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Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression

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Post-Transcriptional Gene Regulation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2404))

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Abstract

Untranslated regions of mRNA (UTRs) are involved in defining the fate of the transcript through processes such as mRNA localization, degradation, translation initiation regulation, and several others: the action of trans-factors such as RNA-binding proteins and non-coding RNAs, combined with the presence of defined sequence and structural cis-elements, ultimately determines protein synthesis levels. Identifying functional regions in UTRs and uncovering post-transcriptional regulators acting upon these is thus of paramount importance to understand this regulatory layer: these tasks can now be approached computationally to reduce the testable hypothesis space and drive the experimental validation in a more effective way.

This chapter will focus on presenting databases and tools allowing to study the various aspects of post-transcriptional regulation, including the profiling of actively translated mRNAs, regulatory network analysis (e.g., RBP and ncRNA binding sites), trans-factor binding sites prediction, motif search (sequence and secondary structure), and other aspects of this regulatory layer: two potential analysis pipelines are also presented as practical examples of how these tools could be integrated and effectively employed.

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Authors and Affiliations

  1. Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

    Eliana Destefanis & Erik Dassi

  2. Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

    Erik Dassi

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  1. Eliana Destefanis
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  2. Erik Dassi
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Correspondence to Erik Dassi .

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  1. Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy

    Erik Dassi

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Destefanis, E., Dassi, E. (2022). Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression . In: Dassi, E. (eds) Post-Transcriptional Gene Regulation. Methods in Molecular Biology, vol 2404. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1851-6_1

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  • DOI: https://doi.org/10.1007/978-1-0716-1851-6_1

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