appressorium. The morphological and physiological transitions that lead to appressorium formation of M. oryzae are stimulated through perception of environmental signals and are tightly regulated by cell cycle checkpoints. External stimuli are internalized by a variety of intracellular MAP kinase signaling pathways, and the major pathway regulating appressorium morphogenesis and plant infection is the Pmk1 MAP kinase signaling pathway. The central kinase, Pmk1, is required for appressorium morphogenesis and the homeobox and C2/H2 Zn-finger domain transcription factor, called Mst12, is required for appressorium formation and tissue invasion. The Mst12 null mutant is able to form melanised appressoria, but it is non-pathogenic. To understand the mechanism of appressorium morphogenesis and penetration peg formation, genome-wide comparative transcriptional profiling analysis was performed for the Δpmk1 and Δmst12 mutant using RNA-seq and HiSeq 2000 sequencing. This thesis reports the identification of gene sets regulated by the Pmk1 signalling pathway and defines the sub-set of these genes regulated by Mst12. I show that a hierarchy of transcription factors is likely to operate downstream of Pmk1 to regulate the main processes required for appressorium morphogenesis and plant infection. I also report the role of Mst12 in cytoskeletal re-organisation and show that it is necessary for septin-dependent F-actin polymerisation at the base on the appressorium prior to plant infection. This is consistent with the major transcriptional changes observed by RNA-seq. The thesis also reports experiments that strongly suggest that appressorium mediated plant penetration is regulated by an S-phase checkpoint which operates independently of the conventional DNA damage and repair response, and the Cds1 and Chk1 checkpoint kinases. Transcriptional profiling results are consistent with the S-phase checkpoint operating downstream of the Pmk1 MAP kinase signalling pathway. An integrated model for the operation of the Pmk1/Mst12 signalling pathways and the hierarchical control of appressorium morphogenesis in the rice blast fungus is presented.

>Magister Scientiae - MSc / INTRODUCTION: Breast cancer is a highly heterogeneous disease. The complexity of achieving an accurate diagnosis and an effective treatment regimen lies within this heterogeneity. Subtypes of the disease are not simply molecular, i.e. hormone receptor over-expression or absence, but the tumour itself is heterogeneous in terms of tissue of origin, metastases, and histopathological variability. Accurate tumour classification vastly improves treatment decisions, patient outcomes and 5-year survival rates. Gene expression studies aided by transcriptomic technologies such as microarrays and next-generation sequencing (e.g. RNA-Sequencing) have aided oncology researcher and clinician understanding of the complex molecular portraits of malignant breast tumours. Mechanisms governing cancers, which include tumorigenesis, gene fusions, gene over-expression and suppression, cellular process and pathway involvementinvolvement, have been elucidated through comprehensive analyses of the cancer transcriptome. Over the past 20 years, gene expression signatures, discovered with both microarray and RNA-Seq have reached clinical and commercial application through the development of tests such as Mammaprint®, OncotypeDX®, and FoundationOne® CDx, all which focus on chemotherapy sensitivity, prediction of cancer recurrence, and tumour mutational level. The Gene Expression Barcode (GExB) algorithm was developed to allow for easy interpretation and integration of microarray data through data normalization with frozen RMA (fRMA) preprocessing and conversion of relative gene expression to a sequence of 1's and 0's. Unfortunately, the algorithm has not yet been developed for RNA-Seq data. However, implementation of the GExB with feature-selection would contribute to a machine-learning based robust breast cancer and subtype classifier. METHODOLOGY: For microarray data, we applied the GExB algorithm to generate barcodes for normal breast and breast tumour samples. A two-class classifier for malignancy was developed through feature-selection on barcoded samples by selecting for genes with 85% stable absence or presence within a tissue type, and differentially stable between tissues. A multi-class feature-selection method was employed to identify genes with variable expression in one subtype, but 80% stable absence or presence in all other subtypes, i.e. 80% in n-1 subtypes. For RNA-Seq data, a barcoding method needed to be developed which could mimic the GExB algorithm for microarray data. A z-score-to-barcode method was implemented and differential gene expression analysis with selection of the top 100 genes as informative features for classification purposes. The accuracy and discriminatory capability of both microarray-based gene signatures and the RNA-Seq-based gene signatures was assessed through unsupervised and supervised machine-learning algorithms, i.e., K-means and Hierarchical clustering, as well as binary and multi-class Support Vector Machine (SVM) implementations. RESULTS: The GExB-FS method for microarray data yielded an 85-probe and 346-probe informative set for two-class and multi-class classifiers, respectively. The two-class classifier predicted samples as either normal or malignant with 100% accuracy and the multi-class classifier predicted molecular subtype with 96.5% accuracy with SVM. Combining RNA-Seq DE analysis for feature-selection with the z-score-to-barcode method, resulted in a two-class classifier for malignancy, and a multi-class classifier for normal-from-healthy, normal-adjacent-tumour (from cancer patients), and breast tumour samples with 100% accuracy. Most notably, a normal-adjacent-tumour gene expression signature emerged, which differentiated it from normal breast tissues in healthy individuals. CONCLUSION: A potentially novel method for microarray and RNA-Seq data transformation, feature selection and classifier development was established. The universal application of the microarray signatures and validity of the z-score-to-barcode method was proven with 95% accurate classification of RNA-Seq barcoded samples with a microarray discovered gene expression signature. The results from this comprehensive study into the discovery of robust gene expression signatures holds immense potential for further R&F towards implementation at the clinical endpoint, and translation to simpler and cost-effective laboratory methods such as qtPCR-based tests.

