The elongation phase starts once assembly of the elongation complex has been completed, and progresses until a termination sequence is encountered. The post-initiation movement of RNA polymerase is the target of another class of important regulatory mechanisms. For example, the transcriptional activator Tat affects elongation rather than initiation during its regulation of HIV transcription. In fact, many eukaryotic genes are regulated by releasing a block to transcription elongation called promoter-proximal pausing. Pausing can influence chromatin structure at promoters to facilitate gene activity and lead to rapid or synchronous transcriptional responses when cells are exposed to an activation signal. Pausing is associated with the binding of two negative elongation factors, DSIF (SPT4/SPT5) and NELF, to the elongation complex. Other factors can also influence the stability and duration of the paused polymerase. Pause release is triggered by the recruitment of the P-TEFb kinase.
Transcription termination has also emerged as an important area of transcriptional regulation. Termination is coupled with the efficient recycling of polymerase. The factors associated with transcription termination can also mediate gene looping and thereby determine the efficiency of re-initiation.