RNA-POLYMERASE-II TERNARY COMPLEXES MAY BECOME ARRESTED AFTER TRANSCRIBING TO WITHIN 10 BASES OF THE END OF LINEAR TEMPLATES

In the presence of elongation factor SII, arrested RNA polymerase II t ernary complexes cleave 7-17 nucleotides from the 3'-ends of their nas cent RNAs. It has been shown that transcription of linear templates ge nerates apparent run-off RNAs, which are nevertheless truncated upon i ncubation with SII. By using high resolution gels, we demonstrate that transcription of blunt or 3'-overhung templates with RNA polymerase I I generates two populations of ternary complexes, The first class paus es 5-10 bases prior to the end of the template strand, These complexes respond to SII by cleaving approximately 9-17 nucleotide RNAs from th eir 3'-ends and therefore may be termed arrested, A second class of co mplexes, which fail to respond to SII, transcribe to within 3 bases of the end of the template strand, These complexes appear to have run of f the template since they have released their nascent RNAs. Run-off tr anscription occurs on all types of templates, but it is the predominan t reaction on DNAs with 5'-overhung ends. Thus, RNA polymerase II tern ary complexes that retain 5-10 bases of contact with the template stra nd downstream of the catalytic site become arrested, Further reduction of downstream template contacts can lead to termination, We also show that the addition of Sarkosyl to the elongation reactions significant ly changes the pattern of transcriptional arrest near the end of linea r templates.