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

Next-generation sequencing (NGS) technologies have revolutionised research into nature and diversity of genomes and transcriptomes. Since the initial description of these technology platforms over a decade ago, massively parallel RNA sequencing (RNA-seq) has driven many advances in the characterization and quantification of transcriptomes. RNA-seq is a powerful gene expression profiling technology enabling transcript discovery and provides a far more precise measure of the levels of transcripts and their isoforms than other methods e.g. microarray. However, the analysis of RNA-seq data remains a significant challenge for many biologists. The data generated is large and the tools for its assembly, analysis and visualisation are still under development. Assemblies of reads can be inspected using tools such as the Integrative Genomics Viewer (IGV) where visualisation of results involves ‘stacking’ the reads onto a reference genome. Whilst sufficient for many needs, when the underlying variance of the genome or transcript assemblies is complex, this visualisation method can be limiting; errors in assembly can be difficult to spot and visualisation of splicing events may be challenging. Data visualisation is increasingly recognised as an essential component of genomic and transcriptomic data analysis, enabling large and complex datasets to be better understood. An approach that has been gaining traction in biological research is based on the application of network visualisation and analysis methods. Networks consist of nodes connected by edges (lines), where nodes usually represent an entity and edge a relationship between them. These are now widely used for plotting experimentally or computationally derived relationships between genes and proteins. The overall aim of this PhD project was to explore the use of network-based visualisation in the analysis and interpretation of RNA-seq data. In chapter 2, I describe the development of a data pipeline that has been designed to go from ‘raw’ RNA-seq data to a file format which supports data visualisation as a ‘DNA assembly graph’. In DNA assembly graphs, nodes represent sequence reads and edges denote a homology between reads above a defined threshold. Following the mapping of reads to a reference sequence and defining which reads a map to a given loci, pairwise sequence alignments are performed between reads using MegaBLAST. This provides a weighted similarity score that is used to define edges between reads. Visualisation of the resulting networks is then carried out using BioLayout Express3D that can render large networks in 3-D, thereby allowing a better appreciation of the often-complex network structure. This pipeline has formed the basis for my subsequent work on the exploring and analysing alternative splicing in human RNA-seq data. In the second half of this chapter, I provide a series of tutorials aimed at different types of users allowing them to perform such analyses. The first tutorial is aimed at computational novices who might want to generate networks using a web-browser and pre-prepared data. Other tutorials are designed for use by more advanced users who can access the code for the pipeline through GitHub or via an Amazon Machine Image (AMI). In chapter 3, the utility of network-based visualisations of RNA-seq data is explored using data processed through the pipeline described in Chapter 2. The aim of the work described in this chapter was to better understand the basic principles and challenges associated with network visualisation of RNA-seq data, in particular how it could be used to visualise transcript structure and splice-variation. These analyses were performed on data generated from four samples of human fibroblasts taken at different time points during their entry into cell division. One of the first challenges encountered was the fact that the existing network layout algorithm (Fruchterman- Reingold) implemented within BioLayout Express3D did not result in an optimal layout of the unusual graph structures produced by these analyses. Following the implementation of the more advanced layout algorithm FMMM within the tool, network structure could be far better appreciated. Using this layout method, the majority of genes sequenced to an adequate depth assemble into networks with a linear ‘corkscrew’ appearance and when representing single isoform transcripts add little to existing views of these data. However, in a small number of cases (~5%), the networks generated from transcripts