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Pausing vs. Poising of RNA Polymerase II on Rapidly Induced Genes

Evaluation of kinetic site occupancy for Pol II bound to human IL1B and TNF genes, as well as the state of CTD Ser5 and Ser2 phosphorylation and NELF and P‐TEFb recruitment following LPS induction, reveals differences between these two rapidly induced human monocyte genes. Pol II is primarily transiently recruited to TNF, whereas it is constitutively pre‐recruited and poised on IL1B. For IL1B, NELF recruitment and P‐TEFb‐dependent release following stimulation is similar to that observed for classical downstream pausing, and continues hours after initial induction. In contrast, TNF recruitment of Pol II is rapidly lost after 30 minutes. Both of these genes differ from a GAPDH control, which reveals constitutive Pol II recruitment, as has been reported by others. These data argue for two novel mechanisms regulating rapidly induced genes that differ from that associated with classical polymerase poising/pausing at TSS‐proximal downstream sites. TNF utilizes de novo recruitment followed by rapid shut‐down, whereas IL1B employs poised polymerase and subsequent continuous expression. The differences between TNF and IL1B are also observed to be manifested at the level of polymerase run‐on and mRNA synthesis, suggesting important distinctions between the kinetic expression of these two immediate‐early inducible genes.