Qi Zhijie, Xue Shuanghong, Chen Junchen, Zhao Wenxin, Johnson Kara, Wen Xingzhao, Richard John Lalith Charles, Zhong Sheng
Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
bioRxiv. 2024 Sep 4:2024.09.04.611288. doi: 10.1101/2024.09.04.611288.
RNA-protein interactions are crucial for regulating gene expression and cellular functions, with their dysregulation potentially impacting disease progression. Systematically mapping these interactions is resource-intensive due to the vast number of potential RNA and protein interactions. Here, we introduce PRIM-seq (Protein-RNA Interaction Mapping by sequencing), a method for the concurrent identification of RNA-binding proteins (RBPs) and the elucidation of their associated RNAs. PRIM-seq works by converting each RNA-protein pair into a unique chimeric DNA sequence, which is then decoded through DNA sequencing. Applied to two human cell types, PRIM-seq generated a comprehensive human RNA-protein association network (HuRPA), consisting of more than 350,000 RNA-proteins pairs involving approximately 7,000 RNAs and 11,000 proteins. The data revealed an enrichment of previously reported RBPs and RNA-protein interactions within HuRPA. We also identified LINC00339 as a protein-associating non-coding RNA and PHGDH as an RNA-associating protein. Notably, PHGDH interacts with BECN1 and ATF4 mRNAs, suppressing their protein expression and consequently inhibiting autophagy, apoptosis, and neurite outgrowth while promoting cell proliferation. PRIM-seq offers a powerful tool for discovering RBPs and RNA-protein associations, contributing to more comprehensive functional genome annotations.
RNA-蛋白质相互作用对于调节基因表达和细胞功能至关重要，其失调可能会影响疾病进展。由于潜在的RNA和蛋白质相互作用数量众多，系统地绘制这些相互作用图谱需要大量资源。在这里，我们介绍了PRIM-seq（通过测序进行蛋白质-RNA相互作用图谱绘制），这是一种同时鉴定RNA结合蛋白（RBP）及其相关RNA的方法。PRIM-seq的工作原理是将每对RNA-蛋白质转化为独特的嵌合DNA序列，然后通过DNA测序进行解码。应用于两种人类细胞类型时，PRIM-seq生成了一个全面的人类RNA-蛋白质关联网络（HuRPA），由超过350,000对RNA-蛋白质组成，涉及约7,000种RNA和11,000种蛋白质。数据显示HuRPA中富集了先前报道的RBP和RNA-蛋白质相互作用。我们还将LINC00339鉴定为一种与蛋白质结合的非编码RNA，将PHGDH鉴定为一种与RNA结合的蛋白质。值得注意的是，PHGDH与BECN1和ATF4 mRNA相互作用，抑制它们的蛋白质表达，从而抑制自噬、凋亡和神经突生长，同时促进细胞增殖。PRIM-seq为发现RBP和RNA-蛋白质关联提供了一个强大的工具，有助于更全面的功能基因组注释。
