Activation of clustered IFN? target genes drives cohesin-controlled transcriptional memory [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: Transcriptome measurements of polyA mRNA for naïve HeLa cells, induced with interferon gamma (50ng/mL) for 24h (priming), 48h after interferon gamma washout (primed) and 24h reinduced with interferon gamma (50ng/mL) (reinduction). Three biological replicates for each condition.

细胞经细胞因子激活后，可诱导参与炎症与免疫反应的基因网络表达。即使在持续转录停止的情况下，一过性的基因激活仍可产生持久影响，该现象被称为长期转录记忆。本研究探究人类细胞经干扰素γ（IFNγ）诱导致敏的建立与维持本质。研究发现，尽管持续转录与局部染色质标记均为一过性现象，但干扰素γ致敏状态可稳定传递至少14个细胞分裂周期。单细胞分析显示，致敏细胞的记忆效应表现为其启动靶基因表达的概率升高，且该概率与初始基因激活的强度呈正相关。进一步研究发现，具有强记忆效应的基因多富集于基因组簇中，且这类基因的长期记忆受黏连蛋白（cohesin）的局部调控限制。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，该成果有助于深入理解增强的先天免疫信号通路。实验设计概要：对四组样本的聚腺苷酸化信使RNA（polyA mRNA）开展转录组检测：未致敏的海拉（HeLa）细胞；经50ng/mL干扰素γ诱导24小时以完成致敏的细胞；干扰素γ洗脱去除48小时后的致敏状态细胞；再次用50ng/mL干扰素γ诱导24小时的再诱导细胞。每组设置3次生物学重复。