Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell types, but obtaining APA maps from individual cell types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2. We further identified a role of APA in switching Araf protein isoforms during microglia activation, impacting production of downstream inflammatory cytokines. Our results demonstrate the broad applicability of cTag-PAPERCLIP and a previously undiscovered role of APA in contributing to protein diversity between different cell types and cellular states within the brain.

中文翻译：

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cTag-PAPERCLIP显示出可替代的聚腺苷酸化可促进细胞类型特异性蛋白质多样性，并通过小胶质细胞活化转移Araf亚型。

越来越多的人认为替代聚腺苷酸化（APA）可以调节不同细胞类型之间的基因表达，但是从单个细胞类型获得APA图通常需要事先纯化，这是一个压力很大的过程，它本身可以改变细胞状态。在这里，我们描述了一个新的平台cTag-PAPERCLIP，它可以从完整组织中的单个细胞群体生成APA配置文件。cTag-PAPERCLIP不需要组织解离，并且可以将转录本保存为原始状态。应用cTag-PAPERCLIP对小鼠大脑中的四种主要细胞类型进行分析，发现与星形胶质细胞和小胶质细胞不同的兴奋性神经元和抑制​​性神经元之间常见的APA偏好，部分受神经元特异性RNA结合蛋白NOVA2和PTBP2的调节。我们进一步确定了小胶质细胞激活过程中APA在转换Araf蛋白同工型中的作用，影响下游炎性细胞因子的产生。我们的结果证明了cTag-PAPERCLIP的广泛适用性以及APA在促进不同细胞类型和大脑内细胞状态之间的蛋白质多样性中所发挥的先前未被发现的作用。