Relevant bibliographies by topics / Transcriptome atla

Academic literature on the topic 'Transcriptome atla'

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Published: 11 March 2023

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Journal articles on the topic "Transcriptome atla"

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Packer, Jonathan S., Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, et al. "A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution." Science 365, no. 6459 (September 5, 2019): eaax1971. http://dx.doi.org/10.1126/science.aax1971.

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Caenorhabditis elegans is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and preterminal cell types, mapping most single-cell transcriptomes to their exact position in C. elegans’ invariant lineage. Using these annotations, we find that (i) the correlation between a cell’s lineage and its transcriptome increases from middle to late gastrulation, then falls substantially as cells in the nervous system and pharynx adopt their terminal fates; (ii) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and (iii) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.
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Callaway, Edward M., Hong-Wei Dong, Joseph R. Ecker, Michael J. Hawrylycz, Z. Josh Huang, Ed S. Lein, John Ngai, et al. "A multimodal cell census and atlas of the mammalian primary motor cortex." Nature 598, no. 7879 (October 6, 2021): 86–102. http://dx.doi.org/10.1038/s41586-021-03950-0.

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AbstractHere we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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Altıntaş, Ali, Rhianna C. Laker, Christian Garde, Romain Barrès, and Juleen R. Zierath. "Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development." Epigenomics 12, no. 8 (April 2020): 701–13. http://dx.doi.org/10.2217/epi-2019-0391.

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Aim: Innate circadian rhythms are critical for optimal tissue-specific functions, including skeletal muscle, a major insulin-sensitive tissue responsible for glucose homeostasis. We determined whether transcriptional oscillations are associated with CpG methylation changes in skeletal muscle. Materials & methods: We performed rhythmicity analysis on the transcriptome and CpG methylome of circadian synchronized myotubes. Results: We identified several transcripts and CpG-sites displaying oscillatory behavior, which were enriched with Gene Ontology terms related to metabolism and development. Oscillating CpG methylation was associated with rhythmic expression of 31 transcripts. Conclusion: Although circadian oscillations may be regulated by rhythmic DNA methylation, strong rhythmic associations between transcriptome and CpG methylation were not identified. This resource constitutes a transcriptomic/epigenomic atlas of skeletal muscle and regulation of circadian rhythms.
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D’Mello, Adonis, Ashleigh N. Riegler, Eriel Martínez, Sarah M. Beno, Tiffany D. Ricketts, Ellen F. Foxman, Carlos J. Orihuela, and Hervé Tettelin. "An in vivo atlas of host–pathogen transcriptomes during Streptococcus pneumoniae colonization and disease." Proceedings of the National Academy of Sciences 117, no. 52 (December 14, 2020): 33507–18. http://dx.doi.org/10.1073/pnas.2010428117.

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Streptococcus pneumoniae (Spn) colonizes the nasopharynx and can cause pneumonia. From the lungs it spreads to the bloodstream and causes organ damage. We characterized the in vivo Spn and mouse transcriptomes within the nasopharynx, lungs, blood, heart, and kidneys using three Spn strains. We identified Spn genes highly expressed at all anatomical sites and in an organ-specific manner; highly expressed genes were shown to have vital roles with knockout mutants. The in vivo bacterial transcriptome during colonization/disease was distinct from previously reported in vitro transcriptomes. Distinct Spn and host gene-expression profiles were observed during colonization and disease states, revealing specific genes/operons whereby Spn adapts to and influences host sites in vivo. We identified and experimentally verified host-defense pathways induced by Spn during invasive disease, including proinflammatory responses and the interferon response. These results shed light on the pathogenesis of Spn and identify therapeutic targets.
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Song, Liting, Shaojun Pan, Zichao Zhang, Longhao Jia, Wei-Hua Chen, and Xing-Ming Zhao. "STAB: a spatio-temporal cell atlas of the human brain." Nucleic Acids Research 49, no. D1 (September 25, 2020): D1029—D1037. http://dx.doi.org/10.1093/nar/gkaa762.

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Abstract The human brain is the most complex organ consisting of billions of neuronal and non-neuronal cells that are organized into distinct anatomical and functional regions. Elucidating the cellular and transcriptome architecture underlying the brain is crucial for understanding brain functions and brain disorders. Thanks to the single-cell RNA sequencing technologies, it is becoming possible to dissect the cellular compositions of the brain. Although great effort has been made to explore the transcriptome architecture of the human brain, a comprehensive database with dynamic cellular compositions and molecular characteristics of the human brain during the lifespan is still not available. Here, we present STAB (a Spatio-Temporal cell Atlas of the human Brain), a database consists of single-cell transcriptomes across multiple brain regions and developmental periods. Right now, STAB contains single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With STAB, the landscape of cell types and their regional heterogeneity and temporal dynamics across the human brain can be clearly seen, which can help to understand both the development of the normal human brain and the etiology of neuropsychiatric disorders. STAB is available at http://stab.comp-sysbio.org.
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Dargahi, Daryanaz, Richard D. Swayze, Leanna Yee, Peter J. Bergqvist, Bradley J. Hedberg, Alireza Heravi-Moussavi, Edie M. Dullaghan, et al. "A Pan-Cancer Analysis of Alternative Splicing Events Reveals Novel Tumor-Associated Splice Variants of Matriptase." Cancer Informatics 13 (January 2014): CIN.S19435. http://dx.doi.org/10.4137/cin.s19435.

