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Identifying Pri-miRNA Transcription Start Sites

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miRNA Biogenesis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1823))

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that can regulate gene expression playing vital role in nearly all biological pathways. Even though miRNAs have been intensely studied for more than two decades, information regarding miRNA transcription regulation remains limited. The rapid cleavage of primary miRNA transcripts (pri-miRNAs) by Drosha in the nucleus hinders their identification with conventional RNA-seq approaches. Identifying the transcription start site (TSS) of miRNAs will enable genome-wide identification of their expression regulators, including transcription factors (TFs), other non-coding RNAs (ncRNAs) and epigenetic modifiers, providing significant breakthroughs in understanding the mechanisms underlying miRNA expression in development and disease. Here we present a protocol that utilizes microTSS, a versatile computational framework for accurate and single-nucleotide resolution miRNA TSS predictions as well as miRGen, a database of miRNA gene TSSs coupled with genome-wide maps of TF binding sites.

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Authors and Affiliations

  1. Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA

    Georgios Georgakilas

  2. Institute for Immunology, University of Pennsylvania, Philadelphia, PA, USA

    Georgios Georgakilas

  3. Epigenetics Institute at Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Georgios Georgakilas

  4. DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece

    Nikos Perdikopanis & Artemis G. Hatzigeorgiou

  5. Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece

    Nikos Perdikopanis & Artemis G. Hatzigeorgiou

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  1. Georgios Georgakilas
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  2. Nikos Perdikopanis
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  3. Artemis G. Hatzigeorgiou
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Editors and Affiliations

  1. Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark

    Ulf Andersson Vang Ørom

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Georgakilas, G., Perdikopanis, N., Hatzigeorgiou, A.G. (2018). Identifying Pri-miRNA Transcription Start Sites. In: Ørom, U. (eds) miRNA Biogenesis. Methods in Molecular Biology, vol 1823. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-8624-8_2

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  • DOI: https://doi.org/10.1007/978-1-4939-8624-8_2

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