美国纽约基因组中心Rahul Satija等研究人员合作完成可变多腺苷酸化调节因子的多重单细胞表征。相关论文于2024年6月25日在线发表在《细胞》杂志上。

研究人员表示，大多数哺乳动物基因都有多个polyA位点，这是受切割和多腺苷酸化（CPA）机制调控的转录本多样性的重要来源。

为了更好地了解这些蛋白是如何调控polyA位点选择的，研究人员引入了CPA-Perturb-seq，这是一个由42个CPA调控因子组成的多重扰动筛选数据集，具有3′ scRNA-seq读数，可以在整个转录组范围内推断polyA位点的使用情况。研究人员建立了一个框架来检测多聚腺苷酸化中的扰动依赖性变化，并确定共调节多聚酶位点模块的特征。研究人员发现内含子polyA位点组受核RNA生命周期不同组成部分的调控，包括延伸、剪接、终止和监控。

研究人员针对串联polyA位点的使用训练并验证了一个深度神经网络（APARENT-Perturb），该网络划定了一个顺式调控代码，可预测扰动响应并揭示调控复合物之间的相互作用。该工作凸显了多重单细胞扰动筛选的潜力，可进一步加深人们对转录后调控的理解。

附：英文原文

Title: Multiplexed single-cell characterization of alternative polyadenylation regulators

Author: Madeline H. Kowalski, Hans-Hermann Wessels, Johannes Linder, Carol Dalgarno, Isabella Mascio, Saket Choudhary, Austin Hartman, Yuhan Hao, Anshul Kundaje, Rahul Satija

Issue&Volume: 2024-06-25

Abstract: Most mammalian genes have multiple polyA sites, representing a substantial sourceof transcript diversity regulated by the cleavage and polyadenylation (CPA) machinery.To better understand how these proteins govern polyA site choice, we introduce CPA-Perturb-seq,a multiplexed perturbation screen dataset of 42 CPA regulators with a 3′ scRNA-seqreadout that enables transcriptome-wide inference of polyA site usage. We developa framework to detect perturbation-dependent changes in polyadenylation and characterizemodules of co-regulated polyA sites. We find groups of intronic polyA sites regulatedby distinct components of the nuclear RNA life cycle, including elongation, splicing,termination, and surveillance. We train and validate a deep neural network (APARENT-Perturb)for tandem polyA site usage, delineating a cis-regulatory code that predicts perturbation response and reveals interactions betweenregulatory complexes. Our work highlights the potential for multiplexed single-cellperturbation screens to further our understanding of post-transcriptional regulation.

DOI: 10.1016/j.cell.2024.06.005

Source: https://www.cell.com/cell/abstract/S0092-8674(24)00645-7