expressed in human fibroblasts possess more complex structures, with ‘loops’, ‘knots’ and multiple ends being observed. In a majority of cases examined, these loops were associated with alternative splicing events, a fact confirmed by RT-PCR analyses. Other DNA assembly networks representing the mRNAs for genes such as MKI67 showed knot-like structures, which was found to be due to the presence of repetitive sequence within an exon of the gene. In another case, CENPO the unusual structure observed was due to reads derived from an overlapping gene of ADCY3 gene present on the opposite strand with reads being wrongly mapped to CENPO. Finally, I explored the use of a network reduction strategy as an approach to visualising highly expressed genes such as GAPDH and TUBA1C. Having successfully demonstrated the utility of networks in analysing transcript isoforms in data derived from a single cell type I set out to explore its utility in analysing transcript variation in tissue data where multiple isoforms expressed by different cells within the tissue might be present in a given sample. In chapter 4, I explore the analysis of transcript variation in an RNA-seq dataset derived from human tissue. The first half of this chapter describes the quality control of these data again using a network-based approach but this time based the correlation in expression between genes and samples. Of the 95 samples derived from 27 human tissues, 77 passed the quality control. A network was constructed using a correlation threshold of r ≥ 0.9, which comprised 6,109 nodes (genes) and 1,091,477 edges (correlations) and clustered. Subsequently, the profile and gene content of each cluster was examined and enrichment of GO terms analysed. In the second half of this chapter, the aim was to detect and analyse alternative splicing events between different tissues using the rMATS tool. By using a false-discovery rate (FDR) cut-off of < 0.01, I found that in comparisons of brain vs. heart, brain vs. liver and heart vs. liver, the program reported 4,992, 4,804 and 3,990 splicing events, respectively. Of these events, only 78 splicing events (52 genes) with more than 50% of exon inclusion level and expression level more than FPKM 30. To further explore the sometimes-complex structure of transcripts diversity derived from tissue, RNAseq assembly networks for KLC1, SORBS2, GUK1, and TPM1 were explored. Each of these networks showed different types of alternative splicing events and it was sometimes difficult to determine the isoforms expressed between tissues using other approaches. For instance, there is an issue in visualising the read assembly of long genes such as KLC1 and SORBS2, using a Sashimi plots or even Vials, just because of the number of exons and the size of their genomic loci. In another case of GUK1, tissue-specific isoform expression was observed when a network of three tissues was combined. Arguably the most complex analysis is the network of TPM1 where the uniquification step was employed for this highly expressed gene. In chapter 5, I perform a usability testing for NGS Graph Generator web application and visualising RNA-seq assemblies as a network using BioLayout Express3D. This test was important to ensure that the application is well received and utilised by the user. / Almost all participants of this usability test agree that this application would encourage biologists to visualise and understand the alternative splicing together with existing tools. The participants agreed that Sashimi plots rather difficult to view and visualise and perhaps would lose something interesting features. However, there were also reviews of this application that need improvements such as the capability to analyse big network in a short time, side-by-side analysis of network with Sashimi plot and Ensembl. Additional information of the network would be necessary to improve the understanding of the alternative splicing. In conclusion, this work demonstrates the utility of network visualisation of RNAseq data, where the unusual structure of these networks can be used to identify issues in assembly, repetitive sequences within transcripts and splice variation. As such, this approach has the potential to significantly improve our understanding of transcript complexity. Overall, this thesis demonstrates that network-based visualisation provides a new and complementary approach to characterise alternative splicing from RNA-seq data and has the potential to be useful for the analysis and interpretation of other kinds of sequencing data.

