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

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  • Yuhui Dou
  • Svetlana Kalmykova, Skolkovo Institute of Science and Technology
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  • Maria Pashkova, Moscow Institute of Physics and Technology
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  • Mehrnoosh Oghbaie, Rockefeller University, University of Groningen
  • ,
  • Hua Jiang, Rockefeller University
  • ,
  • Kelly R. Molloy, Rockefeller University
  • ,
  • Brian T. Chait, Rockefeller University
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  • Michael P. Rout, Rockefeller University
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  • David Fenyö, New York University
  • ,
  • Torben Heick Jensen
  • Ilya Altukhov, Moscow Institute of Physics and Technology
  • ,
  • John LaCava, Rockefeller University, University of Groningen

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.

Original languageEnglish
JournalNucleic Acids Research
Pages (from-to)10456-10469
Number of pages14
Publication statusPublished - Oct 2020

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