Fish with germ cell-specific bait, and you get a new class of RNA.
U Penn researchers CLIPped (Cross-Linked and ImmunoPrecipitated) mouse testis extract with the anti-DNA/RNA-binding protein MSY2, and caught a whole bunch of novel ~30 nt RNAs.
While about 7% of these were known piRNAs, most came from a distinct class of testicular RNAs that are bound by MSY2, a key player in fertility. The MSY-RNAs exhibited some pretty interesting characteristics:
- They turned out to be from annotated genes, and mostly from exons. Yet there doesn’t seem to be any correlation between appearance of the MSY-RNA and transcription of the corresponding gene — many are found in a variety of tissue types, and at developmental stages, that the mRNAs are not.
- Unlike most miRNAs and piRNAs, which tend to have a 5’ U, the Dicer-independent MSY-RNAs tend to lead with 5’ A, and are probably independent of MIWI (the mouse homolog of PIWI) as well.
- MSY-RNAs can be found in both the cytoplasm and the nucleus, but are enriched in chromatin suggesting they may share a similar chromatin remodeling fondness with PIWI-piRNAs.
Are these degradation products, key players in mRNA stability, or are they involved in chromatin modeling? See for yourself at PNAS, July 2009