Genome binding/occupancy profiling by high throughput sequencing
Summary
The response of naive CD8+ T cells to their cognate antigen involves rapid and broad changes in gene expression that are coupled with extensive chromatin remodeling, but the mechanisms governing these changes are not fully understood. In this study, we investigated how this process depends on the activity of the basic leucine zipper ATF-like transcription factor Batf, which is essential for the earliest phase of effector CD8+ T cell differentiation. Through genome scale profiling of multiple modalities, we characterized the role of Batf in chromatin organization at several levels, including the accessibility of key regulatory regions, the expression of nearby genes, and the interactions these regions make with each other and with key transcription factors. We quantified the dependencies between Batf and other transcription factors and identified a core transcription factor network that cooperated with Batf, including Irf4, and the transcription factors Runx3 and T-bet, which tended to co-localize with Batf and bind in regions whose accessibility and long-range interactions were mediated by Batf. We functionally demonstrated the synergistic activity of this network in initiating aspects of the effector T cells’ transcriptional and chromatin accessibility profiles in an ectopically-induced fibroblast system. Using HiChIP, we further found that overexpressing all four factors in fibroblasts was required to recapitulate important aspects of the CD8+ T cell chromatin architecture. Our results provided a comprehensive resource for studying the epigenomic and transcriptomic landscape of effector differentiation of cytotoxic T cells and suggested various modes of dependencies between transcription factors in this process.
Overall design
This submission contains the ATAC-Seq portion of the data. There are three datasets, described below. Ectopic_Expression_In_Fibroblasts These samples are NIH/3T3 fibroblasts which were transduced with a doxycycline-inducible lentivirus consisting of any combination of Batf, Irf4, Runx3 and T-bet (16 combinations altogether). Ectopic expression of the respective TFs in a given sample were induced with doxycycline. Samples with and without doxycycline are included, resulting in 32 different conditions, with two replicates each, resulting in 64 samples. CD8_TCell_In_Vitro These samples are in vitro P14 CD8+ T Cells measured six days after initial stimulation. Samples with and without restimulation are included for Day 6 for WT and Batf KO CD8_TCell_In_Vivo These samples are in vivo P14 CD8+ T Cells with a Cre-Lox system enabling conditional knockout of Batf or Irf4. The samples were obtained 3.5 days after infection with an acute strain of LCMV.
Less...
More...