Degradome Sequencing
Journal
Methods in Molecular Biology
Journal Volume
2900
Start Page
273
End Page
291
ISSN
1064-3745
1940-6029
ISBN
9781071643976
9781071643983
Date Issued
2025
Author(s)
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.
Subjects
5′-RACE
Degradome
microRNA
Next-generation sequencing
RNA degradation
Target RNA
Publisher
Springer US
Type
book part