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RNA Structure Determination by High-Throughput Structural Analysis

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RNA Structure Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2586))

Abstract

RNA functions are closely linked with their structures. Therefore, elucidating the secondary structure of RNAs provides crucial information regarding their function. The chemical modification or RNase-mediated digestion of single-stranded RNA has been utilized to experimentally reveal RNA secondary structures. Owing to advances in high-throughput sequencing technology and chemical analysis, RNA structural analyses that enable structural profiling at the transcriptomic scale in living cells have been developed. Here, we provide an overview of the high-throughput RNA structural (HTS) analyses and describe the computational processing steps of recent HTS analysis pipelines: PROBer, BUMHMM, and reactIDR.

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Author information

Authors and Affiliations

  1. Laboratory of Virology, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan

    Naoki Takizawa

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  1. Naoki Takizawa
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Correspondence to Naoki Takizawa .

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Editors and Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Risa Karakida Kawaguchi

  2. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan

    Junichi Iwakiri

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Takizawa, N. (2023). RNA Structure Determination by High-Throughput Structural Analysis. In: Kawaguchi, R.K., Iwakiri, J. (eds) RNA Structure Prediction. Methods in Molecular Biology, vol 2586. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2768-6_13

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  • DOI: https://doi.org/10.1007/978-1-0716-2768-6_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2767-9

  • Online ISBN: 978-1-0716-2768-6

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