Integrator complex cleaves nascent mRNAs to attenuate transcription

Cellular homeostasis requires transcriptional outputs to be coordinated, and many events post transcription initiation can dictate the levels and functions of mature transcripts. To systematically identify regulators of inducible gene expression, we performed high-throughput RNAi screening of the Drosophila Metallothionein A (MtnA) promoter. This surprisingly revealed that the Integrator complex, which has a well-established role in 3' end processing of small nuclear RNAs (snRNAs), attenuates MtnA transcription during copper stress. Integrator complex subunit 11 (IntS11) endonucleolytically cleaves MtnA transcripts, resulting in premature transcription termination and degradation of the nascent RNAs by the RNA exosome, a complex also identified in the screen (Figure 2). Using RNA-seq, we then identified >400 additional Drosophila protein-coding genes whose expression increases upon Integrator depletion. We focused on a subset of these genes and confirmed that Integrator is bound to their 5' ends and negatively regulates their transcription via IntS11 endonuclease activity. In fact, Integrator catalyzed premature transcription termination events can repress the expression of some full-length mRNAs by more than 100-fold.

Many non-catalytic Integrator subunits, which are largely dispensable for snRNA processing, also have regulatory roles at these protein-coding genes, possibly by controlling Integrator recruitment or RNA polymerase II dynamics. Altogether, our results suggest that attenuation via Integrator cleavage limits production of many full-length mRNAs, allowing precise control of transcription outputs. Going forward, it will be highly interesting to understand how the Integrator complex is recruited and regulated as well as why mutations in Integrator subunits are associated with human diseases.

Figure 2. Integrator cleavage attenuates protein-coding gene expression From Tatomer et al. (2019) Genes Dev 33: 1525-1538.
Figure 2. Integrator cleavage attenuates protein-coding gene expression From Tatomer et al. (2019) Genes Dev 33: 1525-1538.

Key Publications

  • Fujiwara, R., Zhai, S.-N., Liang, D., Shah, A.P., Tracey, M., Ma, X.-K., Fields, C.J., Mendoza-Figueroa, M.S., Meline, M.C., Tatomer, D.C., Yang, L., and Wilusz, J.E. (2023) IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events. Mol Cell 83: 4445-4460.
  • Mendoza-Figueroa, M.S., Tatomer, D.C., and Wilusz, J.E. (2020) The Integrator complex in transcription and development. Trends Biochem Sci 45: 923-934.
  • Tatomer, D.C. and Wilusz, J.E. (2020) Attenuation of eukaryotic protein-coding gene expression via premature transcription termination. Cold Spring Harb Symp Quant Biol 84: 83-93.
  • Tatomer, D.C., Elrod, N.D., Liang, D., Xiao, M.S., Jiang, J.Z., Jonathan, M., Huang, K.L., Wagner, E.J., Cherry, S., and Wilusz, J.E. (2019) The Integrator complex cleaves nascent mRNAs to attenuate transcription. Genes Dev 33: 1525-1538.
  • Elrod, N.D., Henriques, T., Huang, K.L., Tatomer, D.C., Wilusz, J.E., Wagner, E.J., and Adelman, K. (2019) The Integrator complex attenuates promoter-proximal transcription at protein-coding genes. Mol Cell 76:738-752.