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Series GSE234329 Query DataSets for GSE234329
Status Public on Jun 08, 2023
Title PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape [ATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary T cells trigger non-specific signaling pathways to elicit specialized effector functions to eliminate pathogens and cancers. Chromatin accessibility at T effector loci prior to antigen encounter poises cells to couple antigen recognition to the activation of lineage-specific responses. Here, by tracing the chromatin accessibility profiles unique to T effector functions during development, we find that the majority of T effector loci become accessible prior to antigen receptor expression. Epigenomic feature analysis, biochemical studies, and inducible perturbations identified two mechanistic linchpins: the physical association of the mSWI/SNF remodeling complex to the pleiotropic transcription factor (TF) RUNX1, and the cooperativity between RUNX1 and lineage-defining TFs PU.1 and BCL11B that respectively facilitate the establishment and maintenance of chromatin accessibility at T effector loci in early thymocyte progenitors. These findings reflect a design principle that allows distinct cell types to use the same signaling pathways to execute disparate roles which collectively orchestrate the immune response.
Overall design ATAC-seq profiling was performed at various stages of development in wild-type untreated, wild-type FK506-treated, Smarca4 cKO, Bcl11b cKO, and Runx1 cKO murine thymocytes.
Contributor(s) Gamble N, Bradu A, Caldwell JA, McKeever J, Bolonduro O, Kim Y, Parks B, Klemm S, Greenleaf WJ, Crabtree GR, Koh AS
Citation(s) 38632339
BioProject PRJNA971212
Submission date Jun 06, 2023
Last update date May 31, 2024
Contact name Alexandra Bradu
Organization name University Of Chicago
Department Pathology
Lab Koh Lab
Street address 924 East 57th Street
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (69)
GSM7465184 DN1 thymocytes, rep 1
GSM7465185 DN1 thymocytes, rep 2
GSM7465186 DN2a thymocytes, rep 1
This SubSeries is part of SuperSeries:
GSE234331 PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape

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Supplementary file Size Download File type/resource
GSE234329_ATAC_Matrix.Teff_Peaks.TSS_norm.txt.gz 10.9 Mb (ftp)(http) TXT
GSE234329_ATAC_Matrix.Teff_Peaks.TSS_norm_revised20231027.txt.gz 13.2 Mb (ftp)(http) TXT
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Processed data are available on Series record

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