The origins of our current understanding of control of transcription elongation lie in pioneering experiments that mapped RNA polymerase II on viral and cellular genes. These studies first uncovered the surprising excess of polymerase molecules that we now know to be situated at the at the 5′ ends of most genes in multicellular organisms. The pileup of pol II near transcription start sites reflects a ubiquitous bottle-neck that limits elongation right at the start of the transcription elongation. Subsequent seminal work identified conserved protein factors that positively and negatively control the flux of polymerase through this bottle-neck, and make a major contribution to control of gene expression. 1. Introduction The initiation phase of the RNA polymerase II (pol II) transcription cycle involves multiple events, including recruitment of general transcription factors and pol II to the promoter, melting of the DNA template, initiation of RNA synthesis, and pol II promoter clearance, which marks entry into the elongation phase. The stochastic nature of all of these steps poses a potential problem if it becomes necessary to mount a rapid activation of transcription. Following initiation pol II often encounters a rate-limiting barrier that appears to lie between early elongation and productive elongation. The transition between these two phases of the transcription cycle has now been characterized as a powerful regulatory switch used to increase or decrease gene expression in a signal-responsive fashion. Here we review the early discoveries that laid the foundation for a detailed understanding of transcriptional regulation at this transition. 2. Early Evidence of Polymerase Pausing and Premature Termination in DNA Viruses Nearly 30 years ago it was reported by the late Yosef Aloni and colleagues that run-on transcripts made in nuclei from SV40 infected cells were strongly biased toward the 5′ end of the late transcription unit suggesting that pol II accumulated in the promoter-proximal region [1]. Analysis of labeled RNA extended on viral transcription complexes (VTCs) assembled in vivo and purified from infected cells revealed two additional unusual features of transcription from the late promoter. First, two pause sites were mapped around positions +15 and +40 relative to the start site by identifying the junctions between unlabelled RNA made in vivo and labeled RNA extended in vitro [2]. Second, a major product of transcription on VTCs is a discrete 93–95 base RNA, that is, prematurely terminated near a potential hairpin loop structure. Similar
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