Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
Summary
Innate immune responses rely on rapid and precise orchestration of gene regulation mediated by accessibility of regulatory regions to key transcription factors. However, the extent to which acute activation alters accessibility and the roles of distinct classes of transcription factors in this process are unsatisfactorily understood. Here, we investigated and integrated epigenomic modifications and transcriptomic changes occurring upon activation of natural killer (NK) cells.
Overall design
We stimulated splenic NK cells with cytokines IL-2 and IL-12 ex vivo for six hours and performed bulk RNA-seq on both resting and activatd NK cells for transcriptomic analysis, in parellel using ATAC-seq and ChIP-seq (p300, STATs, and histone modifications) for epigenomic profiling. To understand the dynamic chromatin landscapes in vivo, we measured chromatin accessibility of NK cells isolated from mice infected by Toxoplasma gondii for three and seven days using FastATAC-seq. We performed single cell RNA-seq on the infeceted NK cells form the same experiment to study the heterogeniety of immune responses in spleen and peritoneal cavity upon Toxoplasma infection.
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