LIMA, Beatriz de Sousa e. Tolerância de genótipos de Vigna unguiculata ao estresse salino: integração dos mecanismos moleculares, fisiológicos e bioquímicos. 2017. 139 f. Tese (Doutorado em Bioquímica)-Universidade Federal do Ceará, Fortaleza, 2017. / Submitted by Coordenação PGBioquímica (pg@bioquimica.ufc.br) on 2017-11-08T19:30:39Z No. of bitstreams: 1 2017_tese_bselima.pdf: 8023473 bytes, checksum: 3a7160a365e703abea25a6d6c7065072 (MD5) / Approved for entry into archive by Jairo Viana (jairo@ufc.br) on 2017-11-14T17:40:39Z (GMT) No. of bitstreams: 1 2017_tese_bselima.pdf: 8023473 bytes, checksum: 3a7160a365e703abea25a6d6c7065072 (MD5) / Made available in DSpace on 2017-11-14T17:40:39Z (GMT). No. of bitstreams: 1 2017_tese_bselima.pdf: 8023473 bytes, checksum: 3a7160a365e703abea25a6d6c7065072 (MD5) Previous issue date: 2017 / Agricultural production has become a challenge in the arid and semi-arid regions of the world, as a result of the constant incidence of adverse environmental factors, such as abiotic stresses. Among them, the excess of salts in the soil is characterized by severely limiting the growth and development of the plants, causing serious damages due to the low yield of the crops. In this scenario, the selection of cultivars tolerant to salinity and / or genetic engineering of plants emerge as strategies of great importance. However, because stress tolerance is a multigenic phenomenon, the selection / identification of metabolic pathways, molecular markers and potential gene products constitute a challenge for studies on saline stress in plants. The present research was developed with the objective of integrating the molecular, biochemical and physiological mechanisms involved in the tolerance of cowpea (Vigna unguiculata) plants to saline stress. For this, plants of two genotypes of V. unguiculata endowed with differential tolerance to saline stress, Pitiúba and TVU, were used as experimental model. Saline stress promoted severe reductions in plant growth of both genotypes; however, increased biomass production under salinity was observed in TVU genotypes throughout the experimental period (8 and 16 days). The best performance of the TVU plants was attributed to the higher efficiency of the photosynthetic machinery, evidenced by the higher CO2 assimilation rates and by the higher photochemical efficiency of photosystem II (↑ electron transport rate - ETR and ↑ photochemical quenching - qP). In addition, in the presence of NaCl, the high photosynthetic efficiency coincided with the higher pigment content involved in the energy absorption of both chlorophyll a, b and total as well as carotenoids. Such responses were accompanied by increases in the expression of the PGR5-like protein 1A, HEMA (Glutamyl-tRNA reductase-binding protein), Light-harvesting complex I chlorophyll, as well as several structural genes of the thylakoidal CTE. TVU plants also limited the excessive accumulation of Na + in the stems and leaves and, consequently, established a higher K + / Na + ratio under stress. The results suggest that the control of ionic homeostasis was due to the efficient activation of defense routes, involving mechanisms of exclusion and Na + compartmentalization, since there was an increase in the expression of genes encoding SOS route components and V-ATPase genes. In addition, lower oxidative damages (↓ MDA) were observed in plant tissues of the TVU genotype, a result of the effective action of enzymatic and non-enzymatic antioxidants. The higher activity of the SOD, APX and GPX enzymes was correlated with the expression of the DEAD-box and Glutathione peroxidase genes. In this genotype, genes involved in auxin signaling (IAA), jasmonic acid (JA), gibberellins (GA), ethylene (ETHY), abscisic acid (ABA), H2O2, CIPK (CIPK3 and CIPK14) and innumerable transcription factors for example WRKY, MYB and bZIP) may have operated in the intricate network of responses that culminated in greater tolerance to salt stress. In contrast, the higher sensitivity of the Pitiúba genotype to saline stress was associated with the lower efficiency of the photosynthetic machinery and the excessive accumulation of toxic ions in the aerial tissues. Under salinity, decreases in CO2 assimilation rates were due to severe damage to the photosynthetic apparatus, since the maximum quantum efficiency of PSII (Fv / Fm) was seriously compromised shortly after the onset of stress, and this effect was intensified with the imposition of saline treatment. Associated with this, there was a progressive reduction in the effective quantum efficiency of the PSII (φPSII), which was accompanied by decreases in the ETR, as well as by the greater non-photochemical dissipation of electrons, especially in the last times of analysis. Another determinant factor for the