Piwi-interacting RNAs (piRNAs) are transposon silencers that act as guides for a subfamily of Argonaute proteins—PIWI proteins—expressed in germline cells. The authors used flies with ago3 loss-of-function mutations to show that Ago3 increases levels of these piRNAs. The also show a separate, simpler, somatic, piRNA pathway that does not rely on Ago3 amplification. They used the Genome Analyzer for small RNA sequencing.

Investigation of microRNAs, which regulate gene expression, in white leghorn chicken embryo somites (connective tissue precursors) was carried out using the Genome Analyzer. The authors mapped 340,415 reads to the genome, which represented 1701 sequences. They found 85 known miRNAs and, after further investigation via Northern blot, they found eight novel miRNAs, one of which was at a high expression level in the somites.

The authors used ultra highthroughput sequencing on the Genome Analyzer, with analysis using Pipeline software, to investigate small regulatory RNAs in adult bovine kidney cell lines, either control or infected with Bovine herpesvirus 1. Of the 356 known bovine miRNAs they detected 219 and found 115 miRNA* sequences of these expressed genes. They also found “five new bovine orthologs of known mammalian miRNAs,” 268 novel miRNAs, seven mirtron candidates and 10 small nucleolar RNA (snoRNA).