Degradome sequencing provides large amounts of data regarding RNA degradation. The degradome library construction described here is modified from the 5′-rapid amplification of cDNA ends (5′-RACE), and each degradome cDNA is sequenced by next-generation sequencing (NGS). Degradome profiles provide information confirming miRNA-mediated cleavage of target genes and allow the identification of novel targets. Furthermore, degradome sequencing provides additional information for the study of RNA processing, such as information regarding RNA-binding proteins. In this chapter, we describe a detailed optimized protocol for constructing a degradome library with high yield and quality, along with NGS and data mining procedures. We hope that the degradome approach will be applied to further studies of non-model organisms.
CITATION STYLE
Lin, S. S., Chen, Y., & Lu, M. Y. J. (2019). Degradome sequencing in plants. In Methods in Molecular Biology (Vol. 1932, pp. 197–213). Humana Press Inc. https://doi.org/10.1007/978-1-4939-9042-9_15
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