Affinity proteomic dissection of the human nuclear cap-binding complex interactome

Abstract

A 5′,7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed due to its participation in RNA-fate decisions via interactions with RNA productive factors as well as with adapters of the degradative RNA exosome. A novel cap-binding protein, NCBP3, was recently proposed to form an alternative CBC together with NCBP1, and to interact with the canonical CBC along with the protein SRRT. The theme of post-transcriptional RNA fate, and how it relates to co-transcriptional ribonucleoprotein assembly, is abundant with complicated, ambiguous, and likely incomplete models. In an effort to clarify the compositions of NCBP1-, 2- and 3-related macromolecular assemblies, we have applied an affinity capture-based interactome screen where the experimental design and data processing have been modified to quantitatively identify interactome differences between targets under a range of experimental conditions. This study generated a comprehensive view of NCBP-protein interactions in the ribonucleoprotein context and demonstrates the potential of our approach to benefit the interpretation of complex biological pathways.

The effects of NCBP3 on METTL3‐mediated m6A RNA methylation to enhance translation process in hypoxic cardiomyocytes

“… 22 Moreover, NCBP3 can also contribute to RNA splicing and exon–exon junctions coordinated with exon–junction complexes. 23 In our mass spectrum data, the components of NCBP2, eIF4A3, MAGOH, RBM8A ALYREF and DDX39B are all identified both in normoxia and hypoxia H9C2 cells. But we further find the substantial interaction of eIF4A2 and METTL3 with NCBP3 especially in hypoxic stress, indicating a hypoxia‐specific role in cardiomyocytes although the potential connection of these novel binding proteins with NCBP3 is never studied.…”

Cytoplasmic switch of ARS2 isoforms promotes nonsense-mediated mRNA decay and arsenic sensitivity

“…Interestingly, we found a significant enrichment of NCBP3 in the ARS2n data. NCBP3 has been shown to interact with CBC-ARS2 and the EJC post-splicing, and functions to promote multiexonic polyadenylated mRNA export ( 5 , 43 ). The presence of NCBP3, as well as PHAX, in this dataset suggests that the inability to detect NCBP1 and NCBP2 may be due to steric constraints from the placement of the biotin ligase at the N-terminus.…”

Selective Interaction of Sugarcane eIF4E with VPgs from Sugarcane Mosaic Pathogens

“…In A. thaliana , nCBP showed affinity to the cap structure comparable to that shown by eIF(iso)4E [ 64 ]. The cap binding complex comprises many components [ 65 , 66 ]. Considering that ScnCBP was upregulated upon SCMV infection ( Figure 3 ), we speculate that other cap binding components mediate the interaction of ScnCBP with the VPgs of SCMV, SrMV or SCSMV in vivo.…”