lower efficiency of the photosynthetic machinery was the low accumulation of photosynthetic pigments, which probably resulted in the accumulation of energy in PSII and the higher production of reactive oxygen species (ROS). This phenomenon may have caused damage to cell membranes (↑ MDA), which intensified the degradation of the photosynthetic pigments and other structural components of the photosystems. As a result of the lower photochemical efficiency, photosynthetic rates (CO2 assimilation) were seriously compromised by salinity, which consequently restricted plant growth. The results of RNAseq demonstrated that Pitiúba plants also triggered an arsenal of genes in response to stress, including those focused on the control of ionic and redox homeostasis, photosystem repair, hormones, transcription factors, among others. However, such mechanisms were not sufficient to mitigate the deleterious effects of NaCl and the plants were highly sensitive to salt stress. In the present study, the main metabolic pathways involved in the tolerance to salinity of V. unguiculata plants were identified, as well as potential genes for genetic improvement studies. / A produção agrícola tem se tornado um desafio nas regiões áridas e semi-áridas de todo o mundo, resultado da incidência constante de fatores ambientais adversos, como é o caso dos estresses abióticos. Dentre eles, o excesso de sais no solo caracteriza-se por limitar severamente o crescimento e desenvolvimento das plantas, acarretando graves prejuízos devido ao baixo rendimento das culturas. Nesse cenário, a seleção de cultivares tolerantes à salinidade e/ou a engenharia genética de plantas emergem como estratégias de grande importância. Todavia, como a tolerância ao estresse é um fenômeno de natureza multigênica, a seleção/identificação das vias metabólicas, marcadores moleculares e de potenciais produtos gênicos constituem um desafio para os estudos sobre estresse salino em plantas. A presente pesquisa foi desenvolvida com o objetivo de integrar os mecanismos moleculares, bioquímicos e fisiológicos envolvidos na tolerância de plantas de feijão-caupi (Vigna unguiculata) ao estresse salino. Para isso, plantas de dois genótipos de V. unguiculata dotados de tolerância diferencial ao estresse salino, Pitiúba e TVU, foram utilizadas como modelo experimental. O estresse salino promoveu reduções severas no crescimento das plantas de ambos os genótipos, contudo, uma maior produção de biomassa sob salinidade foi observada nas plantas do genótipo TVU, ao longo de todo o período experimental (8 e 16 dias). O melhor desempenho das plantas TVU foi atribuído a maior eficiência da maquinaria fotossintética, evidenciada pelas maiores taxas de assimilação de CO2 e pela maior eficiência fotoquímica do fotossistema II (↑ taxa de transporte de elétrons – ETR e ↑ quenching fotoquímico - qP). Além disso, na presença de NaCl, a elevada eficiência fotossintética coincidiu com o maior conteúdo de pigmentos envolvidos na absorção de energia, tanto de clorofila a, b e total quanto de carotenoides. Tais respostas foram acompanhadas por incrementos na expressão dos genes PGR5-like protein 1A, HEMA (Glutamyl-tRNA reductase-binding protein), Light-harvesting complex I chlorophyll, bem como de vários genes estruturais da CTE tilacoidal. Plantas TVU também limitaram o acúmulo excessivo de Na+ nos caules e folhas e, consequentemente, estabeleceram maior relação K+/Na+ sob estresse. Os resultados sugerem que o controle da homeostase iônica foi decorrente da ativação eficiente de rotas de defesa, envolvendo mecanismos de exclusão e compartimentalização de Na+, pois houve aumento na expressão de genes que codificam componentes da rota SOS e de genes da V-ATPase. Aliado a isso, observou-se menores danos oxidativos (↓ MDA) nos tecidos das plantas do genótipo TVU, resultado da ação efetiva de antioxidantes enzimáticos e não enzimáticos. A maior atividade das enzimas SOD, APX e GPX foi correlacionada com a expressão dos genes DEAD-box e Glutathione peroxidase. Nesse genótipo, os genes envolvidos na sinalização por auxinas (IAA), ácido jasmônico (JA), giberelinas (GA), etileno (ETHY), ácido abscísico (ABA), H2O2, CIPK (CIPK3 e CIPK14) e inúmeros fatores de transcrição (por exemplo, WRKY, MYB e bZIP) podem ter atuado na rede intricada de respostas que culminou na maior tolerância ao estresse salino. Contrariamente, a maior sensibilidade das plantas do genótipo Pitiúba ao estresse salino foi associada com a menor eficiência da maquinaria fotossintética e o acúmulo excessivo de íons tóxicos nos tecidos aéreos. Sob salinidade, os decréscimos nas taxas de assimilação de CO2 foram resultado de danos severos ao aparato fotossintético, pois a eficiência quântica máxima do PSII (Fv/Fm) foi seriamente comprometida logo após o início do