Previously published data have described two different strains of mice with partial deletions of the long arm of Y chromosome (Yq). Several lines of evidence indicate that the male-specific region on long arm of the Y chromosome (MSYq) in mouse is replete with highly repetitive mouse-specific sequences that are expressed in spermatids. Earlier studies have shown that genes involved in sex determination and spermatogenesis are present on the short arm. Y chromosome has come a long way from a single-gene male-determining chromosome to one that houses a few protein-coding genes besides sequences crucial for spermatogenesis and fertility. Taken together, this study provides novel insights into possible role of MSYq-derived ncRNAs in male sterility and speciation. Sperm phenotypes from the Yq-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Our study elucidates a set of autosomal genes that are potentially regulated by MSYq-derived piRNAs in mouse testis. In vitro functional assays reveal putative roles for these piRNAs in regulating autosomal genes. Thus, Pirmy and Pirmy-like RNAs act as templates for several piRNAs. Several lines of experiments show that these short homologous stretches correspond to piRNAs. Pirmy and Pirmy-like RNAs have homology to 5′/3′UTRs of these deregulated autosomal genes. Further, we identified eight differentially expressed autosome-encoded sperm proteins in a mutant mouse strain, XY RIIIqdel (2/3 Yq-deleted). We also identified Pirmy-like RNAs present in multiple copies at different loci on mouse Y chromosome. Pirmy shows a large number of splice variants in testis.
We describe a set of novel mouse male-specific Y long arm (MSYq)-derived long noncoding (lnc) transcripts, named Pirmy and Pirmy-like RNAs. Here we report a set of novel noncoding RNAs from mouse Yq and explore their connection to some of the autosomal genes expressed in testis. While a majority of the genes expressed during spermatogenesis are autosomal, mice with different deletions of the long arm of the Y chromosome (Yq) were previously also shown to be characterized by subfertility, sterility and sperm abnormalities, suggesting the presence of effectors of spermatogenesis at this location. Functions of the noncoding transcripts from Y chromosomal repeats however, remain unclear. Some of these repeats transcribe coding RNAs, the roles of which have been studied. Deciphering the functions of Y chromosome in mammals has been slow owing to the presence of repeats.
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