Figure 5

An intronic cluster of ncRNA genes maps at the variable mfl 3' UTRs. (A) Northern blot analysis of total RNA from male and female adult flies with genomic probes derived from the mfl 3' region (see B for genomic position). Probes 2 and 3 both detect a large transcript of about 4.4 kb (marked by the triangle) and small RNAs of about 100 nt. Note that probe 2, derived from intron 9, strongly cross-hybridizes with rRNA (asterisk on the left) because of bipartite DmSnR60 complementarity to 28S sequences. Since Drosophila 28S rRNA is processed into two fragments that migrate in a similar manner to the 18S rRNA (2.0 kb), cross-reaction labels a band with a mobility similar to that of the mfl 2.2 kb mRNA (indicated by the arrow), which is specifically recognized by probe 3. (B) Genomic organization of the cluster of small ncRNA genes intron-encoded at the mfl 3'UTRs; the four copies of the DmSnR60 C/D box snoRNA gene (a, b, c, d) and the two copies of the snm60 (a, b) exhibit a one gene-per intron organization. (C) Nucleotide sequences of DmSnR60 and snm60 isoforms. Within DmSnR60 sequences (capital letters; flanking sequences are indicated as lower case letters), dark-shaded regions indicate the D and D' boxes, while the 5'-terminal C box is grey-shaded. The D and D' antisenses able to target the Drosophila 28S rRNA are underlined. Positions of nucleotide polymorphisms among the DmSnR60 isoforms are indicated in italics. At the bottom, nucleotide sequences of the snm60 a and b isoforms [GenBank: DQ142641; DQ142642]. The vertical arrows mark the position of the 5' end of the products mapped by primer-extension (see Methods). The putative D and D' boxes are dark-shaded, the 5'-terminal C box is grey-shaded and the internal segment of perfect identity shared by the two snm60 subforms is in italics.