Bulk RNA sequencing of WT (Batf fl/fl) and Batf-/- (Batf fl/fl PLZFcre+) ILC3s sorted from small intestine [bulk RNA-seq]

Group 3 innate lymphoid cells (ILC3s) are crucial for the maintenance of host-microbiota homeostasis in gastrointestinal mucosal tissues. The mechanisms that maintain lineage identity of intestinal ILC3s, and ILC3s-mediated orchestration of microbiota and mucosal T cell immunity are elusive. Here, we identified BATF as a gatekeeper of ILC3s homeostasis in the gut. Depletion of BATF in ILC3s resulted in excessive interferon-? production, dysbiosis, aberrant T cell immune responses and spontaneous inflammatory bowel disease (IBD), which was considerably ameliorated by removal of adaptive immunity or antibiotic treatment. Mechanistically, BATF directly regulates ILC3s identity by globally shapes chromatin landscape of ILC3s. BATF directly binds to the cis-regulatory elements of type 1 effector genes, restrains their chromatin accessibility and inhibits their expression. Conversely, BATF promotes chromatin accessibility of genes involved in MHCII antigen processing and presentation pathways. Collectively, our findings reveal BATF is a promising candidate to maintain ILC3s stability and coordinate ILC3s–mediated control of intestinal homeostasis. Overall design: Bulk RNA sequencing, 2 samples (WT and Batf-/- ILC3s), 3 biological replicates per sample, from small intestine.

3型固有淋巴细胞（Group 3 innate lymphoid cells, ILC3s）在维持胃肠道黏膜组织的宿主-菌群稳态中发挥关键作用。目前，维持肠道3型固有淋巴细胞谱系特性的机制，以及3型固有淋巴细胞介导的菌群与黏膜T细胞免疫调控机制仍尚不明确。本研究证实BATF是肠道3型固有淋巴细胞稳态的核心调控因子。在3型固有淋巴细胞中敲除BATF会导致干扰素-γ过量产生、菌群失调、异常T细胞免疫应答以及自发性炎症性肠病（IBD），该表型可通过清除适应性免疫或抗生素处理得到显著缓解。从机制层面而言，BATF可通过全局重塑3型固有淋巴细胞的染色质景观，直接调控其谱系特性：BATF可直接结合1型效应基因的顺式调控元件，抑制其染色质开放程度并下调其表达；反之，BATF则可提升参与MHCII抗原加工呈递通路的基因的染色质开放程度。综上，本研究结果表明BATF是维持3型固有淋巴细胞稳定性、协调其介导的肠道稳态调控的潜在候选靶点。实验设计：采用批量RNA测序技术，样本取自小鼠小肠，共2组样本（野生型WT与Batf基因敲除Batf-/-的3型固有淋巴细胞），每组设置3次生物学重复。