Activation of clustered IFN? target genes drives cohesin-controlled transcriptional memory [single-cell RNA-seq]

Cytokine activation of cells induces gene networks involved in inflammation and immunity. Transient gene activation can have a lasting impact even in the absence of ongoing transcription, known as long-term transcriptional memory. Here we explore the nature of the establishment and maintenance of IFN?-induced priming of human cells. We find that while both ongoing transcription and local chromatin signatures are short-lived, the IFN?-primed state stably propagates through at least 14 cell division cycles. Single cell analysis reveals that memory is manifested by an increased probability of primed cells to engage in target gene expression, correlating with the strength of initial gene activation. Further, we find that strongly memorized genes tend to reside in genomic clusters and that long-term memory of these genes is locally restricted by cohesin. We define the duration, stochastic nature and molecular mechanisms of IFN?-induced transcriptional memory, relevant to understanding of enhanced innate immune signaling. Overall design: Single cell transcriptome measurements of polyA mRNA for naïve HeLa cells (N=90), induced with interferon gamma (50ng/mL) for 24h (priming) (N=89) and 24h reinduced with interferon gamma (50ng/mL) after 48h washout (reinduction) (N=91).

细胞经细胞因子激活后，会触发参与炎症与免疫反应的基因调控网络。即使在持续转录停止的情况下，一过性基因激活仍可产生持久影响，该现象被称为长期转录记忆（long-term transcriptional memory）。本研究旨在探究人源细胞经干扰素γ（IFNγ）诱导致敏过程的建立与维持机制。研究发现，尽管持续转录与局部染色质特征均为短暂存在的现象，但经干扰素γ致敏的细胞状态可稳定传递至少14次细胞分裂周期。单细胞转录组分析显示，记忆效应体现为致敏细胞激活靶基因的概率升高，且该概率与初始基因激活的强度呈正相关。此外，本研究发现具有强记忆效应的基因多聚集于基因组簇中，且这类基因的长期转录记忆受黏连蛋白（cohesin）的局部限制。本研究明确了干扰素γ诱导的转录记忆的持续时长、随机特性与分子机制，相关结果可为解析增强型先天免疫信号通路提供理论依据。实验整体设计：对三组样本开展聚腺苷酸化mRNA（polyA mRNA）的单细胞转录组测序：未处理的原始海拉细胞（对照组，样本量N=90）、经50ng/mL干扰素γ诱导致敏24小时的细胞（致敏组，N=89）、以及经48小时洗脱后再次用50ng/mL干扰素γ诱导24小时的细胞（再诱导组，N=91）。