The ATAC analysis for Usp18 heterozygous depletion in established AML1/ETO 9a leukemia mouse model

Type I IFN induces IFN stimulated genes (ISGs) and exert varieties of immunomoduratory functions. However, it is not well characterized how ISGs are regulated by negative regulators of IFN signaling. Here, we analyzed the chromatin accessibility when combined with depletion of USP18, one of major negative regulators for IFN signaling. Overall design: Usp18+/f UBCER-Cre AML1/ETO 9a leukemia cells were transplanted into recipient mice. After mice become sick, oil or tamoxifen were injected to heterozygously deplete Usp18. Three days after first injection, Lin- c-kit+ AML cells were sorted from mouse splenocytes. Then performed RNA-sequencing of control (Oil) and USP18KD (Tam) RNA. For RNA-sequencing, 3 biological replicates were prepared for each condition. ATAC-sequencing of Usp18+/f and Usp18+/? AE9a cells. Same biological replicates were processed to RNA-seq as well.

I型干扰素（Type I IFN）可诱导干扰素刺激基因（IFN stimulated genes, ISGs）表达，并发挥多种免疫调节功能。然而，目前对于干扰素信号通路的负调控因子如何调控ISGs的分子机制尚未明确。本研究结合USP18（干扰素信号通路主要负调控因子之一）的敲除实验，分析了染色质开放性（chromatin accessibility）的变化。

整体实验设计：将Usp18+/f UBCER-Cre AML1/ETO 9a白血病细胞移植至受体小鼠体内。待小鼠罹患白血病后，分别注射油剂（oil）与他莫昔芬（tamoxifen）以实现Usp18的杂合敲除。首次注射后第3天，从小鼠脾脏细胞中分选得到Lin- c-kit+ AML细胞。随后对对照组（油剂处理，Oil）与USP18敲低组（他莫昔芬处理，Tam）的RNA开展RNA测序（RNA-sequencing），每组均设置3个生物学重复。此外，本研究还对Usp18+/f与Usp18+/? AE9a细胞进行了ATAC测序（ATAC-sequencing），且上述同一批生物学重复样本也同步完成了RNA测序（RNA-seq）。