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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| 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.
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| 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 |
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| Submission date |
Jun 06, 2023 |
| Last update date |
May 31, 2024 |
| Contact name |
Alexandra Bradu |
| E-mail(s) |
abradu@uchicago.edu
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| Organization name |
University Of Chicago
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| Department |
Pathology
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| Lab |
Koh Lab
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| Street address |
924 East 57th Street
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (69)
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| GSM7465187 |
DN2a thymocytes, rep 2 |
| GSM7465188 |
DN3 thymocytes, rep 1 |
| GSM7465189 |
DN3 thymocytes, rep 2 |
| GSM7465190 |
DN4 thymocytes, rep 1 |
| GSM7465191 |
DN4 thymocytes, rep 2 |
| GSM7465192 |
DP thymocytes, rep 1 |
| GSM7465193 |
DP thymocytes, rep 2 |
| GSM7465194 |
CD8 SP T cells, rep 1 |
| GSM7465195 |
CD8 SP T cells, rep 2 |
| GSM7465196 |
CD8 Naïve T cells, rep 1 |
| GSM7465197 |
CD8 Naïve T cells, rep 2 |
| GSM7465198 |
CD8 Activated T cells, rep 1 |
| GSM7465199 |
CD8 Activated T cells, rep 2 |
| GSM7465200 |
CD4 SP T cells, rep 1 |
| GSM7465201 |
CD4 Naïve T cells, rep 1 |
| GSM7465202 |
CD4 Activated T cells, rep 1 |
| GSM7465203 |
DN1 thymocytes, DMSO-treated, rep 1 |
| GSM7465204 |
DN1 thymocytes, DMSO-treated, rep 2 |
| GSM7465205 |
DN1 thymocytes, FK506-treated, rep 1 |
| GSM7465206 |
DN1 thymocytes, FK506-treated, rep 2 |
| GSM7465207 |
DN2 thymocytes, DMSO-treated, rep 1 |
| GSM7465208 |
DN2 thymocytes, FK506-treated, rep 1 |
| GSM7465209 |
DN3 thymocytes, DMSO-treated, rep 1 |
| GSM7465210 |
DN3 thymocytes, FK506-treated, rep 1 |
| GSM7465211 |
DN1 thymocytes, Smarca4 WT, rep 1 |
| GSM7465212 |
DN1 thymocytes, Smarca4 WT, rep 2 |
| GSM7465213 |
DN1 thymocytes, Smarca4 WT, rep 3 |
| GSM7465214 |
DN1 thymocytes, Smarca4 cKO, rep 1 |
| GSM7465215 |
DN1 thymocytes, Smarca4 cKO, rep 2 |
| GSM7465216 |
DN1 thymocytes, Smarca4 cKO, rep 3 |
| GSM7465217 |
DN2 thymocytes, Smarca4 WT, rep 1 |
| GSM7465218 |
DN2 thymocytes, Smarca4 WT, rep 2 |
| GSM7465219 |
DN2 thymocytes, Smarca4 WT, rep 3 |
| GSM7465220 |
DN2 thymocytes, Smarca4 cKO, rep 1 |
| GSM7465221 |
DN2 thymocytes, Smarca4 cKO, rep 2 |
| GSM7465222 |
DN2 thymocytes, Smarca4 cKO, rep 3 |
| GSM7465223 |
DN3 thymocytes, Smarca4 WT, rep 1 |
| GSM7465224 |
DN3 thymocytes, Smarca4 WT, rep 2 |
| GSM7465225 |
DN3 thymocytes, Smarca4 cKO, rep 1 |
| GSM7465226 |
DN3 thymocytes, Smarca4 cKO, rep 2 |
| GSM7465227 |
DN2 thymocytes, Bcl11b WT, rep 1 |
| GSM7465228 |
DN2 thymocytes, Bcl11b WT, rep 2 |
| GSM7465229 |
DN2 thymocytes, Bcl11b cKO, rep 1 |
| GSM7465230 |
DN2 thymocytes, Bcl11b cKO, rep 2 |
| GSM7465231 |
DN3 thymocytes, Bcl11b WT, rep 1 |
| GSM7465232 |
DN3 thymocytes, Bcl11b WT, rep 2 |
| GSM7465233 |
DN3 thymocytes, Bcl11b cKO, rep 1 |
| GSM7465234 |
DN3 thymocytes, Bcl11b cKO, rep 2 |
| GSM7465235 |
DN1 thymocytes, Runx1 WT, rep 1 |
| GSM7465236 |
DN1 thymocytes, Runx1 WT, rep 2 |
| GSM7465237 |
DN1 thymocytes, Runx1 cKO, rep 1 |
| GSM7465238 |
DN1 thymocytes, Runx1 cKO, rep 2 |
| GSM7465239 |
DN2 thymocytes, Runx1 WT, rep 1 |
| GSM7465240 |
DN2 thymocytes, Runx1 WT, rep 2 |
| GSM7465241 |
DN2 thymocytes, Runx1 cKO, rep 1 |
| GSM7465242 |
DN2 thymocytes, Runx1 cKO, rep 2 |
| GSM7465243 |
DN3 thymocytes, Runx1 WT, rep 1 |
| GSM7465244 |
DN3 thymocytes, Runx1 WT, rep 2 |
| GSM7465245 |
DN3 thymocytes, Runx1 cKO, rep 1 |
| GSM7465246 |
DN3 thymocytes, Runx1 cKO, rep 2 |
| GSM7906510 |
ATAC-seq, DN1 thymocytes, Runx1 cKO, rep 3 |
| GSM7906511 |
ATAC-seq, DN2 thymocytes, Runx1 cKO, rep 3 |
| GSM7906512 |
ATAC-seq, DN3 thymocytes, Runx1 cKO, rep 3 |
| GSM7906513 |
ATAC-seq, DN1 thymocytes, Runx1 WT, rep 3 |
| GSM7906514 |
ATAC-seq, DN2 thymocytes, Runx1 WT, rep 3 |
| GSM7906515 |
ATAC-seq, DN3 thymocytes, Runx1 WT, rep 3 |
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| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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