Northern analysis

A total of 20 μl of gradient fraction was mixed with 30 μl of formamide (final concentration 60%) and 5 μl of 10×load dye (50 mM Tris–HCl, pH 7.6, 0.25% bromophenol blue, 60% glycerol, 1% sodium dodecyl sulphate (SDS)). Samples were incubated at 65°C for 5 min, then immediately chilled on ice for 5 min before fractionation in 1% agarose gels in 0.5× sodium borate buffer at 150V. Following electrophoresis gels were transferred to Hi-Bond N membranes (Amersham) by the vacuum method. Membrane-bound RNAs were probed by hybridizing ³²P 5′-end labeled oligonucleotides at 37°C in ULTRAhyb^®-Oligo buffer (Ambion) according to manufacturers’ specifications, then visualized using a STORM phosphoImager (Molecular Dynamics).

Primer Extension were performed as described in (34).

Peptide-induced pausing and β-galactosidase assays were performed as described previously (38).