RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

We investigated co-transcriptional recruitment of pre-mRNA processing factors to human genes. Capping factors associate with paused RNA polymerase II (pol II) at the 5′ ends of quiescent genes. They also track throughout actively transcribed genes and accumulate with paused polymerase in the 3′ flanking region. The 3′ processing factors cleavage stimulation factor and cleavage polyadenylation specificity factor are maximally recruited 0.5–1.5 kilobases downstream of poly(A) sites where they coincide with capping factors, Spt5, and Ser2-hyperphosphorylated, paused pol II. 3′ end processing factors also localize at transcription start sites, and this early recruitment is enhanced after polymerase arrest with the elongation factor DRB. These results suggest that promoters may help specify recruitment of 3′ end processing factors. We propose a dual-pausing model wherein elongation arrests near the transcription start site and in the 3′ flank to allow co-transcriptional processing by factors recruited to the pol II ternary complex.