Global Profiling and Analysis of 5' Monophosphorylated mRNA Decay Intermediates.

Ai-Ping Chen; Wan-Chieh Chen; Bo-Han Hou; Shu-Jen Chou; Ho-Ming Chen

doi:10.1007/978-1-0716-4176-7_22

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Global Profiling and Analysis of 5' Monophosphorylated mRNA Decay Intermediates.

Ai-Ping Chen·Wan-Chieh Chen·Bo-Han Hou·Shu-Jen Chou·Ho-Ming Chen

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Abstract

During RNA turnover, the action of endo- and exo-ribonucleases can yield RNA decay intermediates with specific 5' ends. These RNA decay intermediates have been demonstrated to be the outcome of decapping, microRNA-directed endo-cleavage, or the protected fragments of ribosomes and exon-junction complexes. Therefore, global analysis of RNA decay intermediates can facilitate studies of many RNA decay pathways. In this chapter, we describe a high-throughput sequencing protocol named parallel analysis of RNA ends (PARE), which allows genome-wide profiling of 5' monophosphorylated mRNA decay intermediates from plants or other eukaryotes. Also, we present the tools and scripts necessary for the proper analysis of RNA degradome data obtained from the PARE method. Details and modifications of library construction procedures and bioinformatic analyses to optimize sequencing quality and cope with emerging sequencing platforms and findings are highlighted.

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RNA Stability RNA, Messenger High-Throughput Nucleotide Sequencing Computational Biology Sequence Analysis, RNA Gene Expression Profiling 5′-3′ RNA decay 5′P end Degradome-seq EJC footprint Endonucleolytic cleavage Ribosome footprint miRNA target Journal Article Research Support, Non-U.S. Gov't

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Ai-Ping Chen, Wan-Chieh Chen, Bo-Han Hou, Shu-Jen Chou, Ho-Ming Chen. 2025. Global Profiling and Analysis of 5' Monophosphorylated mRNA Decay Intermediates.. https://doi.org/10.1007/978-1-0716-4176-7_22

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