NCBP3 is a productive mRNP component

Abstract

<jats:title>Abstract</jats:title><jats:p>The nuclear Cap Binding Complex (CBC), consisting of Nuclear Cap Binding Protein 1 (NCBP1) and 2 (NCBP2), associates with the nascent 5’cap of RNA polymerase II transcripts and impacts RNA fate decisions. Recently, the C17orf85 protein, also called NCBP3, was suggested to form an alternative CBC by replacing NCBP2. However, applying protein-protein interaction screening of NCBP1, 2 and 3, we find that the interaction profile of NCBP3 is distinct. Whereas NCBP1 and 2 identify known CBC interactors, NCBP3 primarily interacts with components of the Exon Junction Complex (EJC) and the TRanscription and EXport (TREX) complex. NCBP3-EJC association <jats:italic>in vitro</jats:italic> and <jats:italic>in vivo</jats:italic> requires EJC core integrity and the <jats:italic>in vivo</jats:italic> RNA binding profiles of EJC and NCBP3 overlap. We further show that NCBP3 competes with the RNA degradation factor ZC3H18 for binding CBC-bound transcripts, and that NCBP3 positively impacts the nuclear export of polyadenylated RNAs and the expression of large multi-exonic transcripts. Collectively, our results place NCBP3 with the EJC and TREX complexes in supporting the productive fate of mRNA.</jats:p>

Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry

“…This data demonstrates that NCPB3 differs from NCBP1 and NCBP2 in selectivity, coprecipitating with members of the THO/TREX complexes. These interactions were later confirmed as supporting a biological role for NCBP3 in mRNA expression that differs from NCBP1 and NCBP2 351. (A) Figure reproduced and adapted with permission from ref 352.…”

“…These interactions were later confirmed as supporting a biological role for NCBP3 in mRNA expression that differs from NCBP1 and NCBP2. 351 isotope labeling methods. These methods rely on the fact that peptides with the same sequence but different isotope enrichment will coelute but be separated in a single spectrum for quantification.…”

ZC3H11A interacts with PABPN1 and alters polyadenylation of viral transcripts

“…ZC3H11A is an RNA-binding protein with three uncharacterized CCCH-type zinc finger motifs (ZFM) motifs present at the N-terminus of the protein (3). Several studies have shown that ZC3H11A is a subunit of the Transcription-Export (TREX) complex, which is responsible for the nuclear mRNA export (4)(5)(6)(7)(8)(9). TREX is a multiprotein complex containing the hexameric core THO complex (THOC1, THOC2, THOC3, THOC5, THOC6, THOC7), which in turn associates with several subunits including ZC3H11A (8).…”