Mars Jean-Clement, Embree Caleb M, Carlile Aidan W B, Gendron Patrick, Borden Katherine L B
Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada.
Department of Pharmacology and Robert H. Lurie Cancer Centre, Northwestern University, Chicago, Illinois, USA.
bioRxiv. 2025 Jul 31:2025.07.25.666897. doi: 10.1101/2025.07.25.666897.
mRNA processing constitutes a series of steps in the nucleus to generate mature mRNAs that can be translated into protein. This relies on the methyl-7-guanosine (mG) "cap" on the 5'end of mRNAs which is bound by the nuclear cap-binding protein NCBP2 with its cofactor NCBP1. The NCBP1/2 complex chaperones capped mRNA through these processing steps. NCBP2 is considered the sole nuclear cap-binding factor and thus its cap-chaperone role is thought to be a constitutive, housekeeping activity. However, another cap-binding protein, the eukaryotic translation initiation factor eIF4E, is also found in the nucleus. Two cap-binding factors co-existing in the nucleus intimate an undiscovered regulatory point in gene expression or, alternatively, redundancy to ensure gene expression fidelity. Consistent with the former possibility, eIF4E and NCBP2 drove distinct gene expression, transcriptomic, and splicing signatures impacting ~2500 transcripts involved in distinct biological programmes with only ~360 transcripts in common and of these only 79 common splicing events. Thus, each cap-chaperone designates distinct mRNA populations for specific processing revealing a new step in gene expression. We denote this mRNA specification of cap-chaperones (SOCCS). We uncovered multiple molecular mechanisms that contribute to SOCCS: distinct spatial localization of eIF4E and NCBP2 within the nucleus, identification of sequence motifs within targeted mRNAs segregated by eIF4E or NCBP2 sensitivity, distinct protein partners for these cap-chaperones and differential impacts on the production of key spliceosome components e.g. U2AF1, PRP31, SF3B1 and SNRNP200 indicative of distinct transcriptomic landscapes produced by eIF4E or NCBP2 overexpression. In all, the realization that multiple cap-binding proteins coexist in the nucleus led us to identify an unexpected gene-expression regulatory point which engaged distinct biological programmes.
mRNA加工在细胞核中构成一系列步骤，以生成可被翻译成蛋白质的成熟mRNA。这依赖于mRNA 5'端的甲基化7-鸟苷（mG）“帽”，它由核帽结合蛋白NCBP2及其辅助因子NCBP1结合。NCBP1/2复合物陪伴带帽的mRNA经历这些加工步骤。NCBP2被认为是唯一的核帽结合因子，因此其帽陪伴作用被认为是一种组成性的看家活动。然而，另一种帽结合蛋白，即真核翻译起始因子eIF4E，也存在于细胞核中。两种帽结合因子共存于细胞核中暗示了基因表达中一个未被发现的调控点，或者是为确保基因表达保真度的冗余机制。与前一种可能性一致，eIF4E和NCBP2驱动了不同的基因表达、转录组和剪接特征，影响了约2500个参与不同生物学程序的转录本，只有约360个转录本是共有的，其中只有79个共同的剪接事件。因此，每个帽陪伴蛋白指定不同的mRNA群体进行特定加工，揭示了基因表达中的一个新步骤。我们将此称为帽陪伴蛋白的mRNA特异性（SOCCS）。我们发现了多种促成SOCCS的分子机制：eIF4E和NCBP2在细胞核内不同的空间定位、识别由eIF4E或NCBP2敏感性区分的靶向mRNA内的序列基序、这些帽陪伴蛋白不同的蛋白质伴侣以及对关键剪接体成分如U2AF1、PRP31、SF3B1和SNRNP200产生的差异影响，这表明eIF4E或NCBP2过表达产生了不同的转录组景观。总之，多种帽结合蛋白共存于细胞核这一认识使我们发现了一个意外的基因表达调控点，它涉及不同的生物学程序。
