Genome-wide Mapping of 5′-monophosphorylated Ends of Mammalian Nascent RNA Transcripts

In eukaryotic cells, RNA biogenesis generally requires processing of the nascent transcript as it is being synthesized by RNA polymerase. These processing events include endonucleolytic cleavage, exonucleolytic trimming, and splicing of the growing nascent transcript. Endonucleolytic cleavage events that generate an exposed 5′-monophosphorylated (5′-PO(4)) end on the growing nascent transcript occur in the maturation of rRNAs, tRNAs, and mRNAs. These 5′-PO(4) ends can be a target of further processing or be subjected to 5′-3′ exonucleolytic digestion that may result in termination of transcription. Here, we describe how to identify 5′-PO(4) ends of intermediates in nascent RNA metabolism. We capture these species via metabolic labeling with bromouridine followed by immunoprecipitation and specific ligation of 5′-PO(4) RNA ends with the 3′-hydroxyl group of a 5′ adaptor (5′-PO(4) Bru-Seq) using RNA ligase I. These ligation events are localized at single nucleotide resolution via highthroughput sequencing, which identifies the position of 5′-PO(4) groups precisely. This protocol successfully detects the 5′monophosphorylated ends of RNA processing intermediates during production of mature ribosomal, transfer, and micro RNAs. When combined with inhibition of the nuclear 5′-3′ exonuclease Xrn2, 5′-PO(4) Bru-Seq maps the 5′ splice sites of debranched introns and mRNA and tRNA 3′ end processing sites cleaved by CPSF73 and RNaseZ, respectively. Key features • Metabolic labeling for brief periods with bromouridine focuses the analysis of 5′-PO(4) RNA ends on the population of nascent transcripts that are actively transcribed. • Detects 5′-PO(4) RNA ends on nascent transcripts produced by all RNA polymerases. • Detects 5′-PO(4) RNA ends at single nucleotide resolution.