estresse, sendo esse efeito intensificado com a imposição do tratamento salino. Associado a isso, houve uma redução progressiva na eficiência quântica efetiva do PSII (ϕPSII), que foi acompanhada por decréscimos na ETR, bem como pela maior dissipação não fotoquímica de elétrons, principalmente nos últimos tempos de análise. Outro fator determinante para a menor eficiência da maquinaria fotossintética foi o baixo acúmulo de pigmentos fotossintéticos, o que provavelmente resultou no acúmulo de energia no PSII e na maior produção de espécies reativas de oxigênio (EROs). Esse fenômeno pode ter ocasionado danos as membranas celulares (↑ MDA), o que intensificou a degradação dos pigmentos fotossintéticos e de outros componentes estruturais dos fotossistemas. Como resultado da menor eficiência fotoquímica, as taxas fotossintéticas (assimilação de CO2) foram seriamente comprometidas pela salinidade o que, consequentemente, restringiu o crescimento das plantas. Os resultados do RNAseq demonstraram que as plantas Pitiúba também acionaram um arsenal de genes em resposta ao estresse, incluindo aqueles voltados para o controle da homeostase iônica e redox, reparo dos fotossistemas, hormônios, fatores de transcrição, dentre outros. Entretanto, tais mecanismos não foram suficientes para mitigar os efeitos deletérios do NaCl e as plantas foram altamente sensíveis ao estresse salino. No presente estudo foram identificadas as principais vias metabólicas possivelmente envolvidas na tolerância à salinidade de plantas de V. unguiculata, além de genes potenciais para estudos de melhoramento genético de plantas

AN ABSTRACT OF THE DISSERTATION OF SOLOMON G. HAILU, for the Doctor of Philosophy degree in Molecular Biology, Microbiology and Biochemistry, presented on August 22, 2017, at Southern Illinois University, School of Medicine. TITLE: DISTINCT GENOME WIDE FUNCTIONS OF CHROMATIN REMODELERS IN NUCLEOSOME ORGANIZATION AND TRANSCRIPTION REGULATION MAJOR PROFESSOR: Dr. Blaine Bartholomew Chromatin remodelers are conserved from yeast to humans and are the gatekeepers of chromatin. They regulate transcription by occluding or exposing DNA regulatory elements globally. They are crucial for DNA processes such as DNA replication, repair and recombination. In addition, they are critical in developmental processes and differentiation. Chromatin remodelers are categorized into several families based on their conserved ATPase domain, an essential component required for their DNA translocation ability. In this study, we investigated the role yeast ISWI and SWI/SNF family of chromatin remodelers play on nucleosome rearrangement and transcription regulation by targeted mutagenesis of domains in accessory subunits and at the C-terminus of the catalytic subunit. All members of the ISWI family (ISW1a, ISW1b, ISW2) share a conserved C-terminal HAND, SANT and SLIDE domains, which are important for sensing linker DNA. We find an auto-regulation of ISWI complexes by the SLIDE domain, independent of the histone H4 Nterminal tail. Our protein-protein chemical crosslinking and mass spectrometry (CX-MS) analysis indicate that the SLIDE domain regulates the ATPase core through N terminal domains of the accessory subunit Itc1. Moreover, we show that the accessory subunits of ISWI modulate the ATPase activity and specificity of ISWI complexes. The DNA sensing ability of the SLIDE domain is required for the in vivo nucleosome spacing and transcription regulation by ISWI. We find that while ISW2 primarily regulates transcription at the 5’ end of genes, ISW1a is important in transcription elongation by rearranging nucleosomes starting at the +2 nucleosome and through the rest of the body of genes towards the 3’ end. ISW1b on the other hand rearrange nucleosomes in the gene body to facilitate suppression of cryptic transcription. For the first time, we show the potential division of labor between ISW1a and ISW1b during transcription elongation. On the other hand, SWI/SNF chromatin remodelers are essential epigenetic factors that are frequently mutated in cancer and neurological disorders. They harbor a C-terminal SnAC and AT hook domains that positively regulate their DNA dependent ATPase activity and nucleosome mobilizing capabilities. By deleting the AT hook motifs, we have identified the role of SWI/SNF in organizing the -1 and +1 nucleosomes at transcription start sites flanking the nucleosome free region (NFR). Our RNA-seq analysis shows SWI/SNF positively regulates the bi-directional transcription of non-coding RNA (ncRNA) which are activated when the AT hook motifs are deleted. Moreover, AT hooks regulate such activities of SWI/SNF through direct protein-protein interactions with the ATPase core as evidenced by our chemical crosslinking and mass spectrometry (CX-MS) analysis.

