Stress granules (SGs) are highly dynamic cytoplasmic membrane-less organelles that assemble when cells are challenged by stress. RNA molecules are sorted into SGs where they play important roles in maintaining the structural stability of SGs and regulating gene expression. Herein, we apply a proximity-dependent RNA labeling method, CAP-seq, to comprehensively investigate the content of SG-proximal transcriptome in live mammalian cells. CAP-seq captures 457 and 822 RNAs in arsenite- and sorbitol-induced SGs in HEK293T cells, respectively, revealing that SG enrichment is positively correlated with RNA length and AU content, but negatively correlated with translation efficiency. The high spatial specificity of CAP-seq dataset is validated by single-molecule FISH imaging. We further apply CAP-seq to map dynamic changes in SG-proximal transcriptome along the time course of granule assembly and disassembly processes. Our data portray a model of AU-rich and translationally repressed SG nanostructure that are memorized long after the removal of stress.

应激颗粒（SG）是高度动态的无细胞质膜的细胞器，当细胞受到应激挑战时，它们会聚集。RNA分子被分类为SG，在维持SG的结构稳定性和调节基因表达方面发挥着重要作用。在此，我们应用邻近依赖性RNA标记方法CAP-seq来全面研究活哺乳动物细胞中SG-近端转录组的含量。CAP-seq 在 HEK293T 细胞中分别捕获亚砷酸盐和山梨醇诱导的 SG 中的 457 个和 822 个 RNA，表明 SG 富集与 RNA 长度和 AU 含量正相关，但与翻译效率负相关。CAP-seq 数据集的高空间特异性通过单分子 FISH 成像得到验证。我们进一步应用 CAP-seq 来绘制 SG-近端转录组随颗粒组装和拆卸过程的动态变化。我们的数据描绘了富含 AU 且翻译抑制的 SG 纳米结构模型，该模型在应力消除后很长时间内仍被记忆。