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 complexe s assembled on oligo(dC)-tailed templates or promoter-initiated (extract-ge nerated) pol II elongation complexes, the precise 3' ends of transcripts pr oduced during transcription in vitro at several human c- and N-myc pause, a rrest and termination sites were determined. Despite a low overall similari ty between the entire c- and N-myc first exon sequences, many positions of pol II pausing, arrest or termination occurred within short regions of rela ted sequence shared between the c- and N-myc templates. The c- and N-myc ge nes showed three general classes of sequence conservation near intrinsic pa use, arrest or termination sites: (i) sites where arrest or termination occ urred after the synthesis of runs of uridines (Us) preceding the transcript 3' end, (ii) sites downstream of potential RNA hairpins and (iii) sites af ter nucleotide addition following either a U or a C or following a combinat ion of several pyrimidines near the transcript 3' end, The finding that reg ions of similarity occur near the sites of pol II pausing, arrest or termin ation suggests that the mechanism of c- and N-myc regulation at the level o f transcript elongation may be similar and not divergent as previously prop osed.