Submitted by Erika Demachki (erikademachki@gmail.com) on 2017-04-27T19:34:22Z No. of bitstreams: 2 Dissertação - Vanessa Cristina da Silva Araújo - 2017.pdf: 2199979 bytes, checksum: f02e05314927339cf3c54225f8ad52db (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-05-03T12:09:43Z (GMT) No. of bitstreams: 2 Dissertação - Vanessa Cristina da Silva Araújo - 2017.pdf: 2199979 bytes, checksum: f02e05314927339cf3c54225f8ad52db (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-05-03T12:09:43Z (GMT). No. of bitstreams: 2 Dissertação - Vanessa Cristina da Silva Araújo - 2017.pdf: 2199979 bytes, checksum: f02e05314927339cf3c54225f8ad52db (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-03-07 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Large-scale sequencing of transcripts via RNA-Seq has been changing paradigms by demonstrating that transcription is prevalent throughout the eukaryotic genome. In these organisms, the vast majority of transcripts are non-coding (ncRNA). One type of RNA that has aroused great interest, given its prevalence, is long non-coding RNAs (lncRNAs), which are ncRNA with more than 200 nucleotides. However, little is known about the role and prevalence of these lncRNAs in plant genomes, even in model species such as Arabidopsis thaliana (L.) Heynh. The objective of this work was to identify lncRNAs in the Arabidopsis genome and to characterize their size, structure and nucleotide diversity. The sequences were obtained from previous work that sequenced total RNA from A. thaliana, grown under different light regimes, using Illumina Hiseq 2000 platform. These sequences were mapped into the reference genome with TopHat and assembled with Cufflinks. The assembled transcripts were compared with the genome annotation with Cuffcompare, to identify non-annotated transcripts. A total of 4,305 long putative RNAs were obtained, with 314 (7%) sense in relation to coding transcripts (mRNAs), 392 (9%) intergenic, 2,216 intronic (52%) and 1,383 (32%) antisense mRNAs. The lncRNAs obtained were filtered to eliminate those with coding potential, as well as those related to rRNA, tRNA and miRNA synthesis. A total of 3,710 high-confidence lncRNAs (HC-lncRNA) were obtained, of which 58.6% were not previously annotated. These HC-lncRNA emcompass a low proportion (~ 1%) lncRNAs in the genome of Arabidopsis thaliana. A functional enrichment analysis of Gene Ontology (GO) categories demonstrated that among genes containing lncRNAs there is a high proportion of categories linked to the localization and transport of proteins within the cell, as well as to nucleic acid binding. A gene expression analyses identified only 22 differentially expressed lncRNAs under the different light conditions in which samples were exposed. Using the SNP data from the 1001 genomes project, identified high nucleotide diversity within lncRNAs regions, indicating low conservation of the primary structure of these transcripts. The nucleotide diversity in regions of long noncoding RNAs is lower than in coding regions, but less than a diversity observed in neutral regions such as pseudogenes. / O sequenciamento em larga escala de transcritos, via RNA-Seq, vêm mudando paradigmas ao demonstrar que a transcrição é prevalente por todo o genoma dos eucariotos. Nesses organismos, a grande maioria dos transcritos não codificam proteínas (ncRNA). Um tipo de RNA que vêm despertando grande interesse, dado sua prevalência, são os RNAs longos não codificantes (lncRNAs), que são ncRNA com mais de 200 nucleotídeos. No entanto, pouco se sabe sobre o seu papel e prevalência nos genomas de plantas, mesmo em espécies modelo como Arabidopsis thaliana (L.) Heynh. O objetivo desse trabalho foi identificar lncRNAs no genoma de Arabidopsis e caracterizar seus tamanhos, estruturas e diversidade genética. As sequências utilizadas foram obtidas de um trabalho que sequenciou RNA total de A. thaliana, sob diferentes regimes de luminosidade, utilizando a plataforma Illumina HiSeq 2000. Estas sequências foram mapeadas no genoma referência com o programa TopHat e montadas com o Cufflinks. Os transcritos montados foram comparados com a anotação do genoma com o Cuffcompare, afim de identificar transcritos ainda não anotados. Um total de 4.305 RNAs longos putativos foi obtido, sendo 314 (7%) senso em relação a transcritos codantes (mRNAs), 392 (9%) intergênicos, 