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High-throughput transcriptome sequencing allows identification of cancer-related changes that occur at the stages of transcription, pre-messenger RNA (mRNA), and splicing. In the current study, we devised a pipeline to predict novel alternative splicing (AS) variants from high-throughput transcriptome sequencing data and applied it to large sets of tumor transcriptomes from The Cancer Genome Atlas (TCGA). We identified two novel tumor-associated splice variants of matriptase, a known cancer-associated gene, in the transcriptome data from epithelial-derived tumors but not normal tissue. Most notably, these variants were found in 69% of lung squamous cell carcinoma (LUSC) samples studied. We confirmed the expression of matriptase AS transcripts using quantitative reverse transcription PCR (qRT-PCR) in an orthogonal panel of tumor tissues and cell lines. Furthermore, flow cytometric analysis confirmed surface expression of matriptase splice variants in chinese hamster ovary (CHO) cells transiently transfected with cDNA encoding the novel transcripts. Our findings further implicate matriptase in contributing to oncogenic processes and suggest potential novel therapeutic uses for matriptase splice variants.
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Wucher, Valentin, Reza Sodaei, Raziel Amador, Manuel Irimia, and Roderic Guigó. "Day-night and seasonal variation of human gene expression across tissues." PLOS Biology 21, no. 2 (February 6, 2023): e3001986. http://dx.doi.org/10.1371/journal.pbio.3001986.

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Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues. Overall, most variation across tissues during day-night and among seasons was unique to each cycle. Although all tissues remodeled their transcriptomes, brain and gonadal tissues exhibited the highest seasonality, whereas those in the thoracic cavity showed stronger day-night regulation. Core clock genes displayed marked day-night differences across multiple tissues, which were largely conserved in baboon and mouse, but adapted to their nocturnal or diurnal habits. Seasonal variation of expression affected multiple pathways, and it was enriched among genes associated with the immune response, consistent with the seasonality of viral infections. Furthermore, they unveiled cytoarchitectural changes in brain regions. Altogether, our results provide the first combined atlas of how transcriptomes from human tissues adapt to major cycling environmental conditions. This atlas may have multiple applications; for example, drug targets with day-night or seasonal variation in gene expression may benefit from temporally adjusted doses.
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Penin, Aleksey A., Anna V. Klepikova, Artem S. Kasianov, Evgeny S. Gerasimov, and Maria D. Logacheva. "Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum." Genes 10, no. 1 (January 15, 2019): 50. http://dx.doi.org/10.3390/genes10010050.

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The knowledge of gene functions in model organisms is the starting point for the analysis of gene function in non-model species, including economically important ones. Usually, the assignment of gene functions is based on sequence similarity. In plants, due to a highly intricate gene landscape, this approach has some limitations. It is often impossible to directly match gene sets from one plant species to another species based only on their sequences. Thus, it is necessary to use additional information to identify functionally similar genes. Expression patterns have great potential to serve as a source of such information. An important prerequisite for the comparative analysis of transcriptomes is the existence of high-resolution expression maps consisting of comparable samples. Here, we present a transcriptome atlas of tomato (Solanum lycopersicum) consisting of 30 samples of different organs and developmental stages. The samples were selected in a way that allowed for side-by-side comparison with the Arabidopsis thaliana transcriptome map. Newly obtained data are integrated in the TraVA database and are available online, together with tools for their analysis. In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes.
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Nomburg, Jason, Wei Zou, Thomas C. Frost, Chandreyee Datta, Shobha Vasudevan, Gabriel J. Starrett, Michael J. Imperiale, Matthew Meyerson, and James A. DeCaprio. "Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses." PLOS Pathogens 18, no. 4 (April 1, 2022): e1010401. http://dx.doi.org/10.1371/journal.ppat.1010401.

