Structural basis for RNA capture and surveillance by the human Nuclear Exosome Targeting (NEXT) complex

Abstract: RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryo-electron microscopy structures of human Nuclear Exosome Targeting (NEXT) complexes bound to RNA, that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 engaging sequences upstream of the 3' end that is bound by MTR4. ZCCHC8 obscures MTR4 surfaces that are important for RNA binding and extrusion as well as surfaces important for MPP6-dependent recruitment and docking onto the RNA exosome core, features of which might contribute to coordinating RNA translocation and extrusion from the helicase to exosome recruitment and decay. Overall design: Total RNA seq comparing the transcriptomes of ZCCHC8 CRISPR knockout HAP1 cells stably transfected with GFP-tagged wild-type ZCCHC8 (WT) and ZCCHC8 with HD deleted (DM). Total RNA seq analysis of non-transfected ZCCHC8 CRISPR knockout HAP1 cells was also performed. Three biological replicates of each sample are included.