Summary Using full-length direct RNA sequencing, this study uncovers a previously unrecognized role for stress granules in promoting selective mRNA decay during cellular stress. The findings show that mRNAs recruited to stress granules undergo preferential degradation, linking stress granule biology to RNA homeostasis.
Summary We developed RNAkinet, a neural network that identifies newly synthesized RNA molecules labeled with 5-ethynyl uridine (5EU) using nanopore direct RNA sequencing, processing raw electrical signals without requiring basecalling or sequence alignment. RNAkinet enables simultaneous analysis of RNA metabolism alongside poly(A) tail length and RNA modifications at single-molecule resolution.
Summary This methods chapter describes a protocol for transcriptome-wide measurement of differential poly(A) tail lengths using nanopore direct RNA sequencing, combined with linear mixed models for statistical analysis. The approach enables quantitative comparison of poly(A) tail dynamics across conditions and provides a framework for studying the role of deadenylation in post-transcriptional gene regulation.
Summary This review covers the post-transcriptional mechanisms by which cells regulate protein synthesis in response to stress, focusing on the roles of RNA-binding proteins, non-coding RNAs, and mRNA modifications in controlling translation. The connections between stress-responsive translational control and aging are discussed.
Summary This study discovers ribothrypsis, a previously unknown mRNA decay process in which ribosomes trigger endonucleolytic cleavage of mRNAs in a ribosome-phased pattern. Ribothrypsis operates during active translation and represents a major pathway of canonical mRNA decay in human cells.