Fig. 4.

Verification of transcripts forming IP-dsRNAs at the 5′ end of transcripts oriented head to tail, termed 5′/intergenic. The IP-dsRNA transcripts were confirmed by Northern blot analyses for msbA. (A) The deep-sequencing results displayed in a coverage map of input and IP libraries in the WT and rnc105 mutant strains. The height at each position indicates the number of reads that mapped to that base. The translucent box indicates the IP-dsRNA. The + strand is always shown on top (in green), and the − strand is on the bottom (in yellow). Note that the y-axis scale differs between the WT and rnc105 mutant strains. (B) Northern blot analyses of total RNA fractionated on a formaldehyde-agarose gel (Right) or a denaturing polyacrylamide gel (Left), blotted to a nylon membrane, and hybridized with oligonucleotides. The red line represents the location of the oligonucleotide probes used for the Northern blot. The predicted transcripts are denoted and marked with the appropriate band in the Northern blot. Three independent experiments were performed, and representative data are shown.