INTAC endonuclease and phosphatase modules differentially regulate transcription by RNA polymerase II

Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription

“…RNAi depletion of IntS8, a key bridging subunit connecting the phosphatase module to the rest of the Integrator, (54,55) led to increased levels of nuclear Ser5ph including at HLBs (fig. S10), consistent with previous studies (53,55,56). However, the intensity of Pol II at the HLBs did not decrease upon IntS8 RNAi (fig.…”

“…IntS11 can facilitate pause release (52,(63)(64)(65), presumably by evicting stalled Pol II on genes; alternatively, it can attenuate transcription by terminating elongation-competent Pol II (66,67). Recent genome-wide analyses (53,68) revealed differential effects across various protein-coding genes upon depleting IntS11, with highly expressed genes showing downregulation and lowly expressed genes showing upregulation (53). Mechanisms underlying the differential regulation remain largely elusive, although it was speculated that IntS11 might preferentially target stalled Pol II at highly expressed promoters where endonuclease activity is more limiting (53).…”

“…Recent genome-wide analyses (53,68) revealed differential effects across various protein-coding genes upon depleting IntS11, with highly expressed genes showing downregulation and lowly expressed genes showing upregulation (53). Mechanisms underlying the differential regulation remain largely elusive, although it was speculated that IntS11 might preferentially target stalled Pol II at highly expressed promoters where endonuclease activity is more limiting (53). Our finding that the Integrator endonuclease module is an essential clustering regulator offers a possible resolution to this conundrum: depletion of the Integrator endonuclease results in the loss of Pol II clusters but its downstream transcriptional effects may depend on whether the Pol II clusters are activated or poised at the time of depletion: for the highly expressed promoters (as was the case with the highly activated S-phase histone loci) where the Pol II clusters are more likely to be active, loss of Pol II clustering would lead to transcriptional downregulation; for the lowly expressed promoters (as was the case with all the G-phase histone loci), loss of clustering would bypass the regulatory transition from poised to activation, causing aberrant transcriptional activation.…”

“…In addition to Spt6 and Spt5, we also examined if Integrator, a multi-subunit complex involved in promoter-proximal regulation of transcription, mediates Pol II clustering at the HLBs. The Integrator complex consists of a phosphatase module and an endonuclease module and has been shown to have both activating and repressive roles in the transcription of protein-coding genes (50)(51)(52)(53). RNAi depletion of IntS8, a key bridging subunit connecting the phosphatase module to the rest of the Integrator, (54,55) led to increased levels of nuclear Ser5ph including at HLBs (fig.…”

Structural basis of the Integrator complex assembly and association with transcription factors

“…More recent studies pointed to its emerging role in several aspects of the transcription of protein-coding genes and other non-coding RNAs [11][12][13][14][15][16][17][18] . Integrator's association with the protein phosphatase PP2A-C counteracts CDK9 kinase of the P-TEFb complex and provides compelling evidence that a fine balance between these two activities plays a key role in determining the outcome of gene expression [19][20][21][22] . Consequently, perturbations of the Integrator function are known to result in severe genetic disorders [23][24][25] .…”