Identification, expression and functional analysis of U3 snoRNA genes from Neurospora crassa

By screening of a cDNA library constructed with small RNAs from Neurospora crassa and genome analysis, three U3 snoRNAs of 262, 270 and 275 nt were identified and named as NcU3A, NcU3B and NcU3C, respectively. Expression of the three U3 snoRNA genes was further analyzed by Northern blot hybridization. Meanwhile, two 5′-truncated U3 transcripts with different sizes were also identified, indicating a complex posttranscriptional processing of the U3 snoRNAs. In addition to the known functional elements complementary to 18S rRNA, a novel antisense sequence to 26S rRNA was found in NcU3A. A primer extension assay showed that the antisense sequence did not guide 2′-O-ribose methylation of 26S rRNA but probably functioned as an rRNA chaperon. In the N. crassa genome, three U3 snoRNA genes are independently transcribed and each of them contains a small intron. The same intron-inserting site in the U3 snoRNA genes among N. crassa and yeasts shows the ancient origin of the intron in these organisms. Our results provide new insights into the structural and functional diversity of U3 snoRNA family.