Fig. 1.

Identification and annotation of conserved CHO miRNAs. (a) Small RNA reads were mapped to the entire set of known miRNA hairpin sequences, in the form of a concatenated sequence leaving spacers of 50 bases (N₅₀) between each hairpin sequence (1). In the second step, miRNA isoforms (isomiRs) were grouped and further represented by the most abundant isomiR sequence (2). For annotation of miRNA reads, three scenarios were differentiated: mapping of both arms of the hairpin duplex (A); mapping of only one arm of the hairpin duplex (B) and mapping of regions adjacent to the duplex (C). For the visualization of short read alignments to the miRNA hairpin reference sequence, VAMP, a software developed at the Center for Biotechnology in Bielefeld, Germany was used: orange bars in the upper section represent annotated hairpin sequences while the lower section shows the single-basepair coverage computed from read alignments; green color indicates perfect coverage with no mismatches, yellow color best-match coverage (containing 1–3 mismatches), and red color represents the complete coverage (reads with 1–3 mismatches that were found to align to a different hairpin at lower mismatch rate). (b) The coverage pattern for hsa-miR-18b at single-basepair level is shown in: both hairpin arms are mapped at high perfect coverage, with more reads mapping to the 5′ arm of the hairpin. (c) A locus in the hairpin genome containing 9 miRNA hairpin sequences from Rattus norvegicus is shown at lower zoom: high perfect coverage is generally observed at the 5′ and 3′ duplex positions within a hairpin. In most cases a predominant hairpin-arm exists (high coverage), while in some cases (mir-106b) both hairpins-arms show equal coverage. In a few cases, antisense alignments (mir-96, mir-98) are observed, indicated by coverage facing downwards. (For interpretation of the references to color in text, the reader is referred to the web version of the article.)