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

• Published in: Nucleic acids research Vol. 48; no. 18; pp. 10456 - 10469
• Main Authors: Dou, Yuhui, Kalmykova, Svetlana, Pashkova, Maria, Oghbaie, Mehrnoosh, Jiang, Hua, Molloy, Kelly R, Chait, Brian T, Rout, Michael P, Fenyö, David, Jensen, Torben Heick, Altukhov, Ilya, LaCava, John
• Format: Journal Article
• Language: English
• Published: Oxford University Press 09.10.2020
• Subjects: RNA and RNA-protein complexes
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkaa743

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.