Evidence for conserved and nonconserved 3′-tailed mirtrons in mammals. (A) The Dlk imprinted region contains a large cluster of miRNAs, at least some of which are associated with the Mirg transcription unit, presumed to be a noncoding RNA. Closeup of mir-668 alignments reveals a conserved hairpin that resides at the 5′ splice donor of Mirg, with a 3′ tail extending to the 3′ splice acceptor; this intron also encodes a branchpoint consensus and a typical 3′ poly-polypyrimidine tract. The top expressed 3p (miRNA) and 5p (star) reads from mmu-mir-668 support this locus as being derived by 5′ splicing and 3′ trimming. (B) Example of a 3′-tailed mirtron in human PTBP1 (hsa-mir-4745), for which the dominant species derives from the 5p arm. Reads were also recovered in two independent Ago-IP data sets, supporting their classification as bona fide miRNAs. Although most 5p reads began with uridine, less abundant reads presumed to be the primary spliced products initiate with the “GU” splice donor. Note that an “aberrant” 3p species produced from a different register was not associated with Ago-IP evidence (arrow). Density plot to the right highlights the specificity of these reads from the intronic hairpin. (C) Example of 3′-tailed mirtron in human FKBP1A (hsa-mir-6869), for which reads were recovered in independent Ago-IP data sets. The secondary structure illustrates that the dominant small RNAs arrange as a duplex with 3′ overhangs.
