Integrator is a global promoter-proximal termination complex

Abstract

Integrator is a metazoan-specific protein complex capable of inducing termination at all RNAPII-transcribed loci. Integrator recognizes paused, promoter-proximal RNAPII and drives premature termination using dual enzymatic activities: an endonuclease that cleaves nascent RNA and a protein phosphatase that removes stimulatory phosphorylation associated with RNAPII pause release and productive elongation. Recent breakthroughs in structural biology have revealed the overall architecture of Integrator and provided insights into how multiple Integrator modules are coordinated to elicit termination effectively. Furthermore, functional genomics and biochemical studies have unraveled how Integrator-mediated termination impacts protein-coding and noncoding loci. Here, we review the current knowledge about the assembly and activity of Integrator and describe the role of Integrator in gene regulation, highlighting the importance of this complex for human health.

Keywords: Integrator; attenuation; elongation control; gene regulation; polymerase pausing; transcription termination.

Figure 1.. Integrator contains modules with both endonuclease and phosphatase activities.

Shown are schematics depicting the balance between pause release by P-TEFb vs. Integrator-mediated termination, depicting the cleavage activity of the Integrator endonuclease, and the phosphatase activity of Integrator-associated PP2A.

Figure 2.. Domain organizations of Integrator and PP2A subunits.

Domains are indicated as boxes while vertical lines indicate boundaries between neighboring domains. The size of each subunit is provided as number of amino acids in the human ortholog. Flexible segments in the subunits are shown in gray. Abbreviations are: N-terminal domain (NTD); Middle domain (MD); C-terminal domain (CTD); N-terminal cap (Ncap); Plant Homeodomain Finger (PHD); Metallo-β-Lactamase (MβL); Metallo-β-Lactamase-associated CPSF73, Artemis, SNM, and PSO (β-CASP); von Willebrand factor type A (vWA); Huntington, Elongation factor 3, Protein Phosphatase A, Tor1 (HEAT). Domains containing α+β or only β secondary structure elements are labeled. Domains in INTS9 and INTS11 contain α+β elements. All other domains contain only α helices.

Figure 3.. The overall architecture of Integrator in an inactive state

(A). (Left) Schematic of the structure of Integrator-PP2A complex in an inactive state, with subunits colored as in Fig. 2. IP₆ observed in the structure of Drosophila ICM is shown in a sphere model. The metal ions in the active site of INTS11 and manganese ions in the active site of PP2A-C are shown as spheres. (Right) Structure shown at left after 90° rotation around the vertical axis. (B). Structures of the individual Integrator modules. Module structures are derived from the structure shown in panel 3A with the exception of the INTS13/INTS14 structure, which is from. Structure figures were produced with PyMOL (www.pymol.org).

Figure 4.. Overall architecture of Integrator in an active state

(A). (Left) Schematic of the structure of Integrator-PP2A-RNAPII PEC complex in an active state . Integrator subunits are colored according to Fig. 2, with RNAPII in gray, NELF and SPT5 in marine. (Right) Structure shown at left after 90° rotation around the vertical axis. (B). Nascent RNA in the active site of INTS11. The RNA is shown in orange, and DNA in olive. The nascent RNA exits RNAPII, and SPT5 helps to direct it to the active site of INTS11. (C) Zoom-in of CTD peptides associated with Integrator subunits with a numbered projections towards the active site of PP2A-C. The black sphere represents residue 1487 of RPB1 and is the last amino acid modeled in the structure. INTS1, INTS6, and INST11 are omitted for clarity.