Gene silencing acts at the level of transcription. (A) Steady state mRNA of parental and integrant plants. Probes for nptII, hpt, and gus mRNA were used in Northern blots. Loading control is large ribosomal RNA stained with ethidium bromide. (B) Run-on transcription from leaf nuclei of active and inactive lines. Radioactive transcripts were used to probe target DNA specific for the full-length ubiquitin, nptII, hpt, and gus genes. In an independent experiment, 5′- and 3′-specific regions of the gus gene were used as target DNA (bottom). The run-on transcripts from the 95g and 95o nuclei were hybridized to the target DNA and the signals from each filter were normalized relative to the ubiquitin signal.