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Polyomaviruses (PyV) are ubiquitous pathogens that can cause devastating human diseases. Due to the small size of their genomes, PyV utilize complex patterns of RNA splicing to maximize their coding capacity. Despite the importance of PyV to human disease, their transcriptome architecture is poorly characterized. Here, we compare short- and long-read RNA sequencing data from eight human and non-human PyV. We provide a detailed transcriptome atlas for BK polyomavirus (BKPyV), an important human pathogen, and the prototype PyV, simian virus 40 (SV40). We identify pervasive wraparound transcription in PyV, wherein transcription runs through the polyA site and circles the genome multiple times. Comparative analyses identify novel, conserved transcripts that increase PyV coding capacity. One of these conserved transcripts encodes superT, a T antigen containing two RB-binding LxCxE motifs. We find that superT-encoding transcripts are abundant in PyV-associated human cancers. Together, we show that comparative transcriptomic approaches can greatly expand known transcript and coding capacity in one of the simplest and most well-studied viral families.
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Wang, Jiabin, Shi Yan, Xiaoli Chen, Aowen Wang, Zhibin Han, Binchao Liu, and Hong Shen. "Identification of Prognostic Biomarkers for Glioblastoma Based on Transcriptome and Proteome Association Analysis." Technology in Cancer Research & Treatment 21 (January 1, 2022): 153303382110352. http://dx.doi.org/10.1177/15330338211035270.

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Objective: Glioblastoma multiforme (GBM) is the most malignant primary brain tumor in adults. This study aimed to identify significant prognostic biomarkers related to GBM. Methods: We collected 3 GBM and 3 healthy human brain samples for transcriptome and proteomic sequencing analysis. Differentially expressed genes (DEGs) between GBM and control samples were identified using the edge R package in R. Functional enrichment analyses, prediction of long noncoding RNA target genes, and protein-protein interaction network analyses were performed. Subsequently, transcriptomic and proteomic association analyses, validation using The Cancer Genome Atlas (TCGA) database, and survival and prognostic analyses were conducted. Then the hub genes directly related to GBM were screened. Finally, the expression of key genes was verified by quantitative polymerase chain reaction (qPCR). Results: Totally, 1140 transcripts and 503 proteins were significantly up- or down-regulated. A total of 25 genes were upregulated and 62 were downregulated at both the transcriptome and proteome levels. Results from TCGA database showed that 84 of these 87 genes matched with transcriptome sequencing results. A Cox regression analysis suggested that Fibronectin 1( FN1) was a prognostic risk factor. The qPCR results showed that FN1 was significantly upregulated in GBM samples. Conclusions: FN1 may play a role in GBM progression through ECM-receptor interaction and PI3K-Akt signaling pathways. FN1 may be considered as a prognostic biomarkers related to GBM.
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Dissertations / Theses on the topic "Transcriptome atla"

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Adekunle, Danielle(Danielle Aduke). "Transcriptome-wide organization of subcellular microenvironments revealed by ATLAS-Seq." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/130189.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, May, 2020
Cataloged from student-submitted PDF of thesis.
Includes bibliographical references.
Subcellular localization of RNAs is a ubiquitous and evolutionarily conserved process that provides an additional layer of transcriptome organization promoting coordinated control of gene expression in both space and time. It has been shown to contribute to processes ranging from cell fate determination and embryonic patterning to local translation and directed cell movement. Elegant efforts focused on a small handful of RNAs have established RNA localization to play key roles in cell function - yet recent studies suggest that specific localization patterns are the rule, not the exception, across the transcriptome. We still lack global maps and organizing principles for how RNAs are localized in cells and tissues.
This dissertation details the findings of a new approach to investigating RNA localization on a transcriptome-wide scale, ATLAS-Seq, a detergent-free method that generates transcriptomes and proteomes from tissue lysates fractionated across a continuous sucrose gradient by density ultracentrifugation. We conducted proteomic analyses of fractions to determine separation of subcellular compartments. Transcriptomic analyses revealed that RNAs sedimenting similarly across gradients encode proteins in similar protein complexes, cellular compartments, or with similar biological functions, suggesting that RNAs that are functionally related are cosegregated to be coregulated. Overall, most RNAs sedimented differently than their encoded protein counterparts, signifying that most RNA compartmentalization is not directed at restricting RNA localization to the final destination of their protein product.
To identify regulatory RNA binding proteins potentially driving these patterns, we correlated their sedimentation profiles to all RNAs, confirming known protein-RNA interactions and predicting new associations. Interestingly, hundreds of alternative RNA isoforms exhibited distinct sedimentation patterns across the gradient, despite sharing most of their coding sequence. These results provide new insights into establishment and maintenance of subcellular organization of the transcriptome.
by Danielle Adekunle.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
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Teixeira, Paulo José Pereira Lima 1986. "Construção de um atlas transcriptômico para o estudo da doença vassoura de bruxa do cacaueiro." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316788.

