Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Mol Cell. 2021 Oct 7;81(19):4091-4103.e9. doi: 10.1016/j.molcel.2021.07.006. Epub 2021 Aug 3.
We describe PROPER-seq (protein-protein interaction sequencing) to map protein-protein interactions (PPIs) en masse. PROPER-seq first converts transcriptomes of input cells into RNA-barcoded protein libraries, in which all interacting protein pairs are captured through nucleotide barcode ligation, recorded as chimeric DNA sequences, and decoded at once by sequencing and mapping. We applied PROPER-seq to human embryonic kidney cells, T lymphocytes, and endothelial cells and identified 210,518 human PPIs (collected in the PROPER v.1.0 database). Among these, 1,365 and 2,480 PPIs are supported by published co-immunoprecipitation (coIP) and affinity purification-mass spectrometry (AP-MS) data, 17,638 PPIs are predicted by the prePPI algorithm without previous experimental validation, and 100 PPIs overlap human synthetic lethal gene pairs. In addition, four previously uncharacterized interaction partners with poly(ADP-ribose) polymerase 1 (PARP1) (a critical protein in DNA repair) known as XPO1, MATR3, IPO5, and LEO1 are validated in vivo. PROPER-seq presents a time-effective technology to map PPIs at the transcriptome scale, and PROPER v.1.0 provides a rich resource for studying PPIs.
我们描述了 PROPER-seq（蛋白质-蛋白质相互作用测序），以大规模绘制蛋白质-蛋白质相互作用（PPIs）图谱。PROPER-seq 首先将输入细胞的转录组转化为 RNA 编码的蛋白质文库，在文库中，所有相互作用的蛋白质对都通过核苷酸条形码连接捕获，记录为嵌合 DNA 序列，并通过测序和映射立即解码。我们将 PROPER-seq 应用于人类胚胎肾细胞、T 淋巴细胞和内皮细胞，鉴定了 210518 个人类 PPI（收集在 PROPER v.1.0 数据库中）。其中，1365 个和 2480 个 PPI 得到了已发表的共免疫沉淀（coIP）和亲和纯化-质谱（AP-MS）数据的支持，17638 个 PPI 是由 prePPI 算法预测的，没有以前的实验验证，100 个 PPI 与人类合成致死基因对重叠。此外，四个以前未被表征的与多聚（ADP-核糖）聚合酶 1（PARP1）（DNA 修复中的关键蛋白）相互作用的新伙伴 XPO1、MATR3、IPO5 和 LEO1 在体内得到了验证。PROPER-seq 是一种在转录组水平上绘制 PPI 的高效技术，而 PROPER v.1.0 为研究 PPI 提供了丰富的资源。
