Degradome Sequencing

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.