加州大学钟声研究小组取得一项新突破。他们提出了通过测序研究RNA-蛋白关联的全基因组图谱。2025年9月9日出版的《自然—生物技术》发表了这项成果。

研究人员介绍了PRIM-seq（蛋白质-RNA相互作用图谱测序），这是一种同时从头鉴定RNA结合蛋白及其相关RNA的方法。PRIM-seq通过RNA与蛋白质连接DNA条形码的近端连接产生独特的嵌合DNA序列，随后通过测序解码。研究人员将PRIM-seq应用于两种人类细胞系，并构建了一个人类RNA-蛋白关联网络（HuRPA），包含35万个关联，涉及约7000种RNA和约1.1万种蛋白质，其中包括2610种蛋白质，每种蛋白质与至少10种不同的RNA相互作用。

课题组人员通过实验验证了与肿瘤发生相关的lincRNA LINC00339是一种蛋白质相关RNA，它是HuRPA中蛋白质关联数量最多的RNA。小组进一步验证了染色质构象调节因子SMC1A、SMC3和RAD21以及代谢酶PHGDH的RNA关联能力。PRIM-seq可以在没有基因或蛋白质特异性试剂的情况下系统地发现和优先排序RNA结合蛋白及其靶标。

据介绍，RNA-蛋白相互作用对基因表达和细胞过程起着至关重要的调节作用，但由于其结构多样性，它们的全面定位仍然具有挑战性。

附：英文原文

Title: Genome-wide mapping of RNA-protein associations through sequencing

Author: Qi, Zhijie, Xue, Shuanghong, Chen, Junchen, Zhao, Wenxin, Johnson, Kara, Wen, Xingzhao, Charles Richard, John Lalith, Lin, Pei, Zhong, Sheng

Issue&Volume: 2025-09-09

Abstract: RNA-protein interactions critically regulate gene expression and cellular processes, yet their comprehensive mapping remains challenging due to their structural diversity. We introduce PRIM-seq (protein-RNA interaction mapping by sequencing), a method for concurrent de novo identification of RNA-binding proteins and their associated RNAs. PRIM-seq generates unique chimeric DNA sequences by proximity ligation of RNAs with protein-linked DNA barcodes, which are subsequently decoded through sequencing. We apply PRIM-seq to two human cell lines and construct a human RNA-protein association network (HuRPA), encompassing >350,000 associations involving ~7,000 RNAs and ~11,000 proteins, including 2,610 proteins that each interact with at least 10 distinct RNAs. We experimentally validate the tumorigenesis-associated lincRNA LINC00339, the RNA with the highest number of protein associations in HuRPA, as a protein-associated RNA. We further validate the RNA-associating abilities of chromatin-conformation regulators SMC1A, SMC3 and RAD21, as well as the metabolic enzyme PHGDH. PRIM-seq enables systematic discovery and prioritization of RNA-binding proteins and their targets without gene- or protein-specific reagents.

DOI: 10.1038/s41587-025-02780-z

Source: https://www.nature.com/articles/s41587-025-02780-z