DSIF, NELF, the Integrator complex, and the promoter-proximal RNA Polymerase II pausing are coupled in metazoans

• The function of Spt4/5, NELF, and Integrator are reassigned. • These complexes are coupled with promoter-proximal Pol II pausing regulation in animals. • This is a unique transcription regulation mechanism only happening in animals. • The transcription termination mechanism of all organisms is revealed. • The transcription expression mechanism of regulatory non-coding RNAs is revealed. Both DSIF (Spt4/5) and the negative elongation factor, NELF, were assigned as two initiators of promoter-proximal RNA Polymerase II (Pol II) pausing in metazoans. Similarly, the Integrator complex is assigned to terminate Pol II pausing and subsequently trigger the release of paused Pol II. Furthermore, the working mechanism (s) of transcription termination of all genes remain controversial. Numerous studies have shown that Spt5 of DSIF is conserved from bacteria to human beings to build up a stable elongation complex of RNA polymerases during elongation. Accumulating data in the past decades showed that NELF is a positive elongation factor acting similarly to that of Paf1c, but specifically for Pol II pausing-regulated genes. Several reports showed that NELF is coupled with elongating Pol II and is essential for the recruitment of the Integrator complex, suggesting that the Integrator complex is a transcription terminator for all Pol II pausing-regulated genes in metazoans, instead of the currently assigned function. The functions of Spt4/5, NELF, and the Integrator are revisited, and a novel relationship between these factors and Pol II pausing is established. More excitingly, the underlying working mechanisms of transcription termination under different scenarios are finally revealed.