Nonadenosine residues in poly(A) tails. (A) Total frequency of reads with poly(A) tails containing nonadenosine residues. (B) Frequency of reads with varying numbers of nonadenosine residues per read. (C) Frequency of nonadenosine residues (cytidine, guanosine, and uridine) in total data sets and in transcripts with CPE motifs. (D) Example nanopore signals with decorated tails. Nonadenosine residues are highlighted. (E) Genome browser-like plot of reads aligned to the 3′UTR of the Nrgn gene, with nanopore signal indicating semi-templated poly(A) tail origin in an isoform using a proximal PAS and internal nonadenosines (guanosines) in fixed positions. The reference sequence and orthologs from various organisms, as well as the reverse complement mRNA sequence, are shown. The signal is not fully aligned (resquiggled) to the sequence (it cannot be done due to technical limitations of available algorithms). (F) Nanopore signals from semi-templated tails of the Nrgn isoform with a shorter 3′ UTR, with fixed-position nonadenosine residues (guanosines) highlighted. (G) Nanopore signals from semi-templated tails of the Tmed9 gene, with fixed-position nonadenosine residues (guanosines and cytidines) highlighted. Results presented in all panels were generated using Ninetails.