2.216 intrônicos (52%) e 1.383 (32%) antisenso de mRNAs. Os lncRNAs obtidos foram filtrados para eliminar aqueles com potencial de codificação, bem como aqueles relacionados com a síntese rRNA, tRNA e miRNA. Após essa filtragem, foram obtidos 3.710 lncRNAs de alta cofiança (HC-lncRNA), sendo que desses 58,6% ainda não foram previamente anotados. Esses HC-lncRNA representam uma baixa proporção (~1%) do genoma de Arabidopsis thaliana. Uma análise de enriquecimento funcional de categorias do Gene Ontology (GO) demonstrou que os genes que contém lncRNAs apresentam enriquecimento para processos ligados à localização e transporte de proteínas dentro da célula, bem como para ligação a ácidos nucléicos. Uma análise de expressão gênica identificou apenas 22 lncRNAs diferencialmente expressos entre as diferentes condições de luminosidade em que as amostras foram expostas. Utilizando os SNPs do projeto 1001 genomes, identificou-se alta diversidade nucleotídica em regiões de lncRNAs, indicando baixa conservação da estrutura primária destes transcritos. A diversidade nucleotídica em regiões de RNAs longos não codificantes é menor do que em regiões codantes, mas menor do que a diversidade observada em regiões neutras como os pseudogenes.

L'ADN génomique des bactéries existe dans un complexe dynamique riche en protéines, le "nucléoïde'', très bien organisé à différentes échelles de longueur. Cette thèse décrit notre modélisation et analyse des données en mettant l'accent sur l'organisation du nucléoïde de \textit{E. coli}, et sur comment cette organisation affecte l'expression des gènes. La première partie du travail est une revue des progrès récents expérimentaux et théoriques quantifiant l'organisation physique (la géométrie et le compactage) du chromosome bactérien. En particulier, nous soulignons le rôle que la physique de la matière molle et la physique statistique jouent dans la description de ce système. Une deuxième partie de l'ouvrage traite d'un modèle de la physique des polymères inspiré par deux caractéristiques du nucléoïde: auto-adhérence osmotique et effet des protéines de pontage. Les résultats sont une caractérisation qualitative du diagramme de phase, qui montre que les nucléoïdes forment des domaines distincts sans interactions intra-spécifiques. La thèse couvre également plusieurs approches d'analyse de données pour tester les connexions entre l'organisation du nucléoïde avec l'expression des gènes (RNA-Seq) et des protéines (ChIP-Seq). Cette dernière partie contient une description de l'outil web NuST, qui permet d'effectuer de simples analyses statistiques sur de multiples échelles. En outre, nous présentons une étude de corrélation d'un grand nombre de mesures d'expression génomique dans différentes conditions de croissance, et nous le comparons avec les cartes d'interaction (Hi-C) spatiale entre le chromosome. / The genomic DNA of bacteria exists in a complex and dynamic protein-rich state, which is highly organized at various lengthscales. This thesis describes a work of physical modeling and data analysis focused on the E. coli genome organization, in the form of the "nucleoid'', and on how nucleoid organization affects gene expression.The first part of the work is a review of the recent experimental andt heoretical advances quantifying the physical organization (compactionand geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance.A second part of the work discusses a simple polymer physics model inspired by two main features of the nucleoid: osmotic self-adhesion and protein bridging. Results are summarized by a qualitative characterization of the phase diagram of this model which shows the general feature that distinct domains may form without the need forintra-specific interactions.The thesis also covers several data analysis approaches to test possible connections between the physical organization of the nucleoid with gene expression (RNA-Seq) and protein binding (ChIP-Seq) datasets. This latter part contains a description of the NuST webtool, which consists of a database which collect datasets from past experiments and an implementation of simple multi scale statistical analysis tools. Additionally, we introduce a correlation study of a large number (about 300) of genome-wide expression data-sets, also compared to the outcome to the published genome interaction map (Hi-C)data.