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. 2025:2900:273-291.
doi: 10.1007/978-1-0716-4398-3_18.

Degradome Sequencing

Shih-Shun Lin  1 , Yihua Chen  2 , Mei-Yeh Jade Lu  3
Affiliations

Degradome Sequencing

Shih-Shun Lin et al. Methods Mol Biol. 2025.

Abstract

Degradome sequencing provides comprehensive insights into RNA degradation profiles. The method described here adapts the 5'-rapid amplification of cDNA ends (5'-RACE) technique, enabling the sequencing of degradome cDNA fragments using short-read next-generation sequencing (NGS). Degradome profiles can validate predicted miRNA-mediated cleavage of target genes and identify novel targets. Additionally, this approach offers valuable insights into RNA processing mechanisms, including the roles of RNA-binding proteins. This chapter outlines an optimized protocol for constructing a high-yield, high-quality degradome library, encompassing NGS and data analysis procedures. We anticipate that the degradome sequencing approach will be highly beneficial for studying RNA dynamics in non-model organisms.

Keywords: 5′-RACE; Degradome; Next-generation sequencing; RNA degradation; Target RNA; microRNA.

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