A noncoding RNA in Saccharomyces cerevisiae is an RNase P substrate

Ribonuclease P (RNase P) is involved in regulation of noncoding RNA (ncRNA) expression in Saccharomyces cerevisiae. A hidden-in-reading-frame antisense-1 (HRA1) RNA in S. cerevisiae, which belongs to a class of ncRNAs located in the antisense strand to verified protein coding regions, was cloned for further use in RNase P assays. Escherichia coli RNase P assays in vitro of HRA1 RNA show two cleavage sites, one major and one minor in terms of rates. The same result was observed with a partially purified S. cerevisiae RNase P activity, both at 30°C and 37°C. These latter cells are normally grown at 30°C. Predictions of the secondary structure of HRA1 RNA in silico show the cleavage sites are canonical RNase P recognition sites. A relatively small amount of endogenous HRA1 RNA was identified by RT-PCR in yeast cells. The endogenous HRA1 RNA is increased in amount in strains that are deficient in RNase P activity. A deletion of 10 nucleotides in the HRA1 gene that does not overlap with the gene coding for a protein (DRS2) in the sense strand shows no defective growth in galactose or glucose. These data indicate that HRA1 RNA is a substrate for RNase P and does not appear as a direct consequence of separate regulatory effects of the enzyme on ncRNAs. Published by Cold Spring Harbor Laboratory Press.