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Orientadores: Gonçalo Amarante Guimarães Pereira, Jorge Maurício Costa Mondego
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: O cacaueiro se destaca como uma das principais culturas perenes na agricultura, sendo economicamente relevante por fornecer a matéria prima para a fabricação do chocolate, um produto que movimenta bilhões de dólares no mercado mundial a cada ano. Apesar de sua importância, o cacaueiro é drasticamente atacado por diversas doenças que diminuem sua produtividade e reduzem a qualidade das amêndoas do cacau. Dentre estas, a vassoura de bruxa, causada pelo basidiomiceto Moniliophthora perniciosa, é um importante fator limitante da produção cacaueira nas Américas. Utilizando tecnologias de sequenciamento de DNA de nova geração, realizamos uma abrangente análise transcriptômica da vassoura de bruxa neste trabalho. Um banco de dados denominado Atlas Transcriptômico da Vassoura de Bruxa foi construído, o qual compreende aproximadamente 60 bibliotecas de RNA-seq representativas dos mais variados estágios de desenvolvimento, condições de crescimento e respostas a estresse do fungo M. perniciosa sob condições in vitro e in planta. O primeiro capítulo desta tese apresenta uma análise global do Atlas Transcriptômico da vassoura de bruxa. Este conjunto de dados tem suportado uma série de estudos específicos relacionados a variados aspectos da doença, os quais são apresentados e detalhados nos demais capítulos da tese. Notavelmente, uma análise detalhada da interação biotrófica entre o cacaueiro e o fungo M. perniciosa (Capítulo II) revelou a ocorrência de intensa reprogramação transcricional e importantes alterações fisiológicas em plantas infectadas, incluindo a ativação de respostas de defesa ineficientes e a ocorrência de privação de carbono. Curiosamente, um processo de senescência prematura se estabelece no tecido infectado e parece ser um evento central no desenvolvimento da doença, possivelmente disparando o início da fase necrotrófica desta interação planta-patógeno. Ainda, nossos dados também permitiram a identificação de potenciais efetores de virulência em M. perniciosa, como também a caracterização do status metabólico do fungo durante a infecção do cacaueiro. Um modelo detalhado que sumariza os aspectos moleculares da vassoura de bruxa foi elaborado. De maneira geral, o Atlas Transcriptômico da Vassoura de Bruxa representa um importante avanço no estudo desta doença e tem servido como ponto de partida para uma série de estudos adicionais. A utilização destes dados na identificação e caracterização de potenciais fatores de patogenicidade de M. perniciosa (Capítulos III, IV e VI) e de mecanismos de defesa do cacaueiro (Capítulo V) também é apresentada nesta tese
Abstract: Cacao stands out as one of the major perennial crops in the world, being economically relevant as the source of chocolate, a multi-billion dollar product appreciated worldwide. Despite its importance, cacao is seriously affected by several diseases that reduce crop yield and decrease the quality of cocoa beans. Among them, the witches' broom disease (WBD), caused by the basidiomycete Moniliophthora perniciosa, is a major constraint for cacao production in the Americas. Using next generation sequencing technologies, a comprehensive transcriptomic analysis of WBD was performed. We developed a database named "WBD Transcriptome Atlas", which comprises approximately 60 RNA-seq libraries that represent a wide range of developmental stages, growth conditions and stress responses of the fungus, either under in vitro or in planta conditions. The first chapter of this thesis presents a global analysis of the WBD Transcriptome Atlas. This data set has supported a number of specific analyses related to several aspects of WBD, which are presented and detailed in the other chapters of the thesis. Strikingly, a detailed analysis of the biotrophic interaction between M. perniciosa and cacao (Chapter I) revealed the occurrence of intense transcriptional reprogramming and remarkable physiological alterations in infected plants, including the activation of ineffective defense responses and the occurrence of carbon deprivation. Curiously, a premature senescence process is established in infected tissues and appears to be a central event in WBD, possibly triggering the onset of the necrotrophic stage of this plant-pathogen interaction. Additionally, our data also allowed the identification of potential virulence effectors in M. perniciosa, as well as the characterization of the metabolic status of the fungus during cacao infection. A detailed model summarizing the molecular aspects of WBD is presented. Overall, the WBD Transcriptome Atlas represents an important advance in the study of this disease and constitutes a starting point for a number of additional studies. The use of these data in the identification and characterization of potential pathogenicity factors of M. perniciosa (Chapters III, IV and VI) and defense mechanisms of cacao (Chapter V) will also be presented in this thesis
Doutorado
Genetica de Microorganismos
Doutor em Genetica e Biologia Molecular
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Rodovalho, Cynara de Melo [UNESP]. "Caracterização do transcriptoma e genoma mitocondrial da formiga cortadeira Atta laevigata (Formicidae : Attini)." Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/100531.

