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What Is the Transcriptome and How It Is Evaluated

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Transcriptomics in Health and Disease

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Abstract

The concept of the transcriptome revolves around the complete set of transcripts present in a given cell type, tissue, or organ and encompasses both coding and noncoding RNA molecules, although we often assume that it consists only of messenger RNAs (mRNAs) because of their importance in encoding proteins. Unlike the nuclear genome, whose composition and size are essentially static, the transcriptome often changes. The transcriptome is influenced by the phase of the cell cycle, the organ, exposure to drugs or physical agents, aging, diseases, and a multitude of other variables, all of which must be considered at the time of its determination. However, it is precisely this property that makes the transcriptome useful for the discovery of gene function and as a molecular signature. In this chapter, we review the beginnings of transcriptome research, the main types of RNA molecules found in a mammalian cell, the methods of analysis, and the bioinformatics pipelines used to organize and interpret the large quantities of data generated by the two current gold-standard methods of analysis: microarrays and high-throughput RNA sequencing (RNA-Seq). Attention is also given to noncoding RNAs, using microRNAs (miRNAs) as an example because they physically interact with mRNAs and play a role in the fine control of gene expression.

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Acknowledgments

Our laboratories are funded by the following agencies: Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, São Paulo, Brazil), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Brasília, Brazil), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Brasília, Brazil, through financial code 001), Institut National de la Santé et de la Recherche Médicale (INSERM, Paris, France), and ARCUS-PACA (Provence-Alpes-Côte d’Azur)-Brésil Cooperation Agreement.

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Authors and Affiliations

  1. Molecular Immunogenetics Group, Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil

    Amanda F. Assis, Ernna H. Oliveira & Geraldo A. Passos

  2. Inflammation and Pain Group, Department of Pharmacology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil

    Paula B. Donate

  3. Bioinformatics Group, Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil

    Silvana Giuliatti

  4. Laboratory TAGC INSERM U1090, National Institute for Health and Medical Research, Scientific Park of Luminy, Marseille, France

    Catherine Nguyen

  5. Laboratory of Genetics and Molecular Biology, Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil

    Geraldo A. Passos

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  1. Amanda F. Assis
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  2. Ernna H. Oliveira
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Correspondence to Geraldo A. Passos .

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    Geraldo A. Passos

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Assis, A.F., Oliveira, E.H., Donate, P.B., Giuliatti, S., Nguyen, C., Passos, G.A. (2022). What Is the Transcriptome and How It Is Evaluated. In: Passos, G.A. (eds) Transcriptomics in Health and Disease. Springer, Cham. https://doi.org/10.1007/978-3-030-87821-4_1

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