PiRNA-like RNAs in the marsupial Monodelphis domestica identify transcription clusters and likely marsupial transposon targets

PIWI-interacting RNAs (piRNAs) are a recently discovered class of small noncoding RNAs that have been detected in human, mouse, rat, zebrafish, and Drosophila genomes. We have utilized a size-directed small-RNA cloning procedure to clone and map more than 300 candidate piRNA-like small RNAs in the genome of the marsupial species Monodelphis domestica. Our results are consistent with those from other species in that the piRNA-like candidate sequences range in size from 28 to 31 nucleotides, show a pronounced preference for uridine at the 5' end, are transcribed from a few large clusters, appear to target transposons, and display virtually no sequence conservation.