Genome-wide profiling of the 3′ ends of polyadenylated RNAs

Alternative polyadenylation (APA) diversifies the 3′ termini of a majority of mRNAs in most eukaryotes, and is consequently inferred to have substantial consequences for the utilization of post-transcriptional regulatory mechanisms. Since conventional RNA-sequencing methods do not accurately define mRNA termini, a number of protocols have been developed that permit sequencing of the 3′ ends of polyadenylated transcripts (3′-seq).

Researchers from Memorial Sloan Kettering Cancer Center present here a experimental protocol to generate 3′-seq libraries using a dT-priming approach, including extensive details on considerations that will enable successful library cloning. They pair this with a set of computational tools that allow the user to process the raw sequence data into a filtered set of clusters that represent high-confidence functional polyadenylation sites. The data are single-nucleotide resolution and quantitative, and can be used for downstream analyses of APA.

Overview of the 3′-seq protocol. IUPAC codes, V=A/C/G; B=C/G/T; N=A/C/G/T