Malaymar Pinar Dicle, Göös Helka, Tan Zenglai, Kumpula Esa-Pekka, Chowdhury Iftekhar, Wang Zixian, Zhang Qin, Salokas Kari, Keskitalo Salla, Wei Gong-Hong, Kumbasar Asli, Varjosalo Markku
Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland; Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.
iCell, Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland.
Mol Cell Proteomics. 2025 Jan;24(1):100890. doi: 10.1016/j.mcpro.2024.100890. Epub 2024 Nov 29.
The Nuclear Factor I (NFI) family of transcription factors (TFs) plays key roles in cellular differentiation, proliferation, and homeostasis. As such, NFI family members engage in a large number of interactions with other proteins and chromatin. However, despite their well-established significance, the NFIs' interactomes, their dynamics, and their functions have not been comprehensively examined. Here, we employed complementary omics-level techniques, i.e. interactomics (affinity purification mass spectrometry (AP-MS) and proximity-dependent biotinylation (BioID)), and chromatin immunoprecipitation sequencing (ChIP-Seq), to obtain a comprehensive view of the NFI proteins and their interactions in different cell lines. Our analyses included all four NFI family members, and a less-studied short isoform of NFIB (NFIB4), which lacks the DNA binding domain. We observed that, despite exhibiting redundancy, each family member had unique high-confidence interactors and target genes, suggesting distinct roles within the transcriptional regulatory networks. The study revealed that NFIs interact with other TFs to co-regulate a broad range of regulatory networks and cellular processes. Notably, time-dependent proximity-labeling unveiled a highly dynamic nature of NFI protein-protein interaction networks and hinted at the temporal modulation of NFI interactions. Furthermore, gene ontology (GO) enrichment analysis of NFI interactome and targetome revealed the involvement of NFIs in transcriptional regulation, chromatin organization, cellular signaling pathways, and pathways related to cancer. Additionally, we observed that NFIB4 engages with proteins associated with mRNA regulation, which suggests that NFIs have roles beyond traditional DNA binding and transcriptional modulation. We propose that NFIs may function as potential pioneering TFs, given their role in regulating the DNA binding ability of other TFs and their interactions with key chromatin remodeling complexes, thereby influencing a wide range of cellular processes. These insights into NFI protein-protein interactions and their dynamic, context-dependent nature provide a deeper understanding of gene regulation mechanisms and hint at the role of NFIs as master regulators.
核因子I（NFI）转录因子家族在细胞分化、增殖和体内平衡中发挥关键作用。因此，NFI家族成员与其他蛋白质和染色质进行大量相互作用。然而，尽管它们具有公认的重要性，但NFI的相互作用组、其动态变化及其功能尚未得到全面研究。在这里，我们采用了互补的组学水平技术，即相互作用组学（亲和纯化质谱分析（AP-MS）和邻近依赖性生物素化（BioID））以及染色质免疫沉淀测序（ChIP-Seq），以全面了解NFI蛋白及其在不同细胞系中的相互作用。我们的分析包括所有四个NFI家族成员，以及一种研究较少的NFIB短异构体（NFIB4），它缺乏DNA结合结构域。我们观察到，尽管表现出冗余性，但每个家族成员都有独特的高可信度相互作用蛋白和靶基因，这表明它们在转录调控网络中具有不同的作用。该研究表明，NFI与其他转录因子相互作用，共同调节广泛的调控网络和细胞过程。值得注意的是，时间依赖性邻近标记揭示了NFI蛋白质-蛋白质相互作用网络的高度动态性质，并暗示了NFI相互作用的时间调控。此外，对NFI相互作用组和靶标组的基因本体（GO）富集分析揭示了NFI参与转录调控、染色质组织、细胞信号通路以及与癌症相关的通路。此外，我们观察到NFIB4与参与mRNA调控的蛋白质相互作用，这表明NFI的作用超出了传统的DNA结合和转录调节。鉴于NFI在调节其他转录因子的DNA结合能力及其与关键染色质重塑复合物的相互作用中的作用，我们提出NFI可能作为潜在的先锋转录因子发挥作用，从而影响广泛的细胞过程。这些对NFI蛋白质-蛋白质相互作用及其动态、上下文依赖性性质的见解为基因调控机制提供了更深入的理解，并暗示了NFI作为主要调节因子的作用。
