Transcriptional pause, arrest and termination sites for RNA polymerase II in mammalian N- and c-myc genes

Using either highly purified RNA polymerase II (pol II) elongation complexes assembled on oligo(dC)-tailed templates or promoter-initiated (extract-generated) pol II elongation complexes, the precise 3' ends of transcripts produced during transcription in vitro at several human c- and N-myc pause, arrest and termination sites were determined. Despite a low overall similarity between the entire c- and N-myc first exon sequences, many positions of pol II pausing, arrest or termination occurred within short regions of related sequence shared between the c- and N-myc templates. The c- and N-myc genes showed three general classes of sequence conservation near intrinsic pause, arrest or termination sites: (i) sites where arrest or termination occurred after the synthesis of runs of uridines (Us) preceding the transcript 3' end, (ii) sites downstream of potential RNA hairpins and (iii) sites after nucleotide addition following either a U or a C or following a combination of several pyrimidines near the transcript 3' end. The finding that regions of similarity occur near the sites of pol II pausing, arrest or termination suggests that the mechanism of c- and N-myc regulation at the level of transcript elongation may be similar and not divergent as previously proposed.