Integrator is a 17 subunit (INTS1-15, PP2Ac, PR65), 1.6 MDa machinery that was originally discovered to be important for snRNA 3'-end processing. Recent studies showed that Integrator mediates the downregulation of a broad collection of mRNAs by cleaving the paused, promoter-proximal Pol II transcripts.

INTS11 and INTS9 are paralogs of CPSF73 and CPSF100, respectively, and INTS11 is the endonuclease for the cleavage activity of Integrator. INTS4-INTS9-INTS11 forms a stable complex, known as the Integrator cleavage module (ICM).

Integrator also contains a protein phosphatase activity (PP2A) that can dephosphorylate the Pol II CTD.

• The crystal structure of the CTD2 complex of INTS11-INTS9 has been determined, revealing tight interactions between them.


• Functional studies show that this complex is important for the cleavage activity of Integrator.


• The structure of Drosophila ICM unexpectedly reveals the binding of an IP6 (inositol hexakisphosphate) molecule, at an allosteric pocket lined with residues from all 3 subunits, 55 A from the dIntS11 active site.


• Binding of IP6 can also be visualized in the structure of human ICM or Integrator.


• This IP6 binding site is important for the function of Integrator.


• CG7044 has been identified as a binding partner of dIntS11 in our collaborator Eric Wagner's lab. This complex is distinct from Integrator. The human homolog of CG7044 if BRAT1.


• The structures of dIntS11-CG7044 and human INTS9-INTS11-BRAT1 complexes have been determined by cryo-EM.


• CG7044/BRAT1 forms a horseshoe-like structure, encircling INTS11 in its center. INTS9 is bound to the side of this horseshoe structure, and has no interaction with INTS11.


• The last three residues at the C-terminal end of CG7044 and BRAT1, DCY, are bound in the active site of INTS11, with the Cys coordinated to the two metal ions. This DCY motif is conserved among all CG7044/BRAT1 homologs. INTS11 is in a semi open state to accommodate these residues.


• The structures suggest CG7044/BRAT1 should be an inhibitor of INTS11 endonuclease activity.


• Surprisingly, CG7044/BRAT1 is required for Integrator function. BRAT1 knockout cells have extensitve snRNA misprocessing.


• CG7044 and BRAT1 are primarily localized in the cytosol, while mature Integrator is nuclear.


• CG7044/BRAT1 is a cytoplasmic binding partner of INTS11 that stabilizes this endonuclease. In the absence of CG7044/BRAT1, INTS11 is unstable and is degraded, leading to Integrator malfunction.


• Inspired by these observations on CG7044/BRAT1, UBE3D has been identified as a cytoplasmic binding partner of CPSF73, with a very similar mechanism of action to stabilize CPSF73 for pre-mRNA 3'-end processing.

Publications from this project

• Y. Wu,* T.R. Albrecht,* D. Baillat, E.J. Wagner$ & L. Tong.$ (2017). Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance. Proc. Natl. Acad. Sci. USA, 114, 4394-4399. (*-equal first authors, $-co-corresponding authors) Reprint(PDF)
• T.R. Albrecht, S.P. Shevtsov, Y. Wu, L.G. Mascibroda, N.J. Peart, K.-L. Huang, I.A. Sawyer, L. Tong, M. Dundr$ & E.J. Wagner.$ (2018). Integrator subunit 4 is a 'symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module. Nucl. Acids Res. 46, 4241-4255. ($-co-corresponding authors)
• M.-H. Lin,* M.K. Jensen,* N.D. Elrod, K.-L. Huang, K.A. Welle, E.J. Wagner$ & L. Tong.$ (2022). Inositol hexakisphosphate is required for Integrator function. Nature Commun. 13, 5742. (*-equal first authors, $-co-corresponding authors)
• L.G. Mascibroda,* M. Shboul,* N.D. Elrod, L. Colleaux, H. Hamamy, K.-L. Huang, N. Peart, M.K. Singh, H. Lee, B. Merriman, J.N. Jodoin, P. Sitaram, L.A. Lee, R. Fathalla, B. Al-Rawashdeh, O. Ababneh, M. El-Khateeb, N. Escande-Beillard, S.F. Nelson, Y. Wu, L. Tong, L.J. Kenney, S. Roy, W.K. Russell, J. Amiel, B. Reversade$ & E.J. Wagner.$ (2022). INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex. Nature Commun. 13, 6054. (*-equal first authors, $-co-corresponding authors)
• E.J. Wagner,$ L. Tong$ & K. Adelman.$ (2023). Integrator is a global promoter-proximal termination complex. Mol. Cell, 83, 416-427. ($-co-corresponding authors)
• M.-H. Lin,* M.K. Jensen,* N.D. Elrod, H.-F. Chu, M. Haseley, A.C. Beam, K.-L. Huang, W. Chiang, W.K. Russell, K. Williams, C. Proschel, E.J. Wagner$ & L. Tong.$ (2024). Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function. Mol. Cell, 84, 2900-2917. (*-equal first authors, $-co-corresponding authors)

Funding for this project

• NIH R35GM118093 (2016-)
• NIH R01NS135070 (2024-)