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Formigas cortadeiras do gênero Atta, popularmente conhecidas como saúvas, são as mais derivadas dentro da tribo Attini. Apresentam grande importância ecológica, porém, pelo hábito de cortarem folhas para manutenção do fungo simbionte e pelo enorme tamanho das colônias, causam muitos prejuízos às lavouras, pastagens e plantações, sendo consideradas pragas agrícolas. Atta laevigata Smith, 1858 apresenta vasta distribuição pelo Brasil e é responsável pela herbivoria de inúmeras plantas dicotiledôneas, gramíneas e espécies nativas de diferentes biomas. O presente trabalho teve como objetivos a caracterização parcial do transcriptoma e do genoma mitocondrial de A. laevigata. Foram caracterizadas 2006 sequências únicas do transcriptoma, a partir de uma biblioteca de cDNA preparada com indivíduos inteiros da formiga. Entre essas sequências, 16 provavelmente representam genes com grande número de transcritos. Esses 16 genes estão relacionados a três funções celulares: (i) conservação de energia através de reações redox na mitocôndria; (ii) estrutural, pelo citoesqueleto e músculos; (iii) regulação da expressão gênica e metabolismo. Considerando o estilo de vida e processos biológicos chaves para essas formigas, 146 sequências foram identificadas com base na sua utilização para o controle de cortadeiras pragas. A partir de dados da biblioteca de cDNA e procedimentos envolvendo primer walking, o genoma mitocondrial de A. laevigata foi parcialmente caracterizado, apresentandose com 17920 pb, maior, portanto, do que outros já descritos em Hymenoptera, mesmo considerando-se a impossibilidade de determinação da sequência de uma pequena porção do mtDNA, envolvendo a região controle, uma parte do 12S e os tRNAs S1, V e M. Como já descrito para outros mitogenomas, o de A. laevigata apresentou alto conteúdo AT, os mesmos 13 genes codificadores...
Leafcutter ants from Atta genus, popularly known as “saúvas”, are the most derived of the tribe Attini. They have major ecological importance, but, because of their habit of cutting leaves for the maintenance of the symbiotic fungus and the huge colony size, they impose severe economic damages to plantations, pastures, and agriculture, being considered as agriculture pests. Atta laevigata shows wide distribution in Brazil and it is responsible for the herbivory of many dicots, grass, and native species from different biomes. The present work aimed to characterize the transcriptome and the mitochondrial genome of A. laevigata. 2,006 unique sequences of the transcriptome were characterized from a cDNA library constructed with whole individuals. Among those sequences, 16 are likely from genes with high number of transcripts. Those 16 genes are related with three cellular functions: (i) energy conservation through redox reactions in mitochondria; (ii) cytoskeleton and muscle structuring; (iii) regulation of gene expression and metabolism. Based on lifestyle and key biological processes of these ants, 146 sequences were identified with potential use for controlling pest leafcutters. Using data from cDNA library and primer walking proceedings, the mitochondrial genome of A. laevigata was partially characterized with 17,920 bp, being larger than the others already described for Hymenoptera. A small part of the mtDNA was not sequenced, including the control region, a portion of 12S and tRNAs S1, V, and M. As described before for other mitogenomes, A. laevigata mtDNA displayed high AT contain, the same 13 proteincoding genes and the two ribosomal subunits with length and location according to the hypothetic ancestral mitogenome. Rearrangements were found for the tRNAs, but the most remarkable difference were the high number and longer length of intergenic regions presented in the mtDNA... (Complete abstract click electronic access below)
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4

Rodovalho, Cynara de Melo. "Caracterização do transcriptoma e genoma mitocondrial da formiga cortadeira Atta laevigata (Formicidae : Attini) /." Rio Claro : [s.n.], 2011. http://hdl.handle.net/11449/100531.

