Analysis and kinase-mediated decay of RNAs with 5´-hydroxyl termini
RNA cleavage by metal ion-independent endoribonucleases and self-cleaving ribozymes produces RNA fragments with 5 ́-hydroxyl (5 ́-OH) and 2 ́,3 ́-cyclic phosphate termini. However, RNAs with 5 ́-OH termini (5 ́-OH RNAs) are not detected by conventional sequencing methods, and 5 ́-OH RNAs cannot be directly degraded by canonical 5 ́-phosphate-dependent 5 ́→3 ́ exoribonucleases. To identify new 5 ́-OH RNA fragments, I exploited the unique ligation mechanism of E. coli RtcB RNA ligase to develop 5OH-seq, a novel method to capture and sequence 5 ́-OH RNAs. I applied 5OH-seq to budding yeast and ...