Cloning and expression profiling of testis-expressed piRNA-like RNAs

Using a novel small RNA cloning method, we identified 630 piRNA-like RNAs (piIRNAs) from the mouse testis, and 498 of them are novel. These piIRNA genes were mapped to all chromosomes as 71 clusters, and the majority of them (similar to 84%) are derived from intergenic, intronic, and exonic sequences. One of the structural characteristics for piIRNAs is that a single locus can encode numerous homologous piIRNAs with overlapping sequences. Hundreds or even thousands of piIRNAs from a single piIRNA gene cluster are all produced from a single long transcript. Expression profiling for 64 piIRNAs revealed that; 14% of all the piIRNAs analyzed displayed a ubiquitous expression pattern, although the majority of (similar to 86%) piIRNAs were preferentially or exclusively expressed in meiotic and haploid male germ cells of the testis. Our semiquantitative analyses also suggest that the testis is the organ with the highest expression of piIRNAs both in number and in abundance. The large number, high abundance, unique genomic locations, and biogenesis all suggest that piIRNAs have important regulatory roles not only in spermatogenesis but also in other biological processes.