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Resumo: Formigas cortadeiras do gênero Atta, popularmente conhecidas como saúvas, são as mais derivadas dentro da tribo Attini. Apresentam grande importância ecológica, porém, pelo hábito de cortarem folhas para manutenção do fungo simbionte e pelo enorme tamanho das colônias, causam muitos prejuízos às lavouras, pastagens e plantações, sendo consideradas pragas agrícolas. Atta laevigata Smith, 1858 apresenta vasta distribuição pelo Brasil e é responsável pela herbivoria de inúmeras plantas dicotiledôneas, gramíneas e espécies nativas de diferentes biomas. O presente trabalho teve como objetivos a caracterização parcial do transcriptoma e do genoma mitocondrial de A. laevigata. Foram caracterizadas 2006 sequências únicas do transcriptoma, a partir de uma biblioteca de cDNA preparada com indivíduos inteiros da formiga. Entre essas sequências, 16 provavelmente representam genes com grande número de transcritos. Esses 16 genes estão relacionados a três funções celulares: (i) conservação de energia através de reações redox na mitocôndria; (ii) estrutural, pelo citoesqueleto e músculos; (iii) regulação da expressão gênica e metabolismo. Considerando o estilo de vida e processos biológicos chaves para essas formigas, 146 sequências foram identificadas com base na sua utilização para o controle de cortadeiras pragas. A partir de dados da biblioteca de cDNA e procedimentos envolvendo primer walking, o genoma mitocondrial de A. laevigata foi parcialmente caracterizado, apresentandose com 17920 pb, maior, portanto, do que outros já descritos em Hymenoptera, mesmo considerando-se a impossibilidade de determinação da sequência de uma pequena porção do mtDNA, envolvendo a região controle, uma parte do 12S e os tRNAs S1, V e M. Como já descrito para outros mitogenomas, o de A. laevigata apresentou alto conteúdo AT, os mesmos 13 genes codificadores... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Leafcutter ants from Atta genus, popularly known as "saúvas", are the most derived of the tribe Attini. They have major ecological importance, but, because of their habit of cutting leaves for the maintenance of the symbiotic fungus and the huge colony size, they impose severe economic damages to plantations, pastures, and agriculture, being considered as agriculture pests. Atta laevigata shows wide distribution in Brazil and it is responsible for the herbivory of many dicots, grass, and native species from different biomes. The present work aimed to characterize the transcriptome and the mitochondrial genome of A. laevigata. 2,006 unique sequences of the transcriptome were characterized from a cDNA library constructed with whole individuals. Among those sequences, 16 are likely from genes with high number of transcripts. Those 16 genes are related with three cellular functions: (i) energy conservation through redox reactions in mitochondria; (ii) cytoskeleton and muscle structuring; (iii) regulation of gene expression and metabolism. Based on lifestyle and key biological processes of these ants, 146 sequences were identified with potential use for controlling pest leafcutters. Using data from cDNA library and primer walking proceedings, the mitochondrial genome of A. laevigata was partially characterized with 17,920 bp, being larger than the others already described for Hymenoptera. A small part of the mtDNA was not sequenced, including the control region, a portion of 12S and tRNAs S1, V, and M. As described before for other mitogenomes, A. laevigata mtDNA displayed high AT contain, the same 13 proteincoding genes and the two ribosomal subunits with length and location according to the hypothetic ancestral mitogenome. Rearrangements were found for the tRNAs, but the most remarkable difference were the high number and longer length of intergenic regions presented in the mtDNA... (Complete abstract click electronic access below)
Orientador: Maurício Bacci Júnior
Coorientador: Henrique Ferreira
Banca: Flavio Henrique da Silva
Banca: Marco Antonio del Lama
Banca: Mariana Lúcio Lyra
Banca: Klaus Hartmann Hartfelder
Doutor
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Salvatico, Jose. "The Expression of MKRN1, an E3 Ubiquitin Ligase for Telomerase Reverse Transcriptase, Is Induced with Differentiation Therapy in Leukemia." Master's thesis, University of Central Florida, 2009. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3744.

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Telomeres are important structural and functional components of chromosomes, serving to provide stability and enabling full replication of the chromosomes. However, a shortening of the telomeres occurs with each cell division that can be fixed by a polymerase activity provided by telomerase, preventing this loss which would otherwise eventually lead to chromosome end-to-end fusions, senescence and cell death. The telomerase activity is present in stem cells and germ line cells, but absent or barely noticeable in adult somatic cells. However, in approximately 80-90% of transformed somatic cells the telomerase activity is recovered, resulting in a "telomerase positive phenotype". This phenotype has been a prime target in cancer research, and recently a novel mechanism for regulating telomerase levels has been uncovered. Makorin 1 RING finger protein (MKRN1) was found to be an E3 ubiquitin ligase for hTERT, the rate-limiting catalytic component of telomerase, leading to the ubiqutin-mediated 26s proteasomal degradation of hTERT and reduced telomerase activity. So, MKRN1 plays a role in telomere homeostasis. In this study we looked at the expression of MKRN1 in numerous tumor cell lines (Hela, HCT116, HL60) and the normal diploid fibroblasts (WI-38). In the latter cell line, basal levels of MKRN1 were found to increase 6-fold when the cells were serum starved and arrested in G1/G0. In contrast, the cancer cell lines expressed MKRN1 at low levels or undetectable. This would indicate that MKRN1 is up-regulated in resting or G1 arrested cells.In one cell line the promyelocytic leukemia, HL-60, showed no protein levels of MKRN1. This cell line is able to be terminally differentiated upon ATRA treatment, when cells are arrested at G1. In this model system of cellular differentiation hTERT mRNA levels and telomerase activity decrease drastically and quickly. We hypothesized that the differentiation of HL-60 induced by ATRA would be accompanied by an increase in MKRN1 levels. MKRN1 mRNA and protein levels were strongly up-regulated during the ATRA-mediated differentiation of HL-60 cells. Although, a decrease in hTERT mRNA is a contributor to telomerase inhibition during cellular differentiation; our data indicate that the up-regulation of MKRN1 ensures the effective removal of residual telomerase activity by the ubiquitin-mediated degradation pathway at the proteasome.
M.S.
Department of Molecular Biology and Microbiology
Burnett College of Biomedical Sciences
Molecular and Microbiology MS
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Tondeur, Sylvie. "Cellule souches hématopoïétiques et cellules souches embryonnaires humaines : analyse du transcriptome et mise en ligne des données par la création d'un atlas d'expression." Montpellier 1, 2009. http://www.theses.fr/2009MON1T012.

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L'étude du transcriptome par les puces à ADN permet de mesurer l'expression globale des gènes et a incontestablement modifié notre manière d'appréhender les questions biologiques. Nous avons appliqué cette technologie à l'étude des cellules souches. Par l'analyse du transcriptome des cellules souches embryonnaires humaines (CSEh), un modèle essentiel de cellules pluripotentes, nous avons pu mieux définir les mécanismes moléculaires de la pluripotence. En particulier, nous avons comparé des CSEh à des ovocytes humains pour identifier les déterminants intrinsèques de la pluripotence. Les puces Affymetrix Exon ST 1. 0 permettent d'étudier le transcriptome avec une résolution jamais atteinte jusqu'à présent, par la mesure de l'expression de l'ensemble des exons du génome. Nous avons utilisé ces nouvelles puces pour cartographier le profil d'expression exonique (exome) des cellules souches hématopoïétiques et des cellules sanguines normales. Ce travail a mis en évidence des évènement d'épissage alternatif spécifiques du tissu hématopoïétique (NEDD9, CD74) et un switch alternatif de certains transcrits au cours de la maturation (INPP4B, PTPLA, CXCL3 et COMMD6). Les gènes présentant ces évènements d'épissage sont particulièrement impliqués dans la mobilité cellulaire et la réponse immunitaire. Enfin, nous avons créé un atlas internet, Amazonia! (http://amazonia. Transcriptome. Eu/), pour un accès aisé à des données publiques de transcriptome. Des profils d'expression géniques peuvent être visualisées sous forme d'histogrammes ou de matrices colorées dans plus de 5000 échantillons répartis dans les différentes pages thématiques, telles que «stem cell», «hematology» ou «exon»
DNA-microarray based transcriptome study can monitor the expression of a whole genome in one experiment and has completely changed our manner to conceive biological questions. We applied this technology to the study of stem cells. The transcriptome analysis of human embryonic stem cells (hESC), a main model of pluripotent stem cells, led us to better define molecular mechanisms of pluripotency. Of note we compared hESC to human oocytes in order to identify intinsic determinants of pluripotency. Affymetrix Exon ST 1. 0 microarrays are high resolution platforms that can measure the expression of all the exons of a genome. We used this new microarray to map exonic expression profile (exome) of hematopoietic stem cells and mature blood cells. Our work showed hematopoietic specific alternative splicing events (NEDD9, CD74) and an alternative switch for some transcripts during maturation (INPP4B, PTPLA, CXCL3, COMMD6). Alternatively spliced genes are notably involved in cell motility and immune response. Finally, we created a web atlas, Amazonia! (http://amazonia. Transcriptome. Eu/), for an easy access to public transciptome data. Gene expression profiles can be visualised as histograms or colored matrixes in more than 5,000 samples regrouped in thematic pages such as «stem cell», «hematology» or «exon»
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Book chapters on the topic "Transcriptome atla"

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Achim, Kaia, Hernando Martínez Vergara, and Jean-Baptiste Pettit. "Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas." In Methods in Molecular Biology, 111–25. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7213-5_7.

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Jin Lee, Dong, and Chang Pyo Hong. "Transcriptome Atlas by Long-Read RNA Sequencing: Contribution to a Reference Transcriptome." In Transcriptome Analysis. IntechOpen, 2019. http://dx.doi.org/10.5772/intechopen.84920.

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van Dam, Pieter-Jan, and Steven Van Laere. "Molecular profiling in cancer research and personalized medicine." In Oxford Textbook of Cancer Biology, edited by Francesco Pezzella, Mahvash Tavassoli, and David J. Kerr, 347–62. Oxford University Press, 2019. http://dx.doi.org/10.1093/med/9780198779452.003.0024.

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Recent efforts by worldwide consortia such as The Cancer Genome Atlas and the International Cancer Genome Consortium have greatly accelerated our knowledge of human cancer biology. Nowadays, complete sets of human tumours that have been characterized at the genomic, epigenomic, transcriptomic, or proteomic level are available to the research community. The generation of these data was made possible thanks to the application of high-throughput molecular profiling techniques such as microarrays and next-generation sequencing. The primary conclusion from current profiling experiments is that human cancer is a complex disease characterized by extreme molecular heterogeneity, both between and within the classical, tissue-defined cancer types. This molecular variety necessitates a paradigm shift in patient management, away from generalized therapy schemes and towards more personalized treatments. This chapter provides an overview of how molecular cancer profiling can assist in facilitating this transition. First, the state-of-the-art of molecular breast cancer profiling is reviewed to provide a general background. Then, the most pertinent high-throughput molecular profiling techniques along with various data mining techniques (i.e. unsupervised clustering, statistical learning) are discussed. Finally, the challenges and perspectives with respect to molecular cancer profiling, also from the perspective of personalized medicine, are summarized.
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Conference papers on the topic "Transcriptome atla"

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You, Sungyong, Jayoung Kim, and Michael R. Freeman. "Abstract A1-49: Prostate cancer classification using a transcriptome atlas." In Abstracts: AACR Special Conference: Translation of the Cancer Genome; February 7-9, 2015; San Francisco, CA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.transcagen-a1-49.

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You, Sungyong, Jayoung Kim, and Michael R. Freeman. "Abstract B1-63: Prostate cancer classification using a transcriptome atlas." In Abstracts: AACR Special Conference: Computational and Systems Biology of Cancer; February 8-11, 2015; San Francisco, CA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.compsysbio-b1-63.

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Hulstaert, Eva, Annelien Morlion, Francisco Avila Cobos, Kimberly Verniers, Justine Nuytens, Eveline Vanden Eynde, Nurten Yigit, et al. "Abstract PR15: Charting extracellular transcriptomes in The Human Biofluid RNA Atlas." In Abstracts: AACR Special Conference on Advances in Liquid Biopsies; January 13-16, 2020; Miami, FL. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3265.liqbiop20-pr15.

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Abdelmoula, Walid M., Ricardo J. Carreira, Reinald Shyti, Benjamin Balluff, Else Tolner, Arn M. J. M. van den Maagdenberg, B. P. F. Lelieveldt, Liam McDonnell, and Jouke Dijkstra. "Automatic registration of imaging mass spectrometry data to the Allen Brain Atlas transcriptome." In SPIE Medical Imaging, edited by Sebastien Ourselin and Martin A. Styner. SPIE, 2014. http://dx.doi.org/10.1117/12.2043653.

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Tsang, Hiu-Gwen, Emily L. Clark, Stephen J. Bush, David A. Hume, Brendan M. Corcoran, Vicky E. MacRae, and Kim M. Summers. "8 Generating a genomic-wide transcriptomic atlas of the mammalian cardiovascular system." In 20th Scottish Cardiovascular, Forum Abstracts, February 4th 2017, University of Glasgow, UK. BMJ Publishing Group Ltd and British Cardiovascular Society, 1997. http://dx.doi.org/10.1136/heartjnl-2017-311433.8.

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Hoang, Margaret L., Michelle Kriner, Zoey Zhou, Zach Norgaard, Kristina Sorg, Chris Merritt, Erin Piazza, et al. "Abstract 1364: Spatially-resolvedin situexpression profiling using the GeoMx™ Cancer Transcriptome Atlas panel in FFPE tissue." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-1364.

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King, Ryan, Azim Amirabad, Amir Bayegan, Joachim Theilhaber, Nicole Acuff, Shannon McGrath, Xiangming Li, Franck Rapaport, Jack Pollard, and Donald Jackson. "1010 A single-cell transcriptomic atlas of human NK cells to guide cancer immunotherapy." In SITC 37th Annual Meeting (SITC 2022) Abstracts. BMJ Publishing Group Ltd, 2022. http://dx.doi.org/10.1136/jitc-2022-sitc2022.1010.

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Sinjab, Ansam, Guangchun Han, Warapen Treekitkarnmongkol, Patrick Brennan, Kieko Hara, Kyle Chang, Elena Bogatenkova, et al. "Abstract 1518: A single-cell transcriptomic atlas of lung adenocarcinoma and adjacent normal-appearing tissue." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-1518.

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Runyon, Jessica, Christian Nievera, and Vijay Baichwal. "151 Using additional morphology markers in NanoString® GeoMx® whole transcriptome atlas assay to assess NSCLC tumor subtype." In SITC 37th Annual Meeting (SITC 2022) Abstracts. BMJ Publishing Group Ltd, 2022. http://dx.doi.org/10.1136/jitc-2022-sitc2022.0151.

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Korkut, Anil, Sobia Zaidi, Rupa Kanchi, Ashton C. Berger, Gordon Robertson, Lawrence N. Kwong, Mike Datto, et al. "Abstract 3413: A pan-cancer atlas of genomic, epigenomic and transcriptomic alterations in the TGF-β pathway." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-3413.

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Reports on the topic "Transcriptome atla"

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Mockler, Todd. A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon. Office of Scientific and Technical Information (OSTI), April 2017. http://dx.doi.org/10.2172/1351713.

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