Jiménez-Ramírez Irma A, Uc-Chuc Miguel A, Zapata Luis Carlos Rodríguez, Castaño Enrique
Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán, Calle 43, No. 130, Chuburná de Hidalgo, Mérida CP 97205, Yucatán, Mexico.
Laboratorio de Biología Celular, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Av. Itzáes, No. 490 x calle 59, Col. Centro, Mérida CP 97000, Yucatán, Mexico.
Noncoding RNA. 2025 Jul 28;11(4):55. doi: 10.3390/ncrna11040055.
: snoRNAs have traditionally been known for their role as guides in post-transcriptional rRNA modifications. Previously, our research group identified several RNAs that may bind to PIP2 with LIPRNA-seq. Among them, snR191 stood out due to its potential specific interaction with this lipid, distinguishing itself from other snoRNAs. However, a detailed study is needed to define the molecular interactions between RNA and lipids, which remain unknown but may serve as a mechanism for transport or liquid-liquid phase separation. This study aimed to determine the interaction between a snoRNA called snR191 and PIP2. : A novel methodology for RNA-PIP2 interaction was carried out. Total RNA from was incubated with PIP2-bound nitrocellulose membranes and RT-PCR reactions. We performed the prediction of snR191-PIP2 interaction by molecular docking and in silico mutations of snoR191. : From LIPRNA-seq analysis, we identified that PIP2-bound RNAs were significantly enriched in diverse biological processes, including transmembrane transport and redox functions. Our RNA-PIP2 interaction approach was successful. We demonstrated that snR191 specifically interacts with PIP2 in vitro. The elimination of DNA ensured that the interaction assay was RNA-specific, strengthening the robustness of the experiment. PIP2 was docked to snR191 in a stem-loop-stem motif. Six hydrogen bonds across four nucleotides mediated the PIP2-snR191 interaction. Finally, mutations in snR191 affected the structural folding. : In this study, we demonstrate the effectiveness of a new methodology for determining RNA-lipid interactions, providing strong evidence for the specific interaction between snR191 and PIP2. Integrating biochemical and computational approaches has allowed us to understand the binding of these biomolecules. Therefore, this work significantly broadens our understanding of snR191-PIP2 interactions and opens new perspectives for further research.
小分子核仁RNA（snoRNAs）传统上因其在转录后rRNA修饰中作为引导分子的作用而为人所知。此前，我们的研究小组通过脂质相互作用RNA测序（LIPRNA-seq）鉴定了几种可能与磷脂酰肌醇-4,5-二磷酸（PIP2）结合的RNA。其中，snR191因其与这种脂质潜在的特异性相互作用而脱颖而出，与其他snoRNAs不同。然而，RNA与脂质之间的分子相互作用仍不清楚，但可能作为运输或液-液相分离的一种机制，因此需要进行详细研究。本研究旨在确定一种名为snR191的snoRNA与PIP2之间的相互作用。：开展了一种用于RNA与PIP2相互作用的新方法。将来自[具体来源未提及]的总RNA与结合有PIP2的硝酸纤维素膜及逆转录聚合酶链反应（RT-PCR）进行孵育。我们通过分子对接和snoR191的计算机模拟突变对snR191与PIP2的相互作用进行了预测。：通过LIPRNA-seq分析，我们发现与PIP2结合的RNA在多种生物学过程中显著富集，包括跨膜运输和氧化还原功能。我们的RNA与PIP2相互作用方法是成功的。我们证明了snR191在体外与PIP中的两个磷酸基团特异性相互作用。DNA的去除确保了相互作用测定是RNA特异性的，增强了实验的稳健性。PIP2以茎-环-茎基序与snR191对接。跨越四个核苷酸的六个氢键介导了PIP2与snR191的相互作用。最后，snR191中的突变影响了结构折叠。：在本研究中，我们证明了一种用于确定RNA与脂质相互作用的新方法的有效性，为snR191与PIP2之间的特异性相互作用提供了有力证据。整合生化和计算方法使我们能够理解这些生物分子的结合。因此，这项工作显著拓宽了我们对snR191与PIP2相互作用的理解，并为进一步研究开辟了新的视角。
