Structure of the catalytic core of the Integrator complex

Wojciech P Galej,Moritz M Pfleiderer

doi:10.1016/j.molcel.2021.01.005

Abstract

SummaryThe Integrator is a specialized 3′ end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator’s catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3′ end-processing machineries points to distinct features and a unique architecture of the Integrator’s catalytic module.

Highlights

30 end processing of nascent RNA polymerase II (RNAPII) transcripts is one of the key steps in gene expression (Proudfoot, 2011; Shi and Manley, 2015)
Modularity of the Integrator complex The Integrator complex consists of 14 different subunits (Baillat et al, 2005; Chen et al, 2012), but little is known about its internal architecture or the assembly mechanism
To gain more insights into the composition of the Integrator complex, we generated a series of stable HEK293F cell lines ectopically overexpressing tagged variants of INTS4, INTS5, INTS7, INTS10, and INTS14

Summary

Introduction

30 end processing of nascent RNA polymerase II (RNAPII) transcripts is one of the key steps in gene expression (Proudfoot, 2011; Shi and Manley, 2015). Most protein-coding RNAPII transcripts are cleaved and polyadenylated by the cleavage and polyadenylation specificity factor (CPSF) (Bienroth et al, 1993; Murthy and Manley, 1992; Preker et al, 1997). The exceptions include replication-dependent histone pre-mRNAs, which are processed by a partially overlapping machinery that depends on the U7 small nuclear ribonucleoprotein particle (snRNP) (Mowry and Steitz, 1987; Pillai et al, 2003), whereas non-coding RNAPII transcripts, such as small nuclear RNAs (snRNAs), are processed by the Integrator complex (Baillat et al, 2005). Most recent studies show that the Integrator can destabilize promoter-proximally paused RNAPII, leading to nascent RNA cleavage and transcription attenuation in a wide range of protein-coding genes (Elrod et al, 2019; Lykke-Andersen et al, 2020; Tatomer et al, 2019)

Results